Introduction

Reprogramming Microbial Realities: My Journey in Engineering the Invisible

I have over 25 years (since June 1999) of diverse work experience in computer systems, inverse problems, medical imaging, and, more recently, microbial informatics. I have led transformative research projects internationally - from pioneering diagnostic imaging algorithms to developing cutting-edge bioinformatics tools and driving sustainable solutions in agriculture, aquaculture, water treatment, and public health. Through my work, I not only push the boundaries of science but also actively contribute to global initiatives such as the United Nations Sustainable Development Goals (UN SDGs), which provide a framework for ensuring a healthier, more equitable, and sustainable future.

From Inverse Problems to Biological Insight

My early career was characterised by a deep engagement with inverse problems - challenging mathematical techniques that require reconstructing hidden parameters from observable data. At Jeju National University, South Korea and later at University of Cambridge, I worked tirelessly on dynamic imaging techniques using electrical impedance tomography and advanced 3D ultrasound systems. I vividly recall the breakthrough moments, such as developing a novel Kalman-filter based reconstruction method (DOI: 10.1088/0957-0233/19/6/065501) and devising dynamic flow measurement techniques (DOI: 10.1016/j.flowmeasinst.2006.12.005). These studies - further led to exploring advances in 3D ultrasound imaging reliability (DOI: 10.7863/ultra.32.4.699) and clinical validations (DOI: 10.1259/bjr/46007369) - provided the quantitative rigor that has shaped my approach to all subsequent research.

Embracing Microbial Ecology: Unveiling the Hidden World

The advent of high-throughput sequencing in the early 2010s revolutionized our ability to study the microbial world. I found myself irresistibly drawn to understanding the dynamic complexity of microbial communities. How do these unseen organisms assemble, adapt, and thrive under fluctuating environmental conditions? I explored ecological null models and taxa-centric analyses to address these questions. My research in this area, including studies that outline statistical frameworks for community assembly (DOI: 10.1002/ece3.8091) and explore microbial resilience (DOI: 10.3389/fmicb.2023.1197838), has not only advanced scientific understanding but also has far-reaching implications for environmental management - directly supporting UN SDG 13 (Climate Action) and UN SDG 15 (Life on Land).

Transforming Theory into Tools: Democratizing Discovery in Microbial Informatics

I have always believed that breakthrough science should be accessible. My commitment to transforming theory into practical tools led me to contribute to a suite of innovative bioinformatics software. One highlight is CONCOCT (DOI: 10.1038/nmeth.3103), a genome binning tool for metagenomic assemblies that contributed to the discovery of the novel Commamox lineage (DOI: 10.1126/science.aad9839). Equally groundbreaking is SEQENV, a text-mining engine that links genomic sequences to environmental contexts using Environmental Ontology (DOI: 10.7717/peerj.2690; DOI: 10.7717/peerj.3827). My suite further expands with microbiomeSEQ (an R package for microbial community analysis in an environmental context; DOI: 10.13140/RG.2.2.17108.71047), NanoAmpli-Seq (a workflow for amplicon sequencing from mixed microbial communities on Oxford Nanopore; DOI: 10.1093/gigascience/giy140), PyTag (a software facilitating systematic reviews using prevalent ontologies; DOI: 10.7287/10.7717/peerj.5047), and CViewer (a Java software for multivariate statistical analysis of shotgun metagenomics datasets with other omics modalities; DOI: 10.1186/s40168-024-01834-9). I have also significantly contributed to RVLAB (an online statistical processing environment for multivariate analysis of microbial communities; DOI: 10.3897/BDJ.4.e8357), and NMGS (a software for fitting unified theory of neutral models to microbial communities; DOI: 10.1109/JPROC.2015.2428213). By making such tools open-source, I support UN SDG 9 (Industry, Innovation, and Infrastructure) and UN SDG 17 (Partnerships for the Goals) by enabling global collaboration and empowering researchers everywhere.

Integrating Data: Crafting a Multi-Dimensional View of Life

Understanding the complexity of life requires merging diverse data streams into a coherent narrative. I have led efforts to integrate microbiome data with metabolomic, transcriptomic, and proteomic profiles using advanced latent variable models and multi-omics methodologies. Such integrative approaches - detailed in publications like DOI: 10.1080/19490976.2021.1930871, DOI: 10.1039/C9FD00020H, and DOI: 10.3389/fsysb.2024.1432791 - provide a panoramic view of how microbial interactions influence cellular function and overall ecosystem health. This work has profound implications for UN SDG 3 (Good Health and Well-Being) and UN SDG 12 (Responsible Consumption and Production), by linking molecular details to systemic outcomes.

Revolutionizing Agriculture and Aquaculture: The Microbial Edge

A major challenge in developing sustainable approaches to agriculture is a lack of fundamental understanding about what allows some plants to adapt better than others to pressures arising from changes in both the biotic and abiotic environments. In the face of the current climate emergency, it will become critical to design crops that will be resilient to the environmental variability resulting from the increasing unpredictability and extremes of local weather during the growing season. However, if we are to achieve long-term sustainable solutions to food security, we also need to move beyond management of single crop species and consider impacts on overall ecosystem health and biodiversity. This is not only important for conservation but will in turn help to simultaneously improve yields of multiple crop species. Moreover, such changes in management practices will only translate into increased food security if they are economically viable: if consumers, supermarkets and growers are willing to engage with a change to more sustainable food sources. My significant contributions in the leading role are as follows: (a) With James Hutton Institute: Centre for Sustainable Cropping (CSC), I am integrating existing data (13 years, to-date the most extensive and long-standing trial in the UK) to quantify fluctuations across space and time in both the abiotic and biotic environments in relation to sustainable vs traditional conventional cropping of different potato varieties. This work builds on the main outcome of a £2M BBSRC UKRI Strategic Priorities Fund - Bacterial Plant Diseases BB/T010657/1, Building a Decision Support Tool for Potato Blackleg Disease (DeS-BL) grant (DOI: 10.1101/2023.06.19.545554); (b) With Forman Christian College (A chartered University), Lahore, Pakistan, we have successfully demonstrated how to suppress Cotton Leaf Curl Disease (CLCuD) by application of Salicylic Acid producing bacteria (DOI: 10.1007/s00284-024-03827-1; DOI: 10.3389/fmicb.2024.1381883; DOI: 10.1038/s41522-023-00470-9), and through interspecies microbiome transplantation (DOI: 10.1038/s42003-025-07812-7). A recent press release, "Microbiota transplantation offers new hope against cotton leaf curl disease", highlights the importance of this work for sustainable agriculture. CLCuD is transmitted by the whitefly Bemisia tabaci, and has devastated Pakistan’s cotton crop for the past three decades with economic losses reaching approximately 2 billion USD per annum in Pakistan. We are currently undertaking on-field trials in Pakistan. All of these works are paving the way toward sustainable, non-chemical plant protection strategies that support UN SDG 2 (Zero Hunger) and UN SDG 15 (Life on Land).

The global demand for food and protein continues to rise as the world’s population is set to hit 9.7 Billion by 2050. Reducing demands on meat protein and increasing fish consumption is good for our health and potentially more environmentally sustainable. Fish consumption has already eclipsed beef consumption globally. Aquaculture production of fish is a booming industry that could eventually satisfy global fish food demands and reduce our reliance on wild resources. However, for some fish species, such as the Atlantic cod, capture fishing remains the dominant means of production (>97%). As a result, many cod stocks are in decline. Consequently, the farming of cod could offer a sustainable and reliable means to meet consumer demand for seafood. In a series of papers directed by me (DOI: 10.1038/s41522-022-00296-x; DOI: 10.1186/s42523-020-00065-1), we have demonstrated the impact of diet supplementation of juvenile Atlantic cod with seaweeds (macroalgae; egg wrack [Ascophyllum nodosum] or sea lettuce [Ulva rigida]) in a typical farming setting. Our work sheds valuable insights into what ecological processes drive the hindgut microbiome in juvenile Atlantic cod. With the advent of novel functional feed supplements from the biotech industries we will need to explore how these additives can benefit farmed fish species like salmon, trout and marine species such as seabass and bream with a view towards producing robust healthy fish for the consumer. Our approach opens the door to a better understanding of these possibilities. As an outreach exercise, we were invited to write a blogpost on Nature Communities, "How do microbial communities assemble in the gut of Atlantic cod in response to diet and novel ingredients?".

In aquaculture, the development of the SalmoSim simulator to replicate the gut microbiome of Atlantic salmon, as well as exploring microbial ecology of Atlantic Salmon (DOI: 10.1186/s40168-021-01134-6; DOI: 10.1128/spectrum.01953-21; DOI: 10.1016/j.aquaculture.2021.736772; DOI: 10.1038/s41522-022-00296-x; DOI: 10.1186/s42523-020-00065-1; DOI: 10.1038/s41598-022-17008-2) represents another breakthrough. This enhances our understanding of fish nutrition and health, contributing directly to the sustainability of global seafood supplies.

The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. With MoyPark (UK’s largest producer of organic and free range chicken, and one of the the UK’s top 15 food companies), three papers on chicken microbiomes (DOI: 10.3389/fmicb.2018.02452; DOI: 10.1186/s40168-020-00908-8; DOI: 10.3389/fmicb.2023.1197838) have led to exploring the diet and their industrial parameters to help control the pathogen Campylobacter, resulting in a press release by Agri-Food & Biosciences Institute, UK Government ("High impact research paper published in Journal of Microbiome"). My current work with MoyPark is towards Alternatives To Antibiotics (ATAs) that can be utilised in animal production for maintenance of gut health, reduction of pathogen load, and improved feed efficiencies (DOI: 10.1101/2024.08.02.606333). Similarly, with National Veterinary Laboratory (NVL), Pakistan (Ministry of National Food Security & Research, Pakistan), I am taking a leading role in understanding the microbial ecology of local/indigenous breeds, improving commercial and backyard farming setups in Pakistan, and reducing antimicrobial resistance (DOI: 10.1186/s13104-025-07220-4; DOI: 10.1016/j.dib.2024.110552; DOI: 10.1016/j.dib.2024.110487; DOI: 10.3389/fmicb.2023.1197838).

Pioneering Water, Wastewater, and Environmental Technologies

I have a significant portfolio in leading and directing research on water and waste-water treatment. Majority of the work is in collaboration with University of Galway, Ireland where I have held a visiting lectureship and where I supervise students and postdocs. My most impactful work has been on understanding Anaerobic Digestion (AD) processes. In the natural environment, organic matter is degraded by diverse communities of microorganisms through AD which can be harnessed for engineered wastewater treatment. Compared to conventional treatment processes, AD is less energy-intensive, reduces land-use requirements, and produces biogas as a renewable energy source. AD is a biological process, reliant on the livelihood and activity of the microbial communities ‘eating’ the organic pollutants. If the bacteria are unable to survive, the system fails. Generally, microorganisms thrive at warm temperatures (around 37°C), but heating wastewater requires significant energy expenditure, especially in temperate climates. In a series of paper below we have shown that we could train or adapt the microbial community to operate at low temperatures with such adaptations would avoid the costs and energy consumption associated with heating, creating meaningful change for the way wastewater is treated in colder climates. My recent work includes: first evidence for temperature influencing the enrichment, assembly and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities (DOI: 10.3389/fsysb.2024.1375472); intI gene abundance as a proxy for antimicrobial resistance (DOI: 10.1128/aem.01071-23); understanding microbial ecology in drinking water treatment and distribution systems (DOI: 10.1016/j.watres.2022.118106); low temperature AD applications (DOI: 10.1016/j.scitotenv.2023.162420; DOI: 10.1016/j.biortech.2021.126098); understanding sulfur-driven denitrification performance and microbial community dynamics (DOI: 10.1016/j.chemosphere.2021.131975); understanding microbial electrosynthesis (DOI: 10.1038/s41522-022-00337-5); understanding granules microbiology and why granules float in AD reactors (DOI: 10.1128/Spectrum.00784-21; DOI: 10.3389/fmicb.2021.666584; DOI: 10.1016/j.jenvman.2021.112229; DOI: 10.1128/mSystems.00323-20; DOI: 10.3389/fmicb.2020.01126); and improving protocols for microbial community detection (DOI: 10.1186/s40168-018-0449-9).

Additionally, my work on employing Rhamnolipid as a biodegradable biosurfactant for oil spill remediation (DOI: 10.1186/s40168-021-01143-5) showcases the transformative potential of microbe-based technologies in environmental crises, aligning with UN SDG 6 (Clean Water and Sanitation) and UN SDG 11 (Sustainable Cities and Communities). The biosurfactant did not suppress the oil-eating bacteria, so more of the aromatic hydrocarbons were degraded when it was used. This is summarised in a video abstract associated with our project and entitled, "Rhamnolipid, a naturally produced oil dispersant, may improve oil spill remediation". The study has environmental impact as ascertained by a press release by Heriot-Watt University, entitled "Oil industry should invest in bio solutions for oil spills".

Microbiomes, Health, and Social Equity: Decoding the Invisible Determinants

The interplay between our microbial communities and our health is profound. I have engaged in extensive collaborations to study how factors such as sanitation, diet, antibiotic use, and socioeconomic status shape the human microbiome. Findings from these studies are pivotal for addressing antimicrobial resistance and chronic diseases while informing public health policy, critical for UN SDG 3 (Good Health and Well-Being). Impactful works in this area include: These efforts underscore that the fight for health equity is inextricably linked with environmental sustainability and social justice.

Revisiting Early Contributions: The Power of Inverse Problems

Before my pivot to microbial informatics, my work in inverse problems provided the analytical bedrock for all that followed. During my PhD (published >40 papers), I focused primarily on the development of static and dynamic algorithms for Inverse Problems that arise in a wide range of engineering areas and worked mainly on Electrical Impedance Tomography (EIT), Electrical Capacitance Tomography (ECT), Mobile Ad hoc Network (MANET), Global Positioning System (GPS), and Inverse Heat Conduction Problem. I have developed novel tomographic imaging methods using EIT and ECT to manipulate measurement data from electrodes attached to the surface of a pipeline in order to estimate the multidimensional distribution of physical parameters inside. As compared to the traditional EIT and ECT, I have considered the scenarios in which the object to be imaged is changing very rapidly during the data acquisition; necessitating a desire for reasonable spatio-temporal resolution. Rather than considering the inverse problem as a traditional tomography reconstruction problem, the problem was formulated as a state estimation problem utilising different kinematic evolution models for the physical parameters along with an observation model based on Finite Element Method (FEM). In particular, I have developed Kalman-type inverse algorithms for: estimation of the concentration distribution by the convection-diffusion equation that allowed for approximation of the velocity field (DOI: 10.1016/j.flowmeasinst.2006.12.005); estimation of time-varying interfacial boundary in stratified flows of immiscible liquids (DOI: 10.1088/0957-0233/19/6/065501; DOI: 10.1088/0957-0233/18/5/012, targeting liquid hydrocarbon transportation in pipelines that often contain free water); imaging of a stirrer vessel for detection of air distribution and detection of air bubbles (DOI: 10.1088/0957-0233/21/3/035501; DOI: 10.1016/j.jcp.2007.12.025; DOI: 10.1088/0957-0233/18/1/008); estimation of settling curves and velocities in the sedimentation process for different layers under the influence of gravity (DOI: 10.1098/rsta.2009.0081, targeting industrial applications such as mining, waste water treatment, and the pulp and paper industry); and visualisation of two-phase flow through rod bundles in nuclear power plants (DOI: 10.1063/1.2747522). These works, though focused on the intricacies of inverse problems, instilled in me the rigorous analytical approach that has been the hallmark of my subsequent research.

Revisiting Early Contributions: Improving Medical Imaging (Computer Vision)

Between 2008 and 2011, I worked as a Post-doc in the University of Cambridge and developed a Hybrid 3D Ultrasound Imaging System. The project focused on: tracking the trajectory of a 3D ultrasound probe based on the image-based registration of acquired data and the output of an inertial position sensor (DOI: 10.1088/0957-0233/21/8/085803; DOI: 10.1243/09544119JEIM586); calibration of the hybrid system; correction of artifacts in the data caused by variations of the pressure from the probe during the scan; differentiation of backscatter into diffuse and directional components using the overlap data from multiple scans (DOI: 10.7863/ultra.32.4.699); and development and evaluation of software tools to enable the system to be used effectively in a hospital environment (DOI: 10.1259/bjr/46007369). The developed system was then shipped to Addenbrookes’ Hospital, Cambridge, where after successfully completing the review by the ethics committee, a clinician explored the range of applications in which such type of a 3D scanner could offer potential benefits. As a proof-of-concept, we carried out a feasibility study recruiting pregnant women attending for routine obstetric ultrasound scans and have obtained promising results (77% to 83% reliability of overlapping scans in clinical trials; DOI: 10.1259/bjr/46007369).

Revisiting Early Contributions: Network Inference

Between 2011 and 2012, I worked as a Senior Post-Doc in the University of Oxford. I scoped a form of dashboard that gives policy makers an integrated view of the state of the UK, both at the current time, and into the past. If we are equipped with a better view of the UK, we can ensure that it is more resilient to shocks. I investigated methods to infer time-varying networks from multiple time signals. The time signals pertain to Google trends, Twitter feeds, stock prices, exchange rates, commodity prices, weather statistics and transport statistics. This project resulted in GlobalView, a software tool for finding both directed and undirected relationships between time signals.

Revisiting Early Contributions: Transition towards understanding biological systems

From 2005 to 2006, I worked on a joint project with the Systems Biology Group at Jeju National University and developed a software, 2D electrophoresis Gel Image Processor for Matlab (DOI: 10.1109/FBIT.2007.95). This software is useful for the analysis of bio-markers by quantifying individual proteins, showing the separation between one or more protein "spots" on a scanned image of a 2D gel, and measuring running differences between several gel images.

What began as a technical challenge - writing image processing algorithms and building analytical tools - soon became something much more meaningful. Immersed in the biological questions driving the project, I found myself increasingly drawn to the science behind the data. This experience marked a pivotal shift in my career trajectory: it was the first time I saw how computational tools could unlock insights into complex biological systems. Working at the interface of engineering and biology, I realized I wanted to move beyond writing code for biology to actually becoming a biologist - someone who could ask the scientific questions, not just support them technically. This project became the bridge that carried me from engineering into the life sciences, reshaping both my professional identity and long-term goals.

Driving Impact Through Innovation and Collaboration

Throughout my career, I have always strived to ensure that my research generates actionable, real-world impact. I have engaged in interdisciplinary collaborations across academia, industry, and governmental agencies to translate scientific discoveries into practical solutions. Whether developing open-source tools that empower thousands of researchers, pioneering sustainable agricultural practices, or revolutionizing water treatment systems, every project is geared toward addressing global challenges as outlined in the UN SDGs. I firmly believe that harnessing microbial intelligence can catalyse progress on many fronts—from combating climate change and ensuring food security to promoting public health and environmental justice.

Looking Forward: A Future Built on Microbial Intelligence

As I reflect on my journey, I am filled with excitement and optimism for the future. In the 21st century, the invisible world of microbes is emerging as a pivotal force in shaping our planet’s destiny. I envision a future where our deep understanding of microbial ecosystems fuels breakthroughs in sustainable agriculture, renewable energy, precision medicine, and environmental resilience. My commitment to advancing microbial informatics - through next-generation computational tools, integrative multi-omics, and robust statistical models - aligns with UN SDG targets and paves the way for a future that is sustainable, equitable, and innovative. Together, by embracing the power of microbial intelligence, we can build a world where the invisible becomes the catalyst for global change.

Grants

I am involved in £22M+ grant money funded as a Principal Investigator(PI)/Co-Investigator(Co-I)/International Participant (with £12M+ brought to University of Glasgow since 2014 that includes £10,577,785 funding from UK Research and Innovation (UKRI) through BBSRC, MRC, EPSRC, and NERC with details available on Gateway to Research (GtR) portal). A noteworthy grant has been my NERC Independent Research Fellowship which over a period of 60 months has resulted in 134 publications with complete list found here. Overall, the grant fundings have resulted in 240+ publications as per my Loop profile: 292992 and ORCID iD iconorcid.org/0000-0001-5780-8551 record.

    Medium Scale to Large Scale Grants

  1. High resolution molecular profiling platform to investigate the role of tumour microbiota in anti-tumour immunity (2025-2027), UKRI Cross Research Council Responsive Mode full stage – Round 1 MR/Z50628X/1 £997,583
    Investigators: H. Yin (PI), U. Z. Ijaz, S. Zanivan, J. Bunch, and W. Huang
    Media coverage:
  2. Combination therapy with biologics and partial enteral nutrition in adults with active ileocolonic Crohn’s disease: The BIOPIC Study (2022-2024), Helmsley Charitable Trust $2,080,024
    Investigators: K. Gerasimidis (PI), J. Macdonald, J. P. Seenan, S. Milling, U. Z. Ijaz, D. Gaya, S. Din, G. -Tzer, C. Mowat, N. Rattray
    Media coverage:
  3. To chlorinate, or not to chlorinate? (2022-2026), EPSRC EP/W037475/1 (University of Glasgow: £862,045), EP/W037270/1 (University of Sheffield: £1,165,060)
    Investigators: J. Boxall (PI), I. Douterelo, K. Fish, V. Speight, C. S. Smith, U. Z. Ijaz, W. T. Sloan, and S. You
  4. Building a Decision Support Tool for Potato Blackleg Disease (DeS-BL) (2020-2023), BBSRC UKRI Strategic Priorities Fund - Bacterial Plant Diseases BB/T010657/1 ~£2M (To Glasgow: ~£360K)
    Investigators: I. Toth (PI), R. Neilson, P. Skelsey, L. Dupuy, J. Milner, B. K. Mable, U. Z. Ijaz, A. Sadanandom, M. Stalham, A. Kleczkowski, G. Jones, D. Walker, G. Saddler, E. Anderson, J. Wilson, S. Alexander, C. Lambourne, and M. Taylor
    Industrial partners: Bayer Crop Science, AHDB, SoilEssentials, SASA, and Scottish Agronomy Ltd
    Twitter: Tweets by Blackleg_Hub
    Media coverage:
  5. A novel dietary therapy to control recurrence of gut inflammation in children with Crohn's disease in remission (01/04/2020-29/03/2025), JP Moulton Charitable Foundation £489,733
    Investigators: K. Gerasimidis (PI), R. Russell, R. Hansen, S. Milling, P. Henderson, D. Wilson, N. Rattray, and U. Z. Ijaz
    Industrial partners: NHS Greater Glasgow and Clyde Health Board
  6. Unravelling the dietary triggers of Crohn's disease and their interplay with the microbiome and host (01/06/2020-01/04/2025), Crohn's & Colitis Foundation £484,924
    Investigators: K. Gerasimidis (PI), R. Russell, R. Hansen, S. Milling, U. Z. Ijaz, and N. Rattray
    Industrial partners: NHS Greater Glasgow and Clyde Health Board
  7. Decentralised water technologies (2021-2026), ESPRC Programme Grant EP/V030515/1 ~£5.9M
    Investigators: W. T. Sloan (PI), S. Connelly, U. Z. Ijaz, Z. Yu, S. You, J. Robbie, A. Clark, J. Amezaga, J. Roberts, R. Ford, C. J. Smith, C. Gauchotte-Lindsay, and A. J. C. Semiao
    Industrial partners (support: £750K): Scottish Water
  8. Gill health in scottish farmed salmon (2018-2022), The Scottish Aquaculture Innovation Centre (SAIC) £2.3M (To Glasgow: £154,694)
    Lead commercial partner: Fish Vet Group
    Lead academic partner: Scotland's Rural College (SRUC)
    Other academic partners: University of Glasgow School of Engineering (C. J. Smith & U. Z. Ijaz)
  9. Optimising decentralised low-cost wastewater infrastructure by managing the microbes (2017-2020), EPSRC Global Challenges Research Fund EP/P029329/1 £1,192,000
    Investigators: W. T. Sloan (PI), T. Koottatep, U. Z. Ijaz, L. Cronin, J. Reboud, and S. Connelly
    Industrial partners (support: £50K): Scottish Water
  10. A microbial basis for Atlantic Salmon energetics (2017-2020), BBSRC-Ireland (SFI) joint funding of research BB/P001203/1 (BBSRC: £587,860; SFI: €638,903)
    BBSRC investigators: M. Llewellyn (PI), U. Z. Ijaz, W. T. Sloan, N. Metcalfe
    SFI investigators: P. McGinnity (PI), P. Connolly, and T. Reed
    Developed system: SalmoSim
    Industrial partners (support: £300K): Alltech, Nofima, Marine Harvest, and SAIC
    Twitter: Tweets by SalmoSim
    Media coverage:
  11. Stable Isotope Probing with Resonance Raman Cell Sorting to profile influence of ocean acidification on microbial carbon fixation (2016-2017), NERC NE/P003826/1 £141,110
    Investigators: H. Yin (PI), M. Cusack, and U. Z. Ijaz
  12. Interactions between the Microbiome, Immunophenotype and Genome in PsA (IMIGPA) (2016-2018), Arthritis Research UK - Microbiome Pathfinder Award £298512.50 (To Glasgow: £139,485)
    Investigators: A. Barton (PI), I. McInnes, C. O'Neil, U. Z. Ijaz, S. Milling, S. Siebert, I. Roberts, A. McBain, and M. Rattray
  13. Molecular epidemiology of Clostridium difficile in Scotland: developing novel, clinically applicable research methods to combine genomic analysis with health informatics (Mar 2014-Aug 2015), Scottish Infection Research Network/Chief Scientist Office £366,638 (To Glasgow: £197,734)
    Investigators: C. Marwick (Co-PI), G. Douce (Co-PI), J. Coia, D. Brown, U. Z. Ijaz, P. Donnan, J. Lindstrom, M. Bennie, C. Wiuff, and P. Davey
    Industrial partners: Health Informatics Centre (University of Dundee), and Scottish Microbiology Reference Laboratories
  14. Late Quaternary Antarctic Cryosphere Interactions (ARCHIE) (2021-2024), FORSKER21 (Norway) NOK 12,000K
    Project manager: S. De Schepper
    Participants: J. L. Ray, A. Larsen, T. Cordier, K. Hakli, C. Guo, and P. Langebroek
    International participants: J. Muller, J. P. Klages, O. Esper, U. Z. Ijaz, S. Belt, and L. Armbrecht
  15. AGENSI - A Genetic View into Past Sea Ice Variability in the Arctic (2019-2023), ERC €2.615M
    PI: S. De Schepper
    Main participants: J. L. Ray, K. S. Skaar, A. Larsen, D. I. Blindheim, The Bjerknes Community, and Nansen Legacy researchers
    International participants: U. Z. Ijaz, R. Stein, and S. Ribeiro
    Project page: norceresearch.no
    Media coverage: Ancient DNA as a new tool for past climate change, November 29, 2018.
  16. Environmental ancient DNA as proxy for sea ice reconstructions (aDNAPROX) (2017-2019), Forskerprosjekt-KLIMAFORSK NOK 8,561K
    Project manager and work package coordinator: S. De Schepper
    Other work package coordinators: J. Stromsoe, and J. L. Ray
    Supporting team: C. Troedsson, K. S. Skaar, H. Sadatzki, T. Dokken, E. Jansens, and Ice2Ice team
    International participants: R. Stein, K. Mertens, and U. Z. Ijaz
    Media coverage: Announcement [Google translated (English)]

  17. Research Fellowships

  18. Lord Kelvin Adam Smith Leadership Fellow: Understanding microbial communities through in situ environmental 'omic data synthesis (Nov 2014-Oct 2019) ~£160K
    Investigator: U. Z. Ijaz (PI)
    Acknowledgement: Received salary from November 2017 to October 2019 (2 years)
  19. NERC Independent Research Fellow: Understanding microbial communities through in situ environmental 'omic data synthesis (Nov 2014-Oct 2019), NERC NE/L011956/1 £425,507
    Investigator: U. Z. Ijaz (PI)
    Acknowledgement: Received salary from November 2014 to October 2017 (3 years)
  20. Research Fellow (Infrastructure & Environment): Characterisation of Gut Microbial Taxonomy and Functionality using Next Generation Sequencing in Children with Crohn's Disease during Exclusive Enteral Nutrition, Crohn's in Childhood Research Association (2013-2014) £34,700
    Acknowledgement: Received 3 months of salary from this grant in 2014 before I started my NERC fellowship
  21. Research Fellow (Infrastructure & Environment): Development of instrumental and bioinformatic pipelines to accelerate commercial applications of metagenomics approaches, Innovate UK (2012-2014) £2,300,000 (To Glasgow: £284,030)
    PI: Yvette Visser (Unilever Plc)
    Acknowledgement: Received salary from 2012 to 2014 (2.5 years)
    Industrial partners: Skalene, Ampliphi, Unilever Plc
  22. Research Fellow (Infrastructure & Environment): To improve the sustainability and affordability of pit latrines, the most common type of on-site sanitation, by developing biotechnology additives and researching pit design and user needs, Bill and Melinda Gates Foundation Grant Number OPP52641 $4,798,496
    PI: J. Ensink
    Acknowledgement: Received salary between 2012 and 2014
  23. Research Fellow (Infrastructure & Environment): Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools, European Union's Earth System Science and Environmental Management ES1103 COST Action
    Acknowledgement: Received support for organization, travel and accommodation for the following hackathons and training school:
    • Cost ES1103: WGs 1 & 2 Inaugural Hackathon: Resolving uncertainty in microbial metagenomics, July 6th-9th 2012, Glasgow, UK
    • From Signals to Environmentally Tagged Sequences" (Ref: ECOST-MEETING-ES1103-050912-018418), September 27th-29th 2012, Hellenic Centre for Marine Research, Crete, Greece
    • COST training school ES1103:Bioinformatics for Microbial Community Analysis , December 11th-14th 2012, University of Liverpool, UK
    • From Signals to Environmentally Tagged Sequences II" (Ref: ECOST-MEETING-ES1103-100613-031037), June 10th-13th 2013, Hellenic Centre for Marine Research, Crete, Greece
    • ProBin: Probabilistic binning for metagenome contigs, June 24th-28th 2013, Instituto Gulbenkian De CieNcia, Lisbon, Portugal
    • WG2 hackathon: Extracting strain level variation from shotgun metagenome data, Isaac Newton Institute, November 7th-11th, Cambridge, UK
    • From signals to environmentally tagged sequences III, September 22nd -25th 2014, Hellenic Centre for Marine Research, Crete, Greece

  24. Small Scale Research Projects, Studentships, and Mobility Grants
    (Primarily Supporting Early Career Researchers)

  25. Applying Shotgun Metagenomics to the NEO-MICROBE BREAST Study (2025-2026), Beatson Cancer Charity Grants Award 2024 ~£27K
    PI: K. Ross (lead), U. Z. Ijaz, and I. Macpherson
  26. Risk Assessment and Spatial Clustering of Infectious Diseases among Afghan Refugees (2023), International Center for Refugee and Migration Studies, Pakistan PKR 600,000
    PI: Z. Noreen, U. Z. Ijaz, and A. khurshid
    Media coverage:
  27. CASDU CROP SOLUTIONS: Developing a commercial bacteriocin-based treatment for protecting seed and ware potatoes against Blackleg disease and soft rot (2022), BBSRC Impact Acceleration Award ~£20,000, IBioIC Spin-out Support Programme ~£10,000
    PI: J. Milner
    Academic Collaborators: D. Walker, B. K. Mable, and U. Z. Ijaz
    Industrial Collaborator: Simon Alexander (SA Consulting)
  28. Integrated one health approach for identification of AMR hotspots within poultry farms in Pakistan (2022), Wellcome Trust Institutional Strategic Support Fund (ISSF) — Feasibility Scheme Application [204820/Z/16/Z](2022), University of Glasgow ~£8,848
    Early career researcher and PI: C. Keating
    PhD Student: Aqsa Ameer
    PhD Supervisors: S. Javed (lead) and U. Z. Ijaz
  29. MVLS/CoSE Workshop - Engineering Biology Pitch (2022), University of Glasgow ~£10K
    Team: A. Kostrytsiia (lead/PI), U. Z. Ijaz (Collaborator), and T. Otto (Collaborator)
  30. Reinvigorating Research Scheme (2022), University of Glasgow ~£40K
    PI: C. Unluer
    Co-Investigators: U. Z. Ijaz, J. MacDonald, and T. Shire
  31. Reinvigorating Research Scheme (2022), University of Glasgow ~£40K
    PI: H. Yin
    Co-Investigators: K. Gerasimidis, U. Z. Ijaz, and J. Reboud
    External-Investigators: C. Probert, W. Huang, and J. Li
    International and industrial collaborators: S. Liu, D. Berry, and Horiba
  32. Bio-engineering of water biofilter communities for enhanced degradation of DOM (2021-2022), Environmental Biotechnology Network (EBNet): Proof of Concept (PoC) Award Application ~£39,999
    Early career researcher and PI: M. Vignola
    Co-Investigators: R. Pereira, U. Z. Ijaz, and C. Smith
  33. How do free-living nematodes (FLN) interact with the microbial populations in soil? (2021-2022), MVLS Wellcome Institutional Strategic Support Fund (ISSF) ECR Catalyst Grant ~£22,346
    Early career researcher and PI: C. Keating
    Co-Investigators: B. Mable, U. Z. Ijaz, J. Milner, and R. Neilson
  34. B-cin Quest: Development of a curated database and workflow for searching for existing and novel bacteriocins produced by bacterial genera associated with plant pathogens (Summer 2021), Society for Applied Microbiology Summer Student Placement ~£2,500
    Student: Scott Saunderson (Glasgow Caledonian University)
    PI: C. Keating
    Supervisors: U. Z. Ijaz (lead and host), C. Keating, B. K. Mable, and J. Milner
  35. B-cin Quest: Developing a curated database and workflow for searching for existing and novel bacteriocins produced by plant pathogenic bacteria (Summer 2021), British Society for Plant Pathology Undergraduate Vacation Bursary ~£3,500
    Student: Alexandru Popescu (University of Glasgow)
    PI: J. Milner
    Supervisors: U. Z. Ijaz (lead and host), C. Keating, B. K. Mable, and J. Milner
  36. Pump Priming Grant (Hand Transplant Microbiome) - Royal College of Surgeons of England (2021-2022) ~£10K
    Investigator: D. Leonard
    Partners: S. Milling, K. Gerasimidis, M. Castelino, and U. Z. Ijaz
  37. International Research Support Initiative Program (2023), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2023/12790 ~£7K
    PhD. student: Aqsa Ameer (COMSATS University, Islamabad, Pakistan)
    Foreign supervisor: U. Z. Ijaz
    Co-supervisor: C. Keating
  38. International Research Support Initiative Program (2023), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2023/12777 ~£7K
    PhD. student: Rhea Aqueel (Forman Christian College, Lahore, Pakistan)
    Foreign supervisor: U. Z. Ijaz
  39. International Research Support Initiative Program (2022), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2022/11998 ~£7K
    PhD. student: Maria Batool (COMSATS University, Islamabad, Pakistan)
    Foreign supervisor: U. Z. Ijaz
    Co-supervisor: C. Keating
  40. International Research Support Initiative Program (2021-2022), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2021/10904 ~£7K
    PhD. student: Zainy (COMSATS University, Islamabad, Pakistan)
    Foreign supervisor: U. Z. Ijaz
    Co-supervisor: C. Keating, A. Kostrytsiia
  41. International Research Support Initiative Program (2022), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2021/11509 ~£7K
    PhD. student: Sara Bibi (COMSATS University, Islamabad, Pakistan)
    Foreign supervisor: U. Z. Ijaz
    Co-supervisor: C. Keating, A. Kostrytsiia
  42. International Research Support Initiative Program (2020), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2020/10901 ~£7K (Deferred)
    PhD. student: Habiba Tariq (COMSATS University, Islamabad, Pakistan)
    Foreign supervisor: U. Z. Ijaz
    Co-supervisor: C. Keating
  43. International Research Support Initiative Program (2019-2020), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2019/8794 ~£7K
    PhD student: Alam Khan (Quaid-i-Azam University, Islamabad, Pakistan)
    Foreign supervisor: U. Z. Ijaz
    Co-supervisor: C. Keating, A. Kostrytsiia
  44. Growing up (and old) with the help of little friends: understanding the role of gut microbiota in the growth-lifespan trade-off (2019-2020), MVLS Wellcome Institutional Strategic Support Fund (ISSF) ECR Catalyst Grant £19,800
    Early career researcher and PI: P. Salmon
    Other co-applicants: U. Z. Ijaz, K. Gerasimidis, and M. Lewellyn
  45. Use of novel mixomics tools to investigate intestinal fungi in Crohn's disease (2019-2020), Royal Liverpool and Broadgreen University NHS Hospital Trust Application for Funding 2019/2020 £16,500
    Early career researcher and co-investigator: A. Frau (University of Liverpool)
    PI: C. Probert (University of Liverpool)
    Partners: S. Allen (Alder Hey), and U. Z. Ijaz
  46. Analysis pipeline for sea ice reconstructions using ancient environmental DNA (2018), 6 months research visit under Forskerprosjekt-KLIMAFORSK Project No. 273455 NOK 124K (~£12K)
    Early career researcher and PI: J. L. Ray (NORCE, Norway)
    Host: U. Z. Ijaz
  47. Exploring the inter-kingdom relationships of gut microbiota in Crohn's disease (01/02/17-01/02/18), Joint BSPGHAN / Crohn's and Colitis UK Start-up Research Grant £9,980
    Investigators: K. Gerasimidis (PI), G. Ramage, R. K. Russell, R. Hansen, and U. Z. Ijaz
  48. Leadership Training Bursaries for NERC fellows (2016) £23,100
    Note: Tuition fee for Cambridge Advanced Leadership Programme (Judge Business School, University of Cambridge, UK)
  49. Cabbages, microbes and diversity, Glasgow Polyomics ISSF Consolidator Funding, Wellcome Trust grant 105614/Z/14/Z £7,000
    PI and lead supervisor: B. K. Mable
    PhD student: Elizabeth Mittel
    Co-supervisor: U. Z. Ijaz
  50. Variation in the human pharyngeal microbiome in health and disease, ISSF Catalyst Funding, Wellcome Trust £20,300
    PI and lead supervisor: J. Lindstrom
    PhD student: Asha Ram
    Co-supervisor: U. Z. Ijaz
  51. To perform faecal metabolomics and combine with existing whole genome metagenomics, Glasgow Polyomics ISSF Consolidator Funding £6,995
    PI: K. Gerasimidis
    Named collaborator: U. Z. Ijaz
  52. Kelvin Smith PhD Scholarships 2015/16 (~£78,000)
    PhD student: Zihan Dai
    Supervisors: U. Z. Ijaz (lead), and A. J. Pinto
  53. Kelvin Smith PhD Scholarships 2014/15 (~£120,000)
    PhD student: Elizabeth Mittell
    Supervisors: B. K. Mable (lead), U. Z. Ijaz, and C. Cobbold
  54. Kelvin Smith PhD Scholarships 2012/13 (~£106,012)
    PhD student: Asha Ram
    Supervisors: J. Lindstrom (lead), U. Z. Ijaz, and T. Evans
  55. IPP with Nestle Global to fund research exploring the role of gut microbiota in Crohn's disease and changes during exclusive enteral nutrition (~£150,000)
    PhD student: Orges Koci
    Supervisors: K. Gerasimidis (lead), U. Z. Ijaz, and R. K. Russell
  56. To study the gut microbiome of chickens over the course of 35 days and to investigate the onset of Campylobacter (2017), Moy Park, Belfast, UK £50,000
    Early career researcher and investigator: O. Gundogdu (LSHTM, London)
    Other investigators: N. Corcionivoschi (AFBI, Belfast), and N. Dorrell (LSHTM, London)
    Host and partner: U. Z. Ijaz
  57. ENVIRONMENTS: Discovering habitat terms in EOL Contents, Encyclopedia of Life 2013 Rubenstein Research Fellowship $50,000
    Early career researcher and investigator: E. Pafilis
    Named international collaborator: U. Z. Ijaz
    Project page: environments-eol (Blogspot)
  58. Diversity and quantification of microbial communities in terrestrial environments, Resolved project no. CZ.1.07/2.2.00/15.0364 - Molecularisation of biological fields of the Faculty of Science of JU, financed by the European Social Fund and the state budget of the Czech Republic, as part of the Education for Competitiveness Operational Programme $1,100
    Lecturer: U. Z. Ijaz (delivered approximately 14 hours of lectures at Faculty of Science, Ceske Budejovice, Czech Republic on interpretation of metagenomic data in microbial ecology)
    Host: A. Chronakova
  59. Send-A-Newbie Award (YAPC::EU 2012) ~£600

  60. Other Grants

  61. How does the microbiome of the hypochlorhydric stomach promote gastric tumourigenesis? AICR £199,357
    Investigators: M. Pritchard (PI), A. Varro, and N. Hall
    Collaborator: U. Z. Ijaz
  62. Do gut bacteria have a role in the aetiology of type 2 diabetes? European Foundation for the study of Diabetes ISRCTN07813749
    PI: D. Robertson
    Collaborator: U. Z. Ijaz
  63. IDEAS Factory - Global View (2011-2012), EPSRC EP/I005986/1 £199,342
    PI: N. Jones
    Senior PostDoc: U. Z. Ijaz
    Project page: Project Global View (blogspot)
    Acknowledgement: Received salary from 2011 to 2012 (1 year)
  64. Hybrid Three-Dimensional Ultrasound (2008-2011), EPSRC EP/F016476/1 £385,012
    PI: R. Prager
    PostDoc: U. Z. Ijaz
    Project page: Hybrid 3D Ultrasonic Imaging (Medical Imaging Group, Engineering Department, University of Cambridge)
    Acknowledgement: Received salary from 2008 to 2011 (3 years)
  65. The 2nd Phase Brain Korea 21 (BK21) Project (2006-2008)
    PhD student and PI: U. Z. Ijaz
    Scholarship: ₩300,000/month for 12 months (2007-2008)
    Award: Best Researcher of the Year (2008) ₩1,500,000
    Award: Best Researcher of the Year (2007) ₩1,000,000
  66. Korea Science and Engineering Foundation Grant No. R01-2007-000-20155-0 (2007-2008)
    PhD student and PI: U. Z. Ijaz
  67. Research Grant of Jeju National University (2007)
    PhD student and PI: U. Z. Ijaz
  68. Korea Research Foundation Grant No. KRF-2005-013-D00075 (2005)
    PhD student and PI: U. Z. Ijaz
  69. Hyocheon Research Fund of the Cheju National University Development Foundation (2005)
    PhD student and PI: U. Z. Ijaz
  70. Korea Science and Engineering Foundation Grant No. R01-2004-000-0040-0 (2004)
    PhD student and PI: U. Z. Ijaz
  71. 2D Electrophoresis Gel Image Processor for Matlab (2005-2006), Ministry of Commerce, Industry and Energy, Korea Grant No. S1005503
    PhD student and PI: U. Z. Ijaz
    Scholarship: ₩350,000/month for 12 months (2005-2006)
    Award: LG Electronics - Excellent Achievement Award (The Second Prize) (2006) ₩500,000
  72. Korean Government IT Scholarship (2004-2008), Institute of Information Technology Assessment, Korea ₩56,000,000 (~$56,000)
  73. JNU Category-A Scholarship (2004-2006)
    Note: Full tuition fee waiver during PhD coursework
  74. GIKI Merit Scholarship (2001-2003)
    Note: Awarded after standing 2nd in the entrance exam for MPhil; Full tuition fee waiver during MPhil coursework and received a monthly stipend of PKR 5000/month

Supervisions

To date, with my involvement, there is a successful completion of 45 PhD theses. Some of these were enrolled in University of Glasgow, others outside of Glasgow where I have acted in the capacity of a foreign supervisor and/or hosted the students in my lab. In majority of the cases, I have conceded support on bespoke bioinformatics and statistical analyses utilising Orion cluster and my software portfolio.

    Academic Visitors

  1. Dr Aneeba Rashid (Honorary Researcher, Department of Botany/Department of Microbiology, GC University Lahore)
    Global Talent Visa (Exceptional Promise)
    Host(2025-): U. Z. Ijaz
  2. Associate Prof. Dr Mujtaba Hassan (Head of Department of Space Science, Institute of Space Technology, Pakistan)
    Charles Wallace Visiting Fellowship 2024-2025
    Host(2025-): U. Z. Ijaz
  3. Assistant Prof. (MLT) Dr Shahid Aziz (Institute of Allied Health Sciences, Wah Medical College, Pakistan)
    Charles Wallace Visiting Fellowship 2024-2025
    Host(2024-): U. Z. Ijaz
  4. Assistant Prof. Dr Zobia Noreen (COMSATS University, Islamabad, Pakistan)
    Host(2024-): U. Z. Ijaz
  5. Associate Prof. Dr Sundus Javed (COMSATS University, Islamabad, Pakistan)
    Host(2024-): U. Z. Ijaz
  6. Associate Prof. Dr Aamira Tariq (COMSATS University, Islamabad, Pakistan)
    Host(2024-): U. Z. Ijaz
  7. Assistant Prof. Dr. Shawkat A . Yaseen Kochary (Head, Department of Civil Engineering, University of Duhok, Iraq)
    Erasmus+ International Credit Mobility, Host(2022): U. Z. Ijaz
  8. Associate Prof. Dr Ozan Gundogdu (London School of Hygiene & Tropical Medicine, UK)
    Host (2017-): U. Z. Ijaz
    Visitor to Environmental'Omics Lab 2017, 2018, and 2019
    Supervisor on his MSc Bioinformatics Project (Queen Mary University of London), 2020
    Mentor (2017-2020): U. Z Ijaz [Grant: To study the gut microbiome of chickens over the course of 35 days and to investigate the onset of Campylobacter, Moy Park]

  9. Early Career Researchers/Post Docs

    Note: Where known, grants (in some cases I act in the capacity of a collaborator and not formal investigator) supporting the research activities are also acknowledged.
  10. Dr Banaz Star-Shirko (London School of Hygiene & Tropical Medicine)
    Visiting PGR to University of Glasgow under Daphne Jackson Fellowship entitled "Investigating the Chicken Gut Microbiome to Understand Campylobacter Prevalence and Mechanisms to Implement Intervention and Control Strategies" (University of Glasgow Student ID: 2956622)
  11. Dr Simon Mills (NUI Galway, Ireland)
    Mentors (2021-): P. N. L. Lens (lead), and U. Z. Ijaz
  12. Dr Ciara Keating (University of Glasgow, UK)
    Mentors (2020-2023): B. K. Mable (lead), U. Z. Ijaz, and J. Milner [Grant: Building a Decision Support Tool for Potato Blackleg Disease (DeS-BL), BBSRC UKRI Strategic Priorities Fund - Bacterial Plant Diseases BB/T010657/1]
    Mentors (2016-2020): W. T. Sloan (lead), and U. Z. Ijaz [Grant: Optimising decentralised low-cost wastewater infrastructure by managing the microbes, EPSRC Global Challenges Research Fund EP/P029329/1]
  13. Dr Anna Trego (O'Flaherty Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab (2019-)
    Hosted on Orion Cluster (2020-)
    Mentors (2019-): V. O'Flaherty (lead), and U. Z. Ijaz [Grant: Supported by funding to O'Flaherty Lab]
  14. Dr Tristan Cordier (AGENSI Group, NORCE Research, Norway)
    Hosted on Orion Cluster (2020-)
    Mentors (2020-): S. De Schepper (lead), and U. Z. Ijaz [Grant: AGENSI - A Genetic View into Past Sea Ice Variability in the Arctic, ERC]
  15. Dr Tarah Lynch (University of Calgary, Canada)
    Virtual visitor to Environmental'Omics Lab (2019-)
    Mentor (2019-): U. Z. Ijaz
  16. Dr Fauzy Nasher (London School of Hygiene & Tropical Medicine, UK)
    Mentors (2019-2020): O. Gundogdu (lead), and U. Z. Ijaz [Grant: Microbes in the Food Chain, as part of the Quadram Institute BBSRC Strategic Programme]
  17. Dr Ben Nichols (University of Glasgow, UK)
    Hosted on Orion Cluster (2020-)
    Mentors (2018-): U. Z. Ijaz (lead), and K. Gerasimidis [Grant: Supported by grants to BINGO Group]
  18. Dr Bachar Cheaib (University of Glasgow, UK)
    Mentors (2018-2020): U. Z. Ijaz (lead), M. Llewellyn, and W. T. Sloan [Grant: A microbial basis for Atlantic Salmon energetics, BBSRC-Ireland (SFI) joint funding of research BB/P001203/1; Grant: Optimising decentralised low-cost wastewater infrastructure by managing the microbes, EPSRC Global Challenges Research Fund EP/P029329/1]
  19. Dr Paolo Dessi (Collins Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab (2020-)
    Mentor (2020-): U. Z. Ijaz [Grant: "HyBioSol", hybrid bio-solar reactors for CO2 recycling and wastewater treatment (PI: P. Dessi), Science Foundation Ireland]
  20. Dr Marta Vignola (University of Glasgow, UK)
    Mentors (2017-2019): W. T. Sloan (lead), and U. Z. Ijaz [Grant: Synthetic biology applications to water supply and remediation, EPSRC EP/K038885/1 Frontier Engineering]
    Mentor (2019-): U. Z. Ijaz [Grant: Eco-Engineered biofilters for sustainable removal of pesticides in drinking water (PI: M. Vignola), Royal Academy of Engineering for Development Research Fellowship]
  21. Dr Adrian Ho (Leibniz University, Germany)
    Mentor (2015-): U. Z. Ijaz [Adrian's work is supported by Wissenschaftliche Mitarbeiter since 2017]
  22. Dr Suniti Singh (Collins Lab, Tampere University of Technology, Finland)
    Virtual visitor to Environmental'Omics Lab (2019-2020)
    Mentors (2019-2020): G. Collins (lead), and U. Z. Ijaz [Grant: Supported by funding as ABWET Marie-Curie Early Stage Researcher]
  23. Dr Julien Plancq (University of Glasgow, UK)
    Mentors (2017-2019): J. Toney (lead), and U. Z. Ijaz [Grant: Project: ALKENoNE, ERC Starting Grant]
  24. Dr Seung Gu Shin (Gyeongnam National University of Science and Technology, South Korea)
    Mentors (2014-2016): W. T. Sloan (lead), and U. Z. Ijaz [Grant: Synthetic biology applications to water supply and remediation, EPSRC EP/K038885/1 Frontier Engineering]
  25. Dr Katharina Besemer (University of Vienna, Austria)
    Vistor to Water & Environment Research Group (2014-2015)
    Virtual visitor to Environmental'Omics Lab (2016-)
    Hosted on Orion Cluster (2014-)
    Mentor (2014-): W. T. Sloan, and U. Z. Ijaz [Grant: Erwin Schrodinger Fellowship (Austrian Science Fund, J-3542-B22)]
  26. Dr Xiaofei Yuan (University of Glasgow, UK)
    Mentors (2017-2018): H. Yin (lead), U. Z. Ijaz, and M. Cusack [Grant: Stable Isotope Probing with Resonance Raman Cell Sorting to profile influence of ocean acidification on microbial carbon fixation, NERC NE/P003826/1]
  27. Dr Richard Randle-Boggis (University of Glasgow, UK)
    Mentors (2017-2020): S. Connelley (lead), U. Z. Ijaz, and W. T. Sloan [Grant: Optimising decentralised low-cost wastewater infrastructure by managing the microbes, EPSRC Global Challenges Research Fund EP/P029329/1]
  28. Dr Kevin Bayle (University of Glasgow, UK)
    Mentors (2016-2017): U. Z. Ijaz (lead), and C. Gauchotte-Lindsay [Grant: Interactions between the Microbiome, Immunophenotype and Genome in PsA (IMIGPA), Arthritis Research UK - Microbiome Pathfinder Award]
  29. Dr Elizabeth McDonald (University of Glasgow, UK)
    Mentors (2016-2018): S. Milling (lead), and U. Z. Ijaz [Grant: Interactions between the Microbiome, Immunophenotype and Genome in PsA (IMIGPA), Arthritis Research UK - Microbiome Pathfinder Award]
  30. Dr Madhura Castelino (University of Manchester, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2014
    Mentors (2016-2018): A. Barton (lead), U. Z. Ijaz, and S. Milling [Grant: Interactions between the Microbiome, Immunophenotype and Genome in PsA (IMIGPA), Arthritis Research UK - Microbiome Pathfinder Award]
  31. Dr Aoife Duff (University of Glasgow, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2017
    Mentors (2016-2018): C. J. Smith (lead), and U. Z. Ijaz [Grant: Molecular ecology of ammonia oxidation in coastal sediments, Science Foundation Ireland (SFI), Starting Investigator Research Grant (11/SIRG/B2159)]
  32. Dr Camilla Pedersen (University of Surrey, UK)
    Visitor to Environmental'Omics Lab 2015, and 2016
    Mentors (2015-2016): D. Robertson (lead), and U. Z. Ijaz [Grant: Do gut bacteria have a role in the aetiology of type 2 diabetes?, European Foundation for the study of Diabetes ISRCTN07813749]
  33. Dr Anastasiia Kostrytsia (University of Glasgow, UK)
    Mentors (2019-): C. J. Smith (lead), and U. Z. Ijaz [Grant: Biofiltration by biological design, Royal Academy of Engineering-Scottish Water Senior Reserach Fellowship]
  34. Dr Anastasis Oulas (Cyprus Institute of Neurology and Genetics)
    Collaborator (2012-2014): U. Z. Ijaz [Grant: Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools, COST Action ES1103]
  35. Dr Evangelos Pafilis (Hellenic Centre for Marine Research, Greece)
    Collaborator (2012-2014): U. Z. Ijaz [Grant: Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools, COST Action ES1103; Grant: ENVIRONMENTS: Discovering habitat terms in EOL Contents, Encyclopedia of Life 2013 Rubenstein Research Fellowship]
  36. Dr Christina Pavloudi (Hellenic Centre for Marine Research, Greece)
    Collaborator (2012-2014): U. Z. Ijaz [Grant: Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools, COST Action ES1103; Grant: ENVIRONMENTS: Discovering habitat terms in EOL Contents, Encyclopedia of Life 2013 Rubenstein Research Fellowship]
  37. Dr Jo De Vrieze (Ghent University, Belgium)
    Visitor to Environmental'Omics Lab 2016 (3 months)
    Mentor (2016-): U. Z. Ijaz (lead), W. T. Sloan, and A. J. Pinto [Mobility grant: Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools, COST Action ES1103]
  38. Dr Jillian Couto-Phoenix (University of Glasgow, UK)
    Mentors (2013-2019): W. T. Sloan (lead) and U. Z. Ijaz [Grant: Synthetic biology applications to water supply and remediation, EPSRC EP/K038885/1 Frontier Engineering]
  39. Dr Bryony Parsons (University of Liverpool, UK)
    Mentors (2016-2017): M. Pritchard (lead), and U. Z. Ijaz [Grant: How does the microbiome of the hypochlorhydric stomach promote gastric tumourigenesis?, AICR]
  40. Dr Alessandra Frau (University of Liverpool, UK)
    Visitor to Environmental'Omics Lab 2017 and 2018
    Mentors (2017-): C. Probert (lead), and U. Z. Ijaz [Grant: Use of novel mixomics tools to investigate intestinal fungi in Crohn's disease, Royal Liverpool and Broadgreen University NHS Hospital Trust]
  41. Dr Jessica Louise Ray (AGENSI Group, NORCE Research, Norway)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2014
    Visitor to Environmental'Omics Lab 2018 (6 months)
    Mentor (2014-): U. Z. Ijaz (lead) [Mobility grant: COST-EU STSM (2014); Mobility grant: Research Council of Norway KLIMAFORSK Mobility Grant (2018)]
  42. Dr Cosmika Goswami (University of Glasgow, UK)
    Mentors (2014-2015): U. Z. Ijaz (lead), and G. Douce [Grant: Molecular epidemiology of Clostridium difficile in Scotland: developing novel, clinically applicable research methods to combine genomic analysis with health informatics, Scottish Infection Research Network/Chief Scientist Office]
  43. Dr Sarah Buchanan (University of Glasgow, UK)
    Mentors (2014-2015): G. Douce (lead), and U. Z. Ijaz [Grant: Molecular epidemiology of Clostridium difficile in Scotland: developing novel, clinically applicable research methods to combine genomic analysis with health informatics, Scottish Infection Research Network/Chief Scientist Office]

  44. Current PhD Students

  45. Alison Graham (University of Galway, Ireland)
    Research title: Revealing microbiome responses to novel oxygen-releasing ruminant feed additives
    Supervisor: V. O'Flaherty (lead), and U. Z. Ijaz (foreign supervisor)
  46. Kris Anthony Silveira (University of Galway, Ireland)
    Research title: Effect of electroactive taxa on syntrophic propionate oxidisers within Methanogenic consortium under pulsed metal dosing
    Supervisor: V. O'Flaherty (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under funds from University of Galway (University of Glasgow Student ID: 3062947)
  47. Aideen Kearney (University of Galway, Ireland)
    Research title: Enhancing farmed Atlantic salmon (Salmo salar) quality through new production technologies
    Supervisor: M. Johnson (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under funds from University of Galway (University of Glasgow Student ID: 3063241)
  48. Maya Subberwal (University of Glasgow, UK)
    Research title: Understanding the impact of sustainable agricultural practices on crop development by focusing on microbial ecology and the exposome
    Supervisors: U. Z. Ijaz (lead), M. Giles, C. Hawes, A. Holmes, and I. Toth
  49. William Roy (University of Glasgow, UK)
    Supervisors: C. Smith (lead), U. Z. Ijaz, K. Thompson, and D. Price
  50. Yecang Chen (University of Glasgow, UK)
    Supervisors: H. Yin (lead), and U. Z. Ijaz
  51. Hajra Khurshid (COMSATS University, Islamabad, Pakistan)
    Supervisor: A. Tariq (lead)
    Collaborator: U. Z. Ijaz
  52. Nukhba Khan (COMSATS University, Islamabad, Pakistan)
    Supervisors: S. T. A. Shah (lead), S. Javed, and U. Z. Ijaz
  53. Tooba Ashiq Seyal (COMSATS University, Islamabad, Pakistan)
    Supervisors: S. T. A. Shah (lead), M. Y. Khan, and U. Z. Ijaz
  54. Ayesha Badder (Forman Christian College, Pakistan)
    Supervisor: K. A. Malik (lead)
    Collaborator: U. Z. Ijaz
  55. Maria Pangga Gladys (London School of Hygiene and Tropical Medicine)
    Supervisors: O. Gundogdu (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under BBSRC funds (University of Glasgow Student ID: 2956622)
  56. Maria Soledad Martinez Martinez (University of Uruguay; Visiting PGR 2024)
    Supervisors: M. P. Cerdeiras (lead), I. D. Soler, and U. Z. Ijaz (co-supervisor & foreign supervisor)
    Visiting PGR to University of Glasgow under funds from University of Uruguay (University of Glasgow Student ID: 3041532)
  57. Habiba Tariq (COMSATS University, Islamabad, Pakistan)
    Supervisors: H. Bukhari (lead), Z. Noreen, and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2020/10901 (University of Glasgow Student ID: 2697609)
  58. Farrukh Saleem (COMSATS University, Islamabad, Pakistan)
    Supervisors: S. Javed (lead), U. Z. Ijaz

  59. Past PhD Theses

  60. Dr Maria Batool (COMSATS University, Islamabad, Pakistan)
    PhD thesis: Identification and Characterization of Antibiotic resistance patterns In the Pakistani cohort using Predictive Metagenomics and Bioinformatics (2025)
    Supervisors: M. Mudassar (lead), U. Z. Ijaz (co-supervisor & foreign supervisor), A. Nasir, and S. Javed
    Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2023/12790 (University of Glasgow Student ID: 2810125)
  61. Dr Hajra Ashraf (University of Sassari, Italy)
    PhD thesis: Microbiome analysis of MAP-positive and MAP-negative individuals with Multiple sclerosis (2025)
    Supervisors: L. A. Sechi (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under ULISSE International Mobility Grant & ERASMUS+ Traineeship (University of Glasgow Student ID: 2950130)
  62. Dr Aqsa Ameer (COMSATS University, Islamabad, Pakistan)
    PhD thesis: Characterization of Chicken Gut Microbiota in Different Pakistani Breeds with Special Reference to Disease Resistance (2025)
    Supervisors: S. Javed (lead), U. Z. Ijaz (co-supervisor & foreign supervisor), S. Sattar, and Z. Noreen
    Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2023/12790 (University of Glasgow Student ID: 2912085)
  63. Dr Zabish Khaliq (Forman Christian College, Pakistan)
    PhD thesis: Development of bioformulations for the field application of biofertilizers (2024)
    Supervisor: K. A. Malik (lead), and U. Z. Ijaz (foreign supervisor)
  64. Dr Linghui Shi (University of Glasgow, UK)
    PhD thesis: Microbial communities and off-grid wastewater treatment (2024)
    Supervisors: C. J. Smith (lead), W. T. Sloan, U. Z. Ijaz, and S. Connelly
  65. Dr Farzana Gul (COMSATS University, Islamabad, Pakistan)
    PhD thesis: Taxonomic structure, biological functions, and phylogenomic diversity of the Pakistani gastrointestinal microbiota in health and disease (2024)
    Supervisors: S. Javed (lead), and U. Z. Ijaz
  66. Dr Zainy (COMSATS University, Islamabad, Pakistan)
    PhD thesis: Studying molecular mechanism of Wheat-Puccinia striformis interactions (2024)
    Supervisors: S. Farrakh (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2021/10904 (University of Glasgow Student ID: 2697612)
  67. Dr Sara Bibi (COMSATS University, Islamabad, Pakistan)
    PhD thesis: Health impacts of fluoride over exposure in Pakistani population (2024)
    Supervisors: M. Nurulain (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2021/11509
  68. Dr Rhea Aqueel (Forman Christian College, Pakistan)
    PhD thesis: Comparative microbiome analysis for viral disease suppression in cotton (2024)
    Supervisors: K. A. Malik (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2023/12777 (University of Glasgow Student ID: 2914245)
  69. Dr Erin Corbett (University of Strathclyde, UK)
    PhD thesis: Analysis of the chemistry & microbiology of urban stormwater & its treatment by rain gardens (2022)
    Supervisors: V. Phoenix, and R. Lunn
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2021-2022)
  70. Dr Kelly Stewart (University of Glasgow, UK)
    PhD thesis: The role of the microbiome in the gill health of farmed Scottish Atlantic salmon (2022)
    Supervisors: C. J. Smith (lead), G. J. Gunn, A. S. Boerlage, and U. Z. Ijaz
  71. Dr Melissa Elizabeth Moore (University of Glasgow, UK)
    PhD thesis: The effect of acute amoxicillin exposure on anaerobic microbial communities - activity, ecology and resistome (2022)
    Supervisors: S. Connelly (lead), W. T. Sloan, and U. Z. Ijaz
  72. Dr Konstantinos Gkikas (University of Glasgow, UK)
    PhD thesis: Unravelling dietary triggers of gut inflammation in children with Crohn's disease (2022)
    Supervisors: K. Gerasimidis (lead), S. Milling, R. K. Russell, and U. Z. Ijaz
  73. Dr Caroline Kerbiriou (University of Glasgow, UK)
    PhD thesis: Immunopathogenesis of non-IgE-mediated cow’s milk protein allergy and the role of the microbiome (2022)
    Supervisors: K. Gerasimidis (lead), S. Milling, G. Raptis, and U. Z. Ijaz
  74. Dr Fabien Cholet (University of Glasgow, UK)
    PhD thesis: Optimising and applying RNA based approaches to identify active nitrifiers in coastal sediments (2021)
    Supervisors: C. Smith (lead), and W. T. Sloan
    Host, tutor, and collaborator: U. Z. Ijaz (Environmental'Omics Lab 2017-2020)
  75. Dr Aaron McKenna (Queen's University, Belfast, UK)
    PhD thesis: Campylobacter spp. within the UK poultry industry: Prevalence, risk factors and the chicken microbiome (2021)
    Supervisors: B. Green (lead), and N. Corcionivoschi
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2018-2020)
  76. Dr Simon Mills (Collins Lab, NUI Galway, Ireland)
    PhD thesis: Methanogenic sludge granules: Granulation microbiology and potential for selenium reduction (2021)
    Supervisors: G. Collins (lead), and U. Z. Ijaz
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2018-2020)
  77. Dr Alam Khan (Quaid-i-Azam University, Islamabad, Pakistan)
    PhD thesis: Enhancement of biogas production and biogas upgradation in two stage anaerobic digestion process (2021)
    Supervisor: M. Badshah (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2019/8794 (University of Glasgow Student ID: 2509902)
  78. Dr Christina Nikolova (Heriot-Watt University, UK)
    PhD thesis: Characterisation and effectiveness evaluation of microbial biosurfactants for their use in oil spill response (2021)
    Supervisors: T. Gutierrez (lead), and U. Z. Ijaz
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2019-2020)
  79. Dr Eleanor Lindsay (University of Glasgow, UK)
    PhD thesis: Ecophysiological Exploration: The Microbiota, Metabolic Rate and Behaviour of Juvenile Atlantic Salmon (Salmo Salar) (2021)
    Supervisors: M. Llewellyn (lead), U. Z. Ijaz, N. Metcalfe, and W. T. Sloan
  80. Dr Ellen McGrory (NUI Galway, Ireland)
    PhD thesis: Environmental aqueous geochemistry of arsenic in groundwater: occurrence, speciation and biogeochemical processes (2020)
    Supervisors: L. Morrison
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2019-2020)
  81. Dr Orges Koci (University of Glasgow, UK)
    PhD thesis: Development of software framework for the integration of metagenomics with clinical and metadata (2020)
    Supervisors: K. Gerasimidis (lead), U. Z. Ijaz, and R. K. Russell
  82. Dr Michael Logan (University of Glasgow, UK)
    PhD thesis: Compositional analysis of exclusive enteral nutrition and its effects on the paediatric Crohn's disease faecal microbiome and metabolome during treatment and food reintroduction (2020)
    Supervisors: U. Z. Ijaz (lead), and K. Gerasimidis
  83. Dr Hyojin Song (Seoul National University, South Korea)
    PhD thesis: Applications of Transcriptomic Studies in Human Cancers (2020)
    Supervisors: S. -S. Yoon (lead), and U. Z. Ijaz (foreign supervisor)
    Visiting PGR to University of Glasgow under mobility grant from Seoul National University (University of Glasgow Student ID: 2445641)
  84. Dr Kym Bain (University of Glasgow, UK)
    PhD thesis: The immunopathogenesis of Alopecia Areata (2020)
    Supervisors: S. Milling (lead), A. Astrand, and I. McInnes
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2018-2020)
  85. Dr Clare Clark (University of Glasgow, UK)
    PhD thesis: Gut Microbial Taxonomy and Metabolism in Paediatric Crohn’s Disease during Exclusive and Maintenance Enteral Nutrition using OMICS Technologies (2020)
    Supervisors: U. Z. Ijaz (lead), C. Edwards, K. Gerasimidis, and R. K. Russell
  86. Dr Zihan Dai (University of Glasgow, UK)
    PhD thesis: Metagenomic insights into the drinking water microbiome (2020)
    Supervisors: U. Z. Ijaz (lead), and A. J. Pinto
  87. Dr Bianca Cavazzin (University of Glasgow, UK)
    PhD thesis: Climate and environmental variability during the late Holocene in the Canadian Great Plains: a multi–proxy biomarker approach (2020)
    Supervisors: J. Toney (lead), and U. Z. Ijaz
  88. Dr Elizabeth Mittell (University of Glasgow, UK)
    PhD thesis: The ecology and evolution of brassicas in Western Europe, featuring feral populations and underground microbial communities (2019)
    Supervisors: B. K. Mable (lead), U. Z. Ijaz, and C. Cobbold
  89. Dr Szymon Tomasz Calus (University of Glasgow, UK)
    PhD thesis: Evaluation of nanopore-based technology for bacterial gene marker analysis of complex environmental samples: Method development for accurate 16S rRNA amplicon sequencing (2019)
    Supervisors: U. Z. Ijaz (lead), and A. J. Pinto
  90. Dr Anna Trego (Collins Lab, NUI Galway, Ireland)
    PhD thesis: The life-cycle of methanogenic granular biofilms (2019)
    Supervisors: G. Collins (lead), and U. Z. Ijaz
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2017-2019)
  91. Dr Vaios Svolos (University of Glasgow, UK)
    PhD thesis: Novel management of Crohn's disease by dietary manipulation of the gut microbiome: The CD-TREAT diet (2019)
    Supervisors: K. Gerasimidis (lead), U. Z. Ijaz, and R. Hansen
  92. Dr Nick Rhys Thomas (University of Glasgow, UK)
    PhD thesis: Preservation and detection of molecular signs of life under Mars analogue conditions (2018)
    Supervisors: J. Toney (lead), U. Z. Ijaz, and M. Lee
  93. Dr Nicholas Alexander Franklin Ellaby (University of Liverpool, UK)
    PhD thesis: A Large Scale Metagenomic Analysis of the Faecal Microbiota in Preterm Infants Developing Necrotising Enterocolitis (2018)
    Supervisors: C. J. Probert (lead), N. Hall, A. Darby, and A. Ewer
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2017)
  94. Dr Anastasiia Kostrytsia (Collins Lab, Tampere University of Technology, Finland)
    PhD thesis: Bioengineering optimization and microbial characterization of elemental sulfur-fueled denitrifying biofilms (2018)
    Thesis supervisors: G. Esposito (lead), P. N. L. Lens, G. Collins, and S. Papiro
    Thesis instructors: L. Frunzo, M. R. Mattei, U. Z. Ijaz, L. Morrison, and E. Proca
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2018 with support through the Advanced Biological Waste-to-Energy Technologies (ABWET) Marie Sklodowska-Curie European Joint Doctorate)
  95. Dr Quyen Melina de los Santos Bautista (University of Glasgow, UK)
    PhD thesis: Towards a predictive framework for microbial management in drinking water systems (2017)
    Supervisors: A. J. Pinto (lead), and W. T. Sloan
    Collaborators: U. Z. Ijaz, and J. Schroeder-Davis
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2015
  96. Dr John Carey (NUI Galway, Ireland)
    PhD thesis (2017), Taxonomy, parataxonomy, and metabarcoding: an investigation of invertebrate diversity in high nature value wet grasslands (2017)
    Supervisors: M. Gormally (lead), and C. J. Smith
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2017)
  97. Dr Asha Rani (University of Glasgow, UK)
    PhD thesis: Invasions of the oropharynx: microbiome of healthy and infected respiratory tissue (2016)
    Supervisors: J. Lindstrom (lead), U. Z. Ijaz, and T. Evans
  98. Dr Caitlin Jukes (University of Glasgow, UK)
    PhD thesis: An investigation of the factors influencing Clostridium difficile germination, colonisation and persistence (2016)
    Supervisors: G. Douce (lead), and U. Z. Ijaz
  99. Dr Stephanie Connelly (Collins Lab, University of Glasgow, UK)
    PhD thesis: Ecology, physiology and performance in high-rate anaerobic digestion (2016)
    Supervisors: G. Collins (lead), and W. T. Sloan
    Collaborators: U. Z. Ijaz, and S. G. Shin
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2015
  100. Dr Aoife Joyce (NUI Galway, Ireland)
    PhD thesis: Investigation of microbial community structure and function underpinning grass and food waste anaerobic digestion (2016)
    Supervisors: F. Abram (lead), and V. O'Flaherty
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2014)
  101. Dr Inga Reich (NUI Galway, Ireland)
    PhD thesis: The EU-protected slug Geomalacus maculosus: an investigation into its phylogenetics, population densities in conifer plantations and its gut microbial community (2016)
    Supervisors: M. Gormally (lead), and C. J. Smith
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2016)
  102. Dr Christopher Rose (Collins Lab, Cranfield University, UK)
    PhD thesis: Developing a nutrient recovery process for recovering nutrients in anaerobic digestate in low income countries (2015)
    Supervisors: A. Parker, and E. Cartmell
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2014)
  103. Dr Muhammad Jaffar Khan (University of Glasgow, UK)
    PhD thesis: Gut microbiota in obesity of different aetiology: cause or effect? (2014)
    Supervisors: K. Gerasimidis (lead), C. A. Edwards, and G. Sheikh
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2013-2014)
  104. Dr Melanie Schirmer (University of Glasgow, UK)
    PhD thesis: Algorithms for viral haplotype reconstruction and bacterial metagenomics: resolving fine-scale variation in next generation sequencing data (2014)
    Supervisors: C. Quince (lead), and W. T. Sloan
    Collaborators: U. Z. Ijaz, and L. D'Amore

  105. Past MSc by Research Theses

  106. Yuchen Fu (University of Glasgow, UK)
    MPhil in Research, 2021
    MSc thesis: Smart Raman activated cell sorting (sRACS) system
    Supervisors: H. Yin (lead), and U. Z. Ijaz
  107. Konstantina Zafeiropoulou (University of Glasgow, UK)
    MSc in Medicine (Research), 2018
    MSc thesis: The gut microbiota in coeliac disease and the effect of dietary therapy
    Supervisors: K. Gerasimidis (lead), C. A. Edwards, and U. Z. Ijaz

  108. Past Undergraduate Projects

  109. Xingyi Du (University of Glasgow, UK)
    ENG4110P: Individual Project 4 (2022-23)
    Project: Microbial Communities analysis on low and high density polyethylene at different temperatures and salinities
    Supervisors: U. Z. Ijaz (lead) and C. Keating
  110. Michael Logan (University of Glasgow, UK)
    ENG4110P: Individual Project 4 (2022-23)
    Project: Identifying key bacteria in microbiomes of microplastics found in marine environments for possible degradation
    Supervisors: U. Z. Ijaz (lead) and C. Keating

  111. Past MSc Projects

  112. Yi Liu (University of Glasgow, UK)
    MSc Engineering Project, 2023
    Project: Exploring microbial interactions and diversity in contaminated soil
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, Uzma, and K. J. Stewart
  113. Weichen Zhao (University of Glasgow, UK)
    MSc Engineering Project, 2023
    Project: Comparing effects of natural and chemical biosurfactants on microbiome to explore crude oil degradation
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, Uzma, and K. J. Stewart
  114. Wei Xiao (University of Glasgow, UK)
    MSc Engineering Project, 2023
    Project: Exploring microbial correlations and diversity in pit latrines
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, and Uzma
  115. Sanhita Koley (University of Glasgow, UK)
    MSc Engineering Project, 2023
    Project: On understanding diversity and interactions of microbes in obesity
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, Uzma, and K. J. Stewart
  116. Renjie Ding (University of Glasgow, UK)
    MSc Engineering Project, 2023
    Project: On exploring microbial interactions and diversities in granule flotation
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, and Uzma
  117. Ke Zhao (University of Glasgow, UK)
    MSc Engineering Project, 2023
    Project: Exploration of zeta diversities and species interaction in gut microbial profile of Crohn's disease patients when treated with Exclusive Enteral Nutrition
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, Uzma, and K. J. Stewart
  118. Zhengye Li (University of Glasgow, UK)
    MSc Engineering Project, 2022
    Project: Understanding microbial ecology of granule flotation
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: Uzma
  119. Youqi Cheng (University of Glasgow, UK)
    MSc Engineering Project, 2022
    Project: Longitudinal microbiome analysis of healthy chicken ceca
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, Uzma, and K. J. Stewart
  120. Peihan Song (University of Glasgow, UK)
    MSc Engineering Project, 2022
    Project: Microbial determinants of obesity, a cross-sectional study
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: S. Bibi, and Uzma
  121. Yucheng Zhi (University of Glasgow, UK)
    MSc Engineering Project, 2022
    Project: Understanding microbial ecology of gut faecal samples of Crohn's disease patients when treated with exclusive enteral nutrition
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, and F. Saleem
  122. Ayodele Adewale (University of Glasgow, UK)
    MSc Engineering Project, 2022
    Project: Understanding cross-Sectional microbial profiles of pit latrines
    Supervisors: U. Z. Ijaz (lead) Other supervisors: W. Barr and Uzma
  123. Wenhan Chan (University of Glasgow, UK)
    MSc Engineering Project, 2022
    Project: Analyzing the microbial ecology of contaminated soils
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, and F. Saleem
  124. Chenyao Sun (University of Glasgow, UK)
    MSc Engineering Project, 2022
    Project: Understanding microbial activity of biological and chemical dispersants of crude oil
    Supervisors: U. Z. Ijaz (lead)
    Other supervisors: A. Ameer, and F. Saleem
  125. Shubhra Priyadarshini (University of Glasgow, UK)
    MSc Bioinformatics Project, 2021
    Project: Meta-analysis workflow used to unravel the microbial communities in plastisphere
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  126. Dongliang Li (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Whole genome analysis of self-healing concrete bacteria Bacillus subtilis
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  127. Zhen Yuan (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Whole genome functional analysis of Pseudomonas putida
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  128. Feng Ni (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Whole genome functional analysis of Alcanivorax, a genus of oil degrading bacteria
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  129. Kaung Sett (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Whole genome analysis of nitrifying bacteria in construction and the built environment​
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  130. Ruixin Wang (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Plastic degrading microbes (PE/PTE) - Pseudomonas putida
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  131. Steffy Anna Cherian (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Whole Genome Analysis of Acetotrophic and Hydrogenotrophic Methanogenic Archaea
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  132. Qikai Yang (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Comparative genomics of known horse genomes
    Supervisors: U. Z. Ijaz (lead), A. Khan, B. K. Mable, and C. Keating
  133. Fan Zou (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Building a plant sequence reference database
    Supervisors: U. Z. Ijaz (lead), A. Khan, B. K. Mable, and C. Keating
  134. Jiajian You (University of Glasgow, UK)
    MSc Engineering Project, 2021
    Project: Creation of a plant reference database of meta-barcoding genes
    Supervisors: U. Z. Ijaz (lead), A. Khan, B. K. Mable, and C. Keating
  135. Liu Kai (University of Glasgow, UK)
    MSc Engineering Project, 2020
    Project: Snakemake workflows for metagenomics data
    Supervisor: U. Z. Ijaz (lead)
  136. Wang Chen (University of Glasgow, UK)
    MSc Engineering Project, 2020
    Project: Phylogeny-aware metrics for microbial community surveys
    Supervisor: U. Z. Ijaz (lead)
  137. Chuanfei Tang (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2020
    Project: A Mobile Android Application to collect data for the treatment of Crohn's disease [Code]
    Supervisor: U. Z. Ijaz (lead)
  138. Dr Ozan Gundogdu (Queen Mary University of London, UK)
    MSc Bioinformatics Project, 2020
    Project: Omics based approaches to study Campylobacter Jejuni pathogenesis
    Supervisor: U. Z. Ijaz (lead)
  139. Rachel Gray (University of Glasgow, UK)
    MSc Quantitative Methods in Biodiversity, Conservation & Epidemiology Project, 2020
    Project: Bioinformatic challenges for using deep sequencing data for diet analysis of a threatened species
    Supervisors: U. Z. Ijaz (lead), and B. K. Mable
  140. Bozhen Chen (University of Glasgow, UK)
    MSc Civil Engineering and Management Project, 2020
    Project: Plastisphere of marine environment - a meta-analysis
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  141. Keda Li (University of Glasgow, UK)
    MSc Mechanical Engineering Project, 2020
    Project: The plastisphere - difference between fresh and marine water, metadata analysis
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  142. Hongyu Mu (University of Glasgow, UK)
    MSc Civil Engineering Project, 2020
    Project: A survey on microbial diversity in coal tar contaminated media
    Supervisors: U. Z. Ijaz (lead), and C. Keating
  143. Nicole Mendez-Santos (Glasgow School of Arts, UK)
    MSc Product Design Engineering (GSA) Project, 2018
    Project: Washing clothes in natural disaster zones where access to power and water are restricted
    Supervisor: U. Z. Ijaz (lead)
  144. Zhuo Chen (University of Glasgow, UK)
    MSc Civil Engineering & Management Project, 2018
    Project: Microbial diversity of Arsenic and Manganese contaminated groundwater
    Supervisors: C. J. Smith (lead), and U. Z. Ijaz
  145. Yonghong Feng (University of Glasgow, UK)
    MSc Civil Engineering & Management Project, 2018
    Project: Microbiological quality of water derived from Kenyan sand dams
    Supervisors: C. J. Smith (lead), and U. Z. Ijaz
  146. Alfred Ssekagiri (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2018
    Project: An R package for microbial community analysis in an environmental context
    Supervisors: U. Z. Ijaz (lead), and W. T. Sloan
  147. Lang Wu (University of Glasgow, UK)
    MSc Civil Engineering & Management Project, 2017
    Project: Design of molecular tools and database for the detection, quantification and identify of nitrifiers (AOB)
    Supervisors: C. J. Smith (lead), and U. Z. Ijaz
  148. Yixuan Song (University of Glasgow, UK)
    MSc Civil Engineering & Management Project, 2017
    Project: Design of molecular tools and database for the detection, quantification and identify of nitrifiers (AOA)
    Supervisors: C. J. Smith (lead), and U. Z. Ijaz
  149. Orges Koci (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2015
    Project: Metagenomic Contigs Visualisation Tool
    Supervisor: U. Z. Ijaz (lead)
  150. David Meltzer (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2015
    Project: AMPLIpyth: A Python Pipeline for Amplicon Processing
    Supervisor: U. Z. Ijaz (lead)

  151. Summer Placement Students

  152. Scott Saunderson (Glasgow Caledonian University)
    Society for Applied Microbiology Summer Student Placement, Summer 2021
    Project: B-cin Quest: Development of a curated database and workflow for searching for existing and novel bacteriocins produced by bacterial genera associated with plant pathogens
    Supervisors: U. Z. Ijaz (lead and host), C. Keating, B. K. Mable, and J. Milner
  153. Alexandru Popescu (University of Glasgow)
    British Society for Plant Pathology Undergraduate Vacation Bursary, Summer 2021
    Project: B-cin Quest: Developing a curated database and workflow for searching for existing and novel bacteriocins produced by plant pathogenic bacteria
    Supervisors: U. Z. Ijaz (lead and host), C. Keating, B. K. Mable, and J. Milner

  154. Other MSc/MEng Theses in James Watt School of Engineering, Glasgow

  155. Anna Law
    ENG 5041P Project: Analysis of Steel Structures Affected by Fire (2025)
    Supervisors: A. Shvarts (1st), and U. Z. Ijaz (2nd)
  156. Sadie Gordon
    ENG 5041P Project: Sonication by Tube Transducer as a Point of Entry Water Treatment System (2025)
    Supervisors: C. J. Smith (1st), and U. Z. Ijaz (2nd)
  157. Sean Yu
    ENG 5041P Project: Lab quantification of soil energy dissipation for earthquake engineering and offshore foundation design (2025)
    Supervisors: R. Buckley (1st), and U. Z. Ijaz (2nd)
  158. Cormac Tyler
    ENG 5041P Project: How much laughing gas comes out of sewage? Nitrous oxide emissions from wastewater treatment (2025)
    Supervisors: C. Domingo-Felez (1st), and U. Z. Ijaz (2nd)
  159. Wuhao Dong
    ENG 5059P Project: Review and Evaluation of Carbon Sequestration Methods in Concrete Production. (2025)
    Supervisors: Y. Zhang (1st), and U. Z. Ijaz (2nd)
  160. Xiahui Tang
    ENG 5059P Project: Thermal Mapping of FDSOI Devices: Addressing Self-Heating for Cryo-CMOS IP in Quantum Computing. (2024)
    Supervisors: F. Imroze (1st), and U. Z. Ijaz (2nd)
  161. Muhammad Noor Azmi Bin Wahab
    ENG 5059P Project: Engineering a Cleaner Future for Malaysia: An Analysis of Hydrogen-Based Cooking Systems. (2024)
    Supervisors: Y. Liu (1st), and U. Z. Ijaz (2nd)
  162. Liam Guermache
    ENG 5041P Project: A geotechnical design report into the reopening of the Kilmacolm line. (2024)
    Supervisors: A. G. Pagano (1st), and U. Z. Ijaz (2nd)
  163. Conrad Adnan Burton
    ENG 5041P Project: Assessing microbial growth in re-usable drinking water storage vessels: A comparative study of repurposed Kenyan jerry cans and Oxfam jerry buckets. (2024)
    Supervisors: M. Vignola (1st), and U. Z. Ijaz (2nd)
  164. Fiona Andrew
    ENG 5041P Project: Integration of carbon with engineering design: Evaluation and reduction of upfront embodied carbon emissions in the energy sector by utilisation of steel reuse. (2024)
    Supervisors: F. Bradley (1st), and U. Z. Ijaz (2nd)
  165. Chung Teng Yu
    ENG 5041P Project: Design and optimisation of a biofiltration system for drinking water treatment for rural communities in Scotland. (2024)
    Supervisors: C. J. Smith (1st), and U. Z. Ijaz (2nd)
  166. Sam Cresswell
    ENG 5041P Project: Numerical modelling of hyperconcentrated flows in one dimension. (2024)
    Supervisors: M. J. Creed (1st), and U. Z. Ijaz (2nd)
  167. Xinying Li
    ENG 5059P Project: Evaluations of empirical methods to estimate rock mass strength: case study on secondary data. (2023)
    Supervisors: J. Shang (1st), and U. Z. Ijaz (2nd)
  168. Aosheng Duan
    ENG 5059P Project: Numerical/Abaqus/FEA simulations of metamaterial lattices for concrete reinforcement. (2023)
    Supervisors: S. Kumar (1st), and U. Z. Ijaz (2nd)
  169. Xiuwei Chen
    ENG 5059P Project: Exploring bubble dynamics with Rayleigh-Plesset equation. (2023)
    Supervisors: P. Prentice (1st), and U. Z. Ijaz (2nd)
  170. Cerys Stewart
    ENG 5059P Project: Microbial bioremediation of polycyclic aromatic hydrocarbon (PAH) contaminated soil in former manufacturing gasworks sites. (2023)
    Supervisors: C. Gauchotte-Lindsay (1st), and U. Z. Ijaz (2nd)
  171. Caleb Jack
    ENG 5059P Project: A modern approach to the appraisal of existing steel roof structures (2023)
    Supervisors: F. Bradley (1st), and U. Z. Ijaz (2nd)
  172. Joe Green
    ENG 5059P Project: Development of ring stent bundle model and investigation of arterial tissue properties using FEA (2023)
    Supervisors: A. McBride (1st), and U. Z. Ijaz (2nd)
  173. Mathew Hollingham
    ENG 5059P Project: Nuclear applications of novel cementitious materials (2023)
    Supervisors: D. V. Achillopoulou (1st), and U. Z. Ijaz (2nd)
  174. Shaobo Yang
    Project: Jackmix Maintenance Release (2022)
    Supervisors: N. Bailey (1st), and U. Z. Ijaz (2nd)
  175. Pouya Naghshin
    Project: Ground improvement with stone columns: methods of calculating settlement reduction factor (2022)
    Supervisors: S. Wheeler (1st), and U. Z. Ijaz (2nd)
  176. Angus Mohun
    ENG5041P: Individual Project 5 (2021-22)
    Project: Prediction of the compressive strength for recycled aggregate concrete from mix design and aggregate properties by using machine learning models
    Supervisors: C. Unluer (1st), and U. Z. Ijaz (2nd)
  177. Sophie Marie Macfarlane
    ENG5041P: Individual Project 5 (2021-22)
    Project: Elastic deformation of a circular membrane with varying thickness profile
    Supervisors: P. Saxena (1st), and U. Z. Ijaz (2nd)
  178. Shahzada Haris Durrani
    ENG5041P: Individual Project 5 (2021-22)
    Project: Development and application of enhanced assimilable organic carbon method using various water sources
    Supervisors: C. J. Smith (1st), and U. Z. Ijaz (2nd)
  179. Amy Lillico
    Project: An Assessment of the Current Use of Glued Laminated Timber as a Structural and Viable Alternative to Steel Construction in the UK (2021)
    Supervisors: L. Brown (1st), and U. Z. Ijaz(2nd)
  180. Ann-Cathrin Reissmann
    Project: Analysis of Intermodal Interactions at Side Street Junctions (2021)
    Supervisors: A. McCay (1st), and U. Z. Ijaz(2nd)
  181. Lewen Qi
    Project: Comparing the finite element method to peridynnamics (2020)
    Supervisors: A. McBride (1st), and U. Z. Ijaz(2nd)
  182. Chenwei Ji
    Project: Modelling the Failure Mode of Reinforced Concrete Beam Using CDPM2 in LS-DYNA (2020)
    Supervisors: P. Grassl (1st), and U. Z. Ijaz(2nd)
  183. Jinxin Chen
    Project: How will the 5G technology change the geotechnical engineering practice? (2020)
    Supervisors: Z. Gao (1st), and U. Z. Ijaz(2nd)
  184. Han Liu
    Project: A comparative analysis of a reinforced concrete high-rise building using the Eurocodes and Chinese building codes (2019)
    Supervisors: F. Bradley (1st), and U. Z. Ijaz(2nd)
  185. Jinliang Wang
    Project: The effect of dilation angle on slope stability analysis (2019)
    Supervisors: Z. Gao (1st), and U. Z. Ijaz(2nd)
  186. Fernando Ardavin
    Project: Feasibility Study of the Mayan Train in Mexico's Yucatan Peninsula (2019)
    Supervisors: K. Ampountolas (1st), and U. Z. Ijaz(2nd)
  187. Xiaoqian Wang
    Project: Modelling creep and rate effects in soils (2019)
    Supervisors: S. Wheeler (1st), and U. Z. Ijaz(2nd)
  188. Xinyi Zhao
    Project: Greening the grey - Green walls in city to alleviate air pollution: Particles Matter reduction by three species of vegetation in a UK city (2019)
    Supervisors: C. Gauchotte-Lindsay (1st), and U. Z. Ijaz(2nd)
  189. Damien Ohienmhen
    Project: A Techno-Economic Evaluation of Metal Powders for Use in Energy Storage Applications (2019)
    Supervisors: N. Karimi (1st), and U. Z. Ijaz(2nd)
  190. Huaixin Cai
    Project: The effect of surface roughness on the velocity of rockfall, for different surface inclinations (2019)
    Supervisors: M. Valyrakis (1st), and U. Z. Ijaz(2nd)
  191. Chao Zhou
    Project: Computational Modelling of Granular Systems (2018)
    Supervisors: A. McBride (1st), and U. Z. Ijaz(2nd)
  192. Ross Hunter
    Project: Utilisation of Waste Heat and Grid Connection Optimisation using Integrated Collection Distribution and Power Systems at a Large Industrial Site in an Urban Setting (2018)
    Supervisors: N. Burnside (1st), and U. Z. Ijaz(2nd)
  193. Sammy Moore
    Project: On-orbit reflectors to enhance the output of large-scale terrestrial solar power farms (2018)
    Supervisors: C. McInnes (1st), and U. Z. Ijaz(2nd)
  194. Adama Olumo
    Project: Infrastructure deterioration: Modelling of corrosion induced cracking in reinforced concrete using a hydro-mechanical approach (2018)
    Supervisors: P. Grassl (1st), and U. Z. Ijaz(2nd)

  195. Other Undergraduate Projects in James Watt School of Engineering, Glasgow

  196. Huzaifa Mushtaq
    ENG4110P: Individual Project 4 (2022-23)
    Project: Meta Analysis of removal of Microplastics by WWTP
    Supervisors: C. Gauchotte-Lindsay (1st), and U. Z. Ijaz (2nd)
  197. Shicheng Luo
    ENG4110P: Individual Project 4 (2022-23)
    Project: Assessing the ability of flowcytometry fingerprinting analyses to distinguish the compositions of different water microbial communities
    Supervisors: M. Vignola (1st), and U. Z. Ijaz (2nd)
  198. Man, Chun Ho Gary
    ENG4110P: Individual Project 4 (2022-23)
    Project: Optimizing biofiltration in drinking water treatment
    Supervisors: C. J. Smith (1st), and U. Z. Ijaz (2nd)
  199. Daniel Paul
    ENG4110P: Individual Project 4 (2021-22)
    Project: CFD analysis investigating efficiency of both onshore and offshore HAWT's under different conditions.
    Supervisors: M. Vezza (1st), and U. Z. Ijaz (2nd)
  200. Oscar Meunier
    ENG4110P: Individual Project 4 (2021-22)
    Project: Biologically inspired UAV
    Supervisors: K. Worrall (1st), and U. Z. Ijaz (2nd)
  201. Samuel Stribling
    ENG4110P: Individual Project 4 (2021-22)
    Project: Optimising the Aerodynamic Efficiency of Electric Road Vehicles for Improved Range
    Supervisors: M. Vezza (1st), and U. Z. Ijaz (2nd)
  202. Duncan Munro
    ENG4110P: Individual Project 4 (2021-22)
    Project: Investigating Low Reynolds Number Flight for Rotorcraft on Mars
    Supervisors: C. White (1st), and U. Z. Ijaz (2nd)
  203. Ching Long Hung
    ENG4110P: Individual Project 4 (2020-21)
    Project: Glasgow Active Travel Design: Cycle Network Planning for Springburn and Blackhill
    Supervisors: A. McCay (1st), and U. Z. Ijaz (2nd)
  204. Goh Wei Jie
    Individual Project 4S (SIT4017P) (2019-2020)
    Project: Dataset collections and image processing
    Supervisors: T. L. Meng (1st), and U. Z. Ijaz (2nd)
  205. Li Weng Kin
    Individual Project 4S (SIT4017P) (2019-2020)
    Project: Data analytics for patient-based quality control in clinical laboratories (MT19191)
    Supervisors: L. C. Yee (1st), and U. Z. Ijaz (2nd)
  206. Yeoh Ya Yun
    Individual Project 4S (SIT4017P) (2019-2020)
    Project: Depression Analysis: Spectrogram Deep Learning
    Supervisors: H. Nguyen (1st), and U. Z. Ijaz (2nd)
  207. Chu Lixuan
    Individual Project 4S (SIT4017P) (2019-2020)
    Project: MT 19194 IoT enabled PV monitoring system
    Supervisors: R. K. Malar (1st), and U. Z. Ijaz (2nd)
  208. Chua Lye Heng
    Individual Project 4S (SIT4017P) (2018-2019)
    Project: Design of a long endurance multi-copter: Flight Systems
    Supervisors: H. Hesse (1st), U. Z. Ijaz (2nd), and E. Lin (HOPE Technik)
  209. Muhammad Ridzuan Bin Alfie
    Individual Project 4S (SIT4017P) (2018-2019)
    Project: Design/build a high endurance drone with realistic payload capability
    Supervisors: H. Hesse (1st), U. Z. Ijaz (2nd), and E. Lin (HOPE Technik)

  210. Informatics Support (including external visitors)

  211. Valentine Okonkwo (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019-
  212. Claire Thom (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019-
  213. Dominic Quin (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2020-
  214. Alison Graham (O'Flaherty Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab 2020-
  215. Jasmine Connolly (O'Flaherty Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab 2020-
  216. Victor Birlanga (Collins Lab, NUI Galway, Ireland)
    Visitor to Environmental'Omics Lab 2017, 2018
    Virtual visitor to Environmental'Omics Lab 2019-
  217. Ali Z. Ijaz (Hawkesbury Institute for the Environment, Australia)
    Visitor to Environmental'Omics Lab 2015
  218. Marco Kreuzer (University of Reading, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2015
  219. Dr Hussain Jaffery (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2017
  220. Dr Kathryn Jane Gray (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019
  221. Hannah Baer (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2020
  222. Anabelle Ferguson (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018; Undergraduate summer 2018 intern
  223. Hannah Craven (Institute of Cancer Sciences, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2021
  224. Dr Lydia Bach (Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2020-2021
  225. Danielle Grant (AGENSI Group, NORCE Research, Norway)
    Virtual visitor to Environmental'Omics Lab 2020- [Grant: AGENSI - A Genetic View into Past Sea Ice Variability in the Arctic, ERC]
    Foreign supervisor: U. Z. Ijaz
  226. Dr Ranjith Rajendran (Dental School, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2017
  227. Maria Fedrica Carboni (NUI Galway, Ireland; Visiting PGR 2021)
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2021)
  228. Christopher Delaney (Dental School, University of Glasgow, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2017
  229. Mauro Tutino (University of Manchester, UK)
    Visitor to Environmental'Omics Lab 2017
  230. Cadi Davies (London School of Hygiene & Tropical Medicine)
    Virtual visitor to Environmental'Omics Lab 2019
  231. Maria Catalina Sevillano Rivera (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2015-2020)
  232. Irmarie Cotto (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  233. Solize Vosloo (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  234. Katie Vilardi (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  235. Sadia Khan (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)

Teaching

My statement is in view of Professional Standards Framework (2023), and how I use the professional values [V1-V5], utilising core knowledge [K1-K5], and taking part in different activities [A1-A5].

My teaching philosophy, in my opinion, is centred on respecting each individual student and creating a diverse learning environment. Every student has a different learning path, therefore it's critical to provide a welcoming environment where all viewpoints are valued. I have worked with students from a variety of cultural, educational, and disciplinary backgrounds over the years, particularly while I was employed at the GIK Institute of Engineering Sciences and Technology in Pakistan, Queen's College, the University of Cambridge, and the University of Glasgow.

I was especially aware that my students came from a variety of academic backgrounds, including bioinformatics, environmental science, and engineering, when I was teaching BIOL5172: Metagenomics at the University of Glasgow. I modified the curriculum to accommodate their diverse knowledge and abilities in order to make sure the training was open to everyone. To ensure that students acquired both conceptual knowledge and practical experience, I combined theoretical lectures, hands-on laboratory sessions, and computational tools. In order to provide students the opportunity to showcase their talents, I also created exams that are adaptable and representative of their varied learning requirements. This method satisfies the value of respect for various learning communities and individual learners by guaranteeing that each student's unique learning process is honoured [V1].

I serve about 40 postgraduate students annually as an Advisor of Studies at the James Watt School of Engineering, where I place a strong emphasis on pastoral and emotional support in addition to academic supervision. Sometimes, I meet with students on zoom to talk about their development and any difficulties they may be having. By establishing personal connections, I make it easier for students to ask for help when they need it, whether it be for their own wellbeing or the course material. Additionally, I make sure that every student has access to opportunities for collaborative learning, which allow them to tackle challenges together. This further cultivates an atmosphere that values individual contributions by encouraging peer support and making students feel included in the learning process [V1].

A crucial component of my instruction is assisting students in becoming self-sufficient, self-assured learners with transferable abilities. I place a strong emphasis on the development of critical thinking and problem-solving abilities in my work as a supervisor of undergraduate engineering students and MSc and PhD bioinformatics students. I provide advice, particularly for research projects where students plan and carry out their own studies, such as those covered in ENG4110P and ENG5041P. In addition to encouraging them to take responsibility for their work, I help them refine their research questions, methodology, and analysis.

For example, I oversee PhD and MSc students engaged in bioinformatics projects that require interpretation and analysis of data. I support them in overcoming obstacles on their own while also empowering them to make choices on their own. Students in my Metagenomics course work with intricate microbiological datasets, and I help them use bioinformatics tools to critically analyse and interpret the data. I provide an atmosphere where students can consider their own development and learning. I give thorough comments on assignments and support students in using feedback as a means of bettering themselves. This method guarantees that students acquire lifetime learning capabilities in addition to subject-specific information [V2].

My dedication to moral principles is fundamental to both my research and teaching. I make sure that my students understand the value of upholding high ethical standards, especially in bioinformatics where concerns like data integrity and confidentiality are crucial, and I set an example of academic integrity in my own work. I place a strong emphasis on ethical issues in data handling and experimental design when I mentor MSc and PhD students. I make sure that students are aware of their obligation to carry out their studies in an open and accountable way. When assessing students' work, I also provide an example of moral behaviour. I have used strict and unbiased standards as a PhD thesis examiner at universities such as Toronto Metropolitan University and the National University of Science and Technology (Pakistan) to make sure that my assessments are equitable and founded only on the quality of the study. I think that cultivating a culture of trust in academics requires upholding justice and integrity [V3].

I strive to maintain the highest ethical standards in all of my academic dealings by making sure that my students comprehend the significance of justice, openness, and respect. When I oversee student projects, for example, I make sure that all data is handled with integrity and provide them advice on how to manage research data so that their work complies with ethical standards (there are dedicated MS teams channel where I manage history and expectations for students). Students learn not only academic material but also how to be responsible researchers in a respected learning environment that is fostered by this dedication to ethical conduct [V3].

I also have a strong commitment to ongoing professional development because I recognise that providing high-quality instruction requires remaining current with pedagogy and subject-specific knowledge. To be on the cutting edge of advancements in bioinformatics and instructional strategies, I regularly take part in international seminars, conferences, and partnerships. For instance, I have participated in training schools, workshops, and hackathons on bioinformatics and metagenomic data processing, as well as EU COST Actions like ES1103. I am able to include state-of-the-art technologies into my instruction because to these opportunities. In order to keep my own expertise current and to help students and peers alike, I also conducted workshops on microbial diversity and data interpretation.

I incorporate these advancements into my instruction in my capacity as a supervisor. I have produced online learning materials for students, such as video lectures on subjects like machine learning and numerical ecology, which are accessible to a wider audience. I'm using these resources as part of my endeavour to help my students grow and make sure they're exposed to the newest techniques and tools. Furthermore, I urge my students to actively utilise these tools in order to improve their learning. By committing to ongoing professional development, I am able to improve my teaching methods and make sure that my students are receiving the most current and pertinent instruction possible [V4].

I show my dedication to lifelong learning by taking part in group projects, coaching students, and developing instructional materials. Working with international partners and creating custom courses like BIOL5172: Metagenomics demonstrate my commitment to remaining on the cutting edge of my area and using this knowledge to improve my instruction. In order to improve my reflective practice and further my career, I also aggressively solicit input from my students and colleagues. I will keep looking for professional development opportunities as my career progresses to make sure I can give my students the best education possible [V5]. Through all of these initiatives, I hope to create a classroom atmosphere that supports my students' ongoing growth, promotes inclusive learning, and maintains the highest standards of academic integrity. I work to make learning enjoyable and significant for everyone I teach by upholding high ethical standards, fostering students' independence as learners, valuing various learning communities, and pursuing continual professional development.

Area of Activity 1: Design and Plan Learning Activities and/or Programmes of Study

I have continuously created and organised creative, interesting learning activities that meet the demands of students with different academic backgrounds throughout my teaching career. The creation of the Metagenomics Module (BIOL 5172), which I built during my NERC fellowship, is a notable example. This multidisciplinary course bridged the domains of Computer Science and Medical Veterinary and Life Sciences (MVLS) and was designed for MSc students specialising in Bioinformatics, Polyomics, and Systems Biology. It made use of my Orion cluster, giving students practical exposure with metagenomics and bioinformatics. Other universities throughout the world have highly cited the course material, which includes Linux command-line exercises for processing Next Generation Sequencing (NGS) data and lessons on R code for ecological data analysis [A1]. Because it integrated active learning using real-world data analysis and computational tools, the course design was based on core knowledge (how learners learn [K1]), enabling students to interact meaningfully with the material. By making my materials available online through sites like Biostars, I made sure they could be accessed from anywhere in the world, which increased their reach. Through this method, students were able to acquire both transferable computational biology abilities and fundamental metagenomics principles. As evidence of its enduring significance, my course design has impacted university curriculum across the globe over the years, and it was included in the University of Edinburgh's Precision Medicine Programme [K1].

After my NERC fellowship ended, I moved into teaching in the field of civil engineering. I revolutionised programming instruction in ENG2079 by introducing Python programming in a Jupyter notebook format. By enabling students to run code locally or through Google Colaboratory, this innovation saved up university computing resources while offering students a dynamic, interactive learning experience [A1]. The response I received from students demonstrated the success of this course, as they expressed gratitude for the approach's flexibility and clarity. This course has grown to be essential to the field of civil engineering, serving as a foundation for later courses like finite element analysis and structural mechanics 3. In line with core knowledge (use of digital technology in teaching K4), the move to Python and Jupyter notebooks as teaching aids improves student learning and gets them ready for difficulties in a sector that is changing quickly [K4].

Area of Activity 2: Teach and Support Learning

At the core of my work is teaching and facilitating student learning, where I actively interact with students to guarantee their comprehension and development. As the coordinator of the ENG5322 (Engineering Skills M) course, I offer a mix of tutorials, lectures, and hands-on activities aimed at fostering the development of fundamental engineering skills. At first, only students studying civil engineering could enrol in this course. But during the last two years, ENG5322 has grown to include students studying mechanical engineering, and now there are around 150 students in the class. Due to space limitations, it became increasingly difficult to oversee the practical sessions in conventional computer labs as the student body increased. In order to accommodate growth, I shifted to a hybrid teaching paradigm for the course. This model makes learning accessible and guarantees that they can continue their education without interruption [A2, K4]. The course offers opportunities for practical, hands-on learning [A2]. I modified my teaching to accommodate various learning styles, offering drop-in sessions to help students develop their Python programming skills throughout the COVID-19 epidemic. By providing adaptable and responsive support, this exemplifies core knowledge (appropriate teaching and support practices [K2]). I employ a mixed learning approach when instructing ENG2079 (Programming in Python), where students study through sample code and conduct independent lab exercises in Jupyter notebooks. Because of this flexibility, they may learn at their own speed and still receive focused feedback. I use Zoom for screen sharing during lab sessions to offer prompt support for coding problems, creating a responsive and cooperative learning environment [A2]. This is an illustration of how to use digital resources to enhance student learning and engagement (core knowledge [K4]).

We employ a novel strategy in the ENG2078 course, asking students to produce two-to-three-minute videos of their work. These movies provide them a chance to summarise the main ideas they have learnt throughout the course and reflect their learning experience. After that, on special presentation days, the students show their videos and get helpful criticism from the course instructors (myself and Caroline Gauchotte-Lindsay) and peers. This helps students improve their communication skills and their capacity to convey complicated ideas clearly and concisely, in addition to encouraging them to think critically about their work [A2]. This approach encourages active learning and allows me to give them focused, helpful criticism on their individual work while creating a cooperative and encouraging atmosphere.

I also participated in the Cambridge Advanced Leadership Programme at the University of Cambridge's Judge Business School in 2016. I gained a deeper grasp of leadership, instructional techniques, and the significance of creating a welcoming and cooperative learning environment as a result of this experience. In order to give students a well-rounded and interesting educational experience, I have used the leadership and management concepts I learnt from the program into my teaching practice, especially when organising classes and guiding students [V5].

Area of Activity 3: Assess and Give Feedback to Learners

Two essential elements of my teaching methodology are assessment and feedback. In order to give students quick feedback and enable them to make the required adjustments, I employ a formative assessment technique in all of my courses. I use peer assessments in lab sessions for ENG2079 and ENG5322, where students evaluate one another's code to promote group learning and peer assistance [A3]. This feedback mechanism aids students in critical self-evaluation and reflection on their work. In order to help students identify their areas of strength and growth, I also give them thorough written and verbal feedback on their lab exercises. Previously, I gave students feedback on their research projects in the Metagenomics course, offering guidance on design, data processing, and interpretation. I assisted students in honing their computational analysis and biological interpretation skills by providing focused feedback on particular project components [K3]. Furthermore, I make sure that my feedback is in line with core knowledge (quality assurance and enhancement [K5]), guaranteeing openness and equity in all evaluation standards and preserving uniformity throughout all courses. A key component of my teaching approach is the feedback loop, which encourages critical thinking and lifelong learning in addition to helping students perform better.

Area of Activity 4: Develop Effective Learning Environments and Approaches to Teaching and Learning

In all of my teaching positions, I place a high priority on creating a productive and welcoming learning atmosphere. Students can interact with the materials in a variety of ways that best fit their learning preferences thanks to the usage of digital tools in classes like ENG2079 and ENG5322. I modified my teaching methods during the COVID-19 epidemic by adding lectures that were recorded for students to view whenever it was convenient for them and setting up extra drop-in sessions for one-on-one assistance [A4]. This illustrated my capacity to modify my instruction in response to outside events and to keep using adaptable strategies to enhance students' learning objectives.

I pay close attention to fostering an environment that celebrates variety. For example, I recognised that students in ENG5322 (with sizeable majority of international students) had a variety of academic backgrounds and programming experience. I promoted equality of opportunity and inclusion in the learning environment by making sure that all students could interact with the content and advance at their own speed by offering extra learning tools including online lessons and access to coding platforms (core Knowledge [K1]). This illustrates my dedication to collaboration and professional development [V5], as I constantly collaborate with co-workers, students, and outside specialists to establish the best possible learning environment.

Area of Activity 5: Engage in Continuing Professional Development (CPD)

In order to improve my teaching, I regularly participate in continuing professional development, or CPD. To make sure that my practice stays up to date and efficient, I have participated in workshops on cutting-edge teaching strategies (some were offered as trainings for NERC fellows, others were offered by University of Glasgow), pedagogical approaches, and technology developments. I gained important leadership insights from my 2016 participation in the Cambridge Advanced Leadership Programme, which improved my capacity to lead teams, work with colleagues, and assist students in a multidisciplinary setting. My leadership, team-building, and mentoring abilities have all improved as a result of this experience and have been crucial to my teaching [V5].

In addition, I am a Fellow of the Royal Society for Public Health, a Fellow of the Royal Society of Biology, a Fellow of the Royal Statistical Society, a Fellow of the British Computing Society, a Fellow of the Royal Society for Arts, Manufacture and Commerce, a Fellow of the Institute of Biomedical Science, a Fellow of Institute of Leadership, a Visiting Lecturer at University of Galway, Ireland, and an Honorary Visiting Professor at the University of Liverpool, among other fellowships and advisory positions. In addition to giving me professional recognition, these positions enable me to participate in and gain knowledge from best practices within the international academic community.

I frequently interact with co-workers and outside specialists to share best practices, which I then include into my instruction. Specifically, I have collaborated with academics through Pakistan's Higher Education Commission to help PhD students from Pakistan receive research training, opening doors for global cooperation. In order to stay current with the newest developments in bioinformatics education, I also keep up with global networks like Biostars and other platforms. In addition to improving my own profession, this interaction with the larger academic community also helps others grow [A5, V5].

Teaching History

  • In University of Glasgow:
  • Continuous Professional Development:
  • Previously:
    • Worked as a Teaching Associate for Queen's College, University of Cambridge for a year (2008-2009) where I was the tutor for the first year engineering students for Michaelmas term 2008 and Lent/Easter term 2009 (4 hours / week teaching) for the following courses:
      • P3: Physical Principles of Electronics and Electromagnetics
      • P3: Linear Circuits and Devices
      • P3: Digital Circuits and Information Processing
      • P4: Mathematics
      • P4: Computing
    • Worked as a Graduate Assistant at Faculty of Computer Sciences and Engineering, GIK Institute of Engineering Sciences and Technology (GIK), Pakistan for two years (2001-2003) where I was a teaching assistant (20 hours / week teaching) for the following courses (in addition to being a laboratory demonstrator for programming languages such as CLIPS, PROLOG, LISP, Small Talk and C++):
      • CS-221: Data Structures and Algorithms
      • CS-211: Operating Systems
      • CS-433: Computer Graphics
      • CS-504: Concepts of Programming Languages
      • CS-564: Pattern Recognition
      • CS-562: Expert Systems and Knowledge Engineering

Profile

Expertise: Information Engineering
Competencies: Collegiality, Collaboration, and Communication
Current research theme: Microbial Informatics (Numerical Ecology and Machine Learning), Chemometrics, Text Mining, Population Genomics, and Computational Immunology
Past research themes: Network Inference, Ultrasound Imaging, Computer Vision, Inverse Problems, Electrical Tomography, Adhoc Networks, Global Positioning Systems, Control Engineering, and Artificial Intelligence
Nationality: Dual: British;Pakistani
25+ years of work experience since June 1999 with no career breaks


Appointments


Orion Cluster

At the heart of my Environmental'Omics lab is a bioinformatics cluster called Orion that I regularly administer and that run the workflows and the software I develop in collaboration with my colleagues as well as the most frequently used third-party software.

Summary statistics

Principal Investigator and sysadmin: U. Z. Ijaz (for correspondence/issues/usage)
IT technician and sysadmin: G. Quinn
Naming convention: We like to name our servers after famous musicians as it is easier to remember this way
Total number of servers: 19
Cores: 500+
Disk space: 800TB+
Software: 500+
Capacity: ~70 PGR/T
Money generated for cluster (to date): ~£222K+:
  • Innovate UK Project with Unilever entitled "Development of instrumental and bioinformatic pipelines to accelerate commercial applications of metagenomics approaches": ~£40K
  • In-kind support from W. T. Sloan & A. J. Pinto: £6,400
  • SIRN Project entitled "Molecular epidemiology of Clostridium difficile in Scotland: developing novel, clinically applicable research methods to combine genomic analysis with health informatics": £8,000
  • Industrial partnership with Nestle Global to fund research exploring the role of gut microbiota in Crohn's disease and changes during exclusive enteral nutrition: £12,000
  • Arthritis UK project entitled "Interactions between the Microbiome, Immunophenotype and Genome in PsA (IMIGPA)": £8,000
  • Support from J. Toney: £1,500
  • Support from C. J. Smith: £6,000
  • NERC project entitled "Understanding microbial communities through in situ environmental 'omic data synthesis": £10,000
  • BBSRC-SFI project entitled "A microbial basis for Atlantic Salmon energetics" and "Scottish Aquaculture Innovation Centre Money in Future Funding": £12,000
  • EPSRC project entitled "Optimising decentralised low-cost wastewater infrastructure by managing the microbes": £17,500
  • EPSRC project entitled "Sythetic biology applications to the water industry": £60,000
  • SAIC project entitled "Gill health in scottish farmed salmon": £8,000
  • University of Glasgow, Infrastructure & Environment Division Fund (Head of Division: A. McBride): £2,000
  • Royal Academy of Engineering-Scottish Water Senior Reserach Fellowship (PI: C. J. Smith) entitled "Biofiltration by biological design": £12,000
  • BBSRC project entitled "Building a Decision Support Tool for Potato Blackleg Disease (DeS-BL)": £8,000
  • FORSKER21 (Norway) project entitled "Late Quaternary Antarctic Cryosphere Interactions (ARCHIE)": NOK 12,000K
  • EPSRC project entitled "To chlorinate, or not to chlorinate?": £10,000
  • Helmsley Charitable Trust project entitled "Combination therapy with biologics and partial enteral nutrition in adults with active ileocolonic Crohn's disease: The BIOPIC Study": ~£5,000

Compute nodes (Orion)

These are the nodes that you login to using ssh -Y [USER]@[NODE].eng.gla.ac.uk. Please note that due to security reason, Orion cluster is only accessible through University of Glasgow VPN (install the client from this link). Those with Windows machines can use MobaXterm as a telnet client. To upload/download the data to/from Orion, use Cyberduck for FTP/SFTP.

pitrelli.eng.gla.ac.uk (48 cores)
becker.eng.gla.ac.uk (64 cores)
hammett.eng.gla.ac.uk (64 cores)
poland.eng.gla.ac.uk (64 cores)
young.eng.gla.ac.uk (64 cores)
tafolla.eng.gla.ac.uk (96 hyperthreaded cores; 2TB RAM)
macalpine.eng.gla.ac.uk (96 hyperthreaded cores; 2TB RAM)
moore.eng.gla.ac.uk (96 hyperthreaded cores)
howe.eng.gla.ac.uk (96 hyperthreaded cores)
rhoads.eng.gla.ac.uk (64 cores)

Storage nodes (Orion)

mustaine.eng.gla.ac.uk
friedman.eng.gla.ac.uk
drover.eng.gla.ac.uk
broderick.eng.gla.ac.uk
loureiro.eng.gla.ac.uk
skolnick.eng.gla.ac.uk
chastain.eng.gla.ac.uk

Legacy nodes (Old)

quince-nas.eng.gla.ac.uk
network drive

Impact

Developing analytical strategies have played a pivotal role in identifying and analyzing critical patterns in datasets from diverse sources. These advancements whilst working with national and international research groups have directly contributed to the creation of groundbreaking products and engineered systems, while also supporting the publication of key research papers that have advanced scientific understanding and discovery in the field. Below, find some of the impact:

Impact Type: Influencing Policy/Clinical Guidelines



Impact Type: Instrumental (Technology and Product Development)

  • CD-Treat Diet [project page]:

    Significance: In 2012, I co-founded Bacteria Immunology, Nutrition, Gastroenterology and Omics (BINGO) group with colleagues at Human Nutrition Department, as well as NHS (4 academic principal investigators including me; 5 clinical principal investigators). Through ~£8M grant funding to the BINGO group, and using my software and hardware infrastructure, we have developed CD-TREAT Diet, a solid diet for initial treatment of active Crohn’s disease, that received significant press coverage (coverage in 88 news outlets), an Altmetric score of 798 and reaching an attention score of 12 out of 14,089 output from Gastroenterology journal as well as academic citations (DOI: 10.1053/j.gastro.2018.12.002; I contributed to the study design, advised on bioinformatics and statistical analysis, supervised the PDRA, and co-supervised the PhD student). Recently, being a Co-I on a $1,143,065.00 (2019-) fund by Hemsley Trust, we are currently conducting clinical effectiveness of CD-TREAT at NHS and its microbial mechanism of action in patients with active Crohn's disease.
  • Spin Off: SalmoSim Simulator: [project page]
    [Technology Brochure (I am co-author on two of the case studies as proof-of-concept of the technology enabled by my software portfolio; one of the four investigators on a BBSRC BB/P001203/1 grant that led to the development of technology)]
    Technology Demo:

    Significance: This technology further led to commercial and research contracts: supporting trials conducted by California-based Calysta for an alternative protein source with potential applications across the global aquaculture industry; as well as the feed simulator to be used by feed ingredient maker Royal DSM.
  • Spin Off: CASDU CROP SOLUTIONS: Developing a commercial bacteriocin-based treatment for protecting seed and ware potatoes against Blackleg disease and soft rot.
    Significance: Informed by the bioinformatics workflows on Orion Cluster, we have identified and characterized two bacteriocins from Pectobacterium spp. (Pba; causing Potato Blackleg disease and responsible for losses of £50m annually in the UK alone). We found that one of these is highly effective in killing nearly all UK isolates of Pba and at concentrations lower than conventional antibiotics. Our work on bacteriocins to develop a biocontrol method for blackleg disease is going through commercialisation and a business case has been developed, e.g., a startup (BBSRC Impact Acceleration Program, IBioIC Spin-out Support Programme; 2023; see “further funding” section on BBSRC BB/T010649/1 (I am one of the three investigators) on developing a commercial bacteriocin-based treatment for protecting seed and ware potatoes against Blackleg disease and soft rot.
    Associated Impact Case Study: The impact narrative of our work is independently assessed and released by Bacterial Plant Diseases UK as a case study of DES-BL project (we are particularly highlighted for 41 engagement activities and spinouts). The key stakeholders engaged were: Growers; Agronomists, groups such as the Agronomy Group, Potato companies; Seed Potato Organisation, Scotland; GB Potatoes; Potato Processors Association; CUPGRA (Cambridge University Potato Growers Association); Biocontrol businesses; and Policymakers, Regulators. Note that the assessors have acknowledged "that steps have occurred with potential to contribute to longer-term policy impacts; for example, the team has held discussions with policy advisors and Chief Scientific Advisors, as well as contributing to national consultation".
  • Spin Off: Low temperature Anaerobic Digestion (LtAD) technology: [company page]
    Technology demo:
    Significance: A wastewater treatment technology that removes organic pollution (chemical oxygen demand and biological oxygen demand) while producing renewable energy in the form of biogas. The technology is a sustainable and cost effective wastewater treatment approach for a wide range of industries such as – food and drink (meat processing, dairy, brewing, distilling, malting and bottling) and municipal water industries. The process can reduce energy costs by as much as 95% and reduce sludge production by 95% when compared to activated sludge treatment installations.
    My role: Software strategies on my NERC fellowship grant (NERC NE/L011956/1) utilising microbiomeSEQ led to the ground breaking proof-of-concept publication demonstrating that the technology works (DOI: 10.1016/j.biortech.2021.125786 (I am a corresponding author as well as contributed to conceptualization, methodology, software, formal analysis, investigation, data curation, writing – review & editing, visualization, supervision, and funding acquisition). This technology created 15 new specialist jobs in Ireland): "Transforming Sustainable Water Management: Creating Jobs and Saving Energy". The technology is very successful and has won several national and international awards.
  • Hybrid 3D Ultrasonic Imaging System: [relevant software: StradWin]
    StradWin Demo:

    Significance: At University of Cambridge, I developed the Hybrid 3D Ultrasonic Imaging System which was subsequently delivered to Addenbrookes' Hospital, Cambridge, where it successfully completed the review by the ethics committee. It was then used by a clinician to explore the range of applications in which this type of scanner could offer particular benefit. Our feasibility study (DOI:10.1259/bjr/46007369) on pregnant women regularly attending for routine obstetric ultrasound scans demonstrated that the technology has promising results (77% to 83% reliability in clinical trials). The system led to acquisition of further grants and devleopment of other high definition 3D ultrasound systems.


Impact Type: Instrumental (Third-party workflows built on our software)

CONCOCT was assimilated in MetaWRAP suite in 2018 (DOI: 10.1186/s40168-018-0541-1); and ANVIO suite in 2020 (DOI: 10.1038/s41564-020-00834-3.

Impact Type: Discovery (Academic Impact)

Esteem

  • Visiting UK academic appointments
    • Honorary Visiting Professor (Research Track) (2022-2027), Department of Molecular and Clinical Cancer Medicine, University of Liverpool, UK
      Significance:High throughput DNA sequencing is now fundamental to the microbiology of everything from environmental engineering through medicine to agriculture. Prior to my research comparing different sequencing technologies, starting in 2014 and funded by Innovate UK (Project No. 100969, £2.3M), no one knew which technology was the most accurate or what were the optimal strategies for sample processing. In a series of, now highly cited (>1400 citations) papers, I helped to establish the Illumina platforms as the leaders in the field. My recommendations on next generation sequencing technology and protocols for microbial community profiling are being adopted by many sequencing centres including Centre for Genome Research, Liverpool. An SME (Eagle Genomics), subsequently implemented my algorithms in Unilever’ R&D centre's systems to facilitate them in their search of next generation personal care products involving microbiology. For these reasons, and contribution to a growing shared research portfolio with several investigators at University of Liverpool, I was awarded the position to recognize my impact.
  • Visiting international academic appointments
    • Visiting Lecturer (2022-2023), University of Galway, Ireland
      Significance: I acquired this honorary visiting position by supporting PhD students and staff in largely anaerobic digestion projects (since 2014) at University of Galway, Ireland. The position reinforces my standing in the academic community, and is a significant recognition of my expertise and contributions to the field. The position also enables me to foster collaboration between myself and key academic investigators at the University of Galway, by enhancing the quality of research through the exchange of knowledge and practical experience. My position also allows for the mentorship of emerging researchers, shaping the next generation of experts and ensuring the continuity of high-quality research. At the moment, my major association is with the O'Flaherty Lab where we have shared access to collective resources.
  • Track record of invited talks at international conferences and/or UK HEIs
    • I have published with some of the best known research groups across the world. I have concentrated on showing international academic leadership in the field of bioinformatics, and microbial informatics. Invitations to teach on the prestigious STAMPs course at Woods Hole USA and on EU's ES1103 COST Action training school, is evidence that I am perceived by my peers to be a leader in the field. My organisation of Bioinformatics Hackathons through EU's ES1103 COST Action have given me a high profile in Europe. Noteable talks (including plenary/keynote talks) are given at outreach.
  • Fellowship of subject-specific society
    • Fellow of British Computing Society (Elected 2024; Membership No: 995153327)
      Significance: This fellowship is the highest membership grade, and is recognition of influential professionals in the digital industry, particularly those who are "IT leader and role model in the field".
    • Fellow of Royal Society for Public Health (Elected 2024; Membership No: 137506)
      Significance: This fellowship is the highest membership grade, and is granted to individuals who are adjudged to have "worked in public health for over five years and/or are a registered Member of the UK Public Health Register (UKPHR)".
    • Fellow of Royal Statistical Society (2024-; Membership No: 236289)
      Significance: This fellowship is open to anyone with an interest in statistics and data science at any stage of their career, from students through to retirees.
    • Fellow of Royal Society of Biology (Elected 2025; Membership No: P0160412)
      Significance: This fellowship is the highest membership grade, and is granted to individuals who are adjudged to have made a "prominent contribution to the advancement of the biological sciences, and have gained no less than five years of experience in a position of senior responsibility".
    • Fellow of Royal Society for Arts, Manufacture & Commerce (2025-; Membership No: 8405844)
      Significance: Fellows are committed to inspiring better ways of thinking, acting and delivering change. An integral part of the RSA in creating a better future, Fellows champion new ideas, drive social change, deliver practical solutions and support the RSA mission.
    • Fellow of Institute of Biomedical Science (Elected 01/04/2025)
      Significance: This fellowship is the highest grade of membership in the Institute of Biomedical Science (IBMS). This designation is awarded to individuals "at the most senior levels of the biomedical science profession, including biomedical and clinical scientists, as well as senior academics and researchers not requiring HCPC registration, and have a biomedical science related PhD together with five years professional experience in an area related to biomedical science".
    • Fellow of Institute of Leadership (Elected 2025; Membership No: 20635445)
      Significance: This fellowship is the highest grade of membership in the Institute of Leadership (IoL). This designation is "recommended for highly experienced leaders who are passionate about the positive impact great leadership has on individuals, teams, organisations or the wider community. A senior leader operating at a strategic level and able to demonstrate the real impact they make at this level to deliver success. Passionate about their own leadership learning and eager to help others to become successful leaders too. In addition, having completed a Level 7 qualification OR an equivalent Institute Approved programme OR mapped Military rank, OR evidence of 3 years appropriate CPD to become one of our Fellows".
  • Membership of subject-specific society
  • Chair of editorial board of leading journal(s) or book series
  • Membership of editorial board of leading journal(s) or book series
  • I was Nominated for People Make Research 2023 – recognising those who make a positive difference to our research culture, and recognised for impact on Collaboration and Career
  • I have received Exceptional Contribution Award 2020/2021 from James Watt School of Engineering, University of Glasgow (£1,000)
  • I have received Exceptional Contribution Award 2017/2018 from James Watt School of Engineering, University of Glasgow (£1,000)
  • 2021/2022: MVLS/CoSE Engineering Biology Workshop, University of Glasgow, UK (team led by PDRA, Anastasiia Kostrytsiia, with myself as collaborator was winner of ~£10K pitch)
  • Poster by PhD student (Rhea Aqueel) entitled "Cotton Microbiome Profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum" was winner of the First Prize at Advances in Plant Genomics for Climate Mitigation Conference 2024
  • Talk by PhD Student (Gladys Maria Pangga) entitled "Integrative omics reveals distinct metabolic and microbial signatures in broilers under gut health interventions" was winner of Best Oral Presentation Award at World's Poultry Science Association (WPSA) UK Branch Meeting 2025.
  • Poster by PhD student (Aideen Kearney) entitled "Influence of hatchery rearing system on intestinal microbiome communities during the smoltification process of Atlantic Salmon (Salmo Salar)" was winner of the Best Poster Award at European Association of Fish Pathologists (EAFP) conference 2025
  • Alexandru Popescu (undergraduate student placement on British Society for Plant Physiology Summer Vacation Bursary) presented his work in the prestigious British Society for Plant Pathology Conference (December, 2021) and was subsequently winner of 2022 Sandwich Student Recruitment at The Francis Crick Institute
  • PDRA (Anastasiia Kostrytsia) was the Overall Winner (Presentation) in the 3rd annual Early Career Researcher Conference by EBNET for her presentation entitled "DNA-SIP metagenomics to recover active ammonia- and nitrite oxidisers".
  • MSc in Medicine Research Student (Konstantina Zafeiropoulou) was winner of the Yorkhill Postgraduate Research 1st Prize, 2020 upon the publication of K. Zaferopoulou et al. Gastroenterology, 159(6):2039-2051.e20, 2020. DOI: 10.1053/j.gastro.2020.08.007
  • PhD Student (Vaios Svolos) was winner of the Yorkhill Postgraduate Research 1st Prize, 2019 upon the publication of V. Svolos et al. Gastroenterology, 156(5):1354-1367.e6, 2019. DOI: 10.1053/j.gastro.2018.12.002
  • Poster by PhD student (Anna Trego) entitled Size matters for structure and function of anaerobic sludge granules, supporting a biofilm life-cycle model was winner of the prestigious ISME Student Poster Award at ISME17 (9/1800+ posters awarded)
  • Poster by PhD student (Konstantinos Gkikas) entitled "The fibre fermentative capacity of the gut microbiota is diminished in children with Crohn's disease and it is independent of disease activity or treatment with exclusive enteral nutrition" was winner of the Best Poster Award at Single Cell Technology meets Microbiomics 2021
  • Paper by the PhD student (Konstantinos Gkikas) entitled "Dietary triggers of colonic inflammation following treatment with exclusive enteral nutrition in children with Crohn's disease" was winner of the prestigious Dr Falk IBD Poster Award at BSPGHAN Annual Meeting
  • Paper by the PhD student (Vaios Svolos) was the winner of the prestigious Best investigator-initiated study (IIS) Award at the 11th Congress of ECCO (2/178 abstracts awarded)
  • I won the Send-A-Newbie Award (~£600) to attend the prestigious YAPC::EU 2012 conference on Perl language
  • I have declined the offer of Tier 1 (Exceptional Talent Visa) and instead opted for British citizenship through the Indefinite Leave to Remain route
  • Past Esteem
    • I have received scholarship throughout my studies. I stood 2nd in the entrance exam for my MPhil, which led to the award of GIKI Merit Scholarship resulting in tuition fee waiver. During my PhD, I was awarded JNU Category-A Scholarship that waived my tuition fee during the PhD coursework (2004-2006). For living allowance, I simultaneously held three scholarships, namely, Korean Government IT Scholarship, IITA, Korea ~$56,000 (2004-2008), 2nd phase Brain Korea-21 Project Scholarship ~$3,600 (2007-2008), and Scholarship from Ministry of Commerce, Industry and Energy, Korea Grant No. S1005503 ~$4,200 (2005-2006).
    • I have secured first position in the university (across all departments) during my MPhil by securing 4.0/4.0 CGPA for which I received Certificate of Excellence from the Dean of Faculty of Computer Science and Engineering; as well as Merit Certificate from Pro-Rector Academics, GIK Institute of Science and Technology, Pakistan.
    • During my MPhil, I have been given Certificates of Appreciation by members (A. M. Mirza; S. A. Hussain) of Faculty of Computer Science and Engineering, GIK Institute of Science and Technology, Pakistan and was recognised for taking part in Aggressive Learning Competitions, where I demonstrated my ability to quickly grasp knowledge in a very short time, often taking three to four days (in a single sitting) to read text books and solve all exercises.
    • I have received the prestigious Excellence in Research Award [English Translation] (only two PhD students are awarded each year) from the Dean of Graduate Studies, Jeju National University. My PhD achievements were adjudged 2nd amongst 37 (across all departments) who were awarded the PhD degree in February 2008.
    • I have received the Best Researcher of the Year Award two years (2007 ₩1,000,000, 2008 ₩1,500,000) in a row being part of the countrywide 2nd Phase Brain Korea 21 project.
    • I have received the prestigious Excellent Achievement Award, The Second Prize (₩500,000) from LG Electronics in 2006. The assessment was done through countrywide competition among ~300 students who received Korean Government IT Scholarship from Institute of Information Technology Assessment (IITA) for their PGR studies.
    • During my PhD, two papers received Excellent Paper Award in a student fair organized by IITA in 2005. Another paper was considered as one of the 11 noteworthy papers and was selected and published in Meas. Sci. Technol. (DOI: 10.1088/0957-0233/18/1/008) from the prestigious Fifth International Conference on Inverse Problems in Engineering: Theory and Practice held in Cambridge, UK (2005)

Leadership

  • Principal investigator of research groups/labs
    • Director, Environmental'Omics Lab (2012-present)
      Significance: An online consortium on analysis of omics datasets in environmental and clinical science. There are 114 current members (Feb 2025) where the primary mode of interaction is through MS Teams channel and Zoom. The lab hosts video tutorials and standard operating procedures on how to go about data analysis from molecular methods. Additionally, the MS Teams page also serves as a journal group on bioinformatics.
    • PI, Water & Environment Group (2014-present; James Watt School of Engineering, University of Glasgow)
      Significance: Under this group, I am working on world's most pressing environmental and public health problems: clean water and sanitation for all; decarbonisation of water and environmental services; sustainable management of the environment; extracting energy and resources form waste; making our rivers, water infrastructure and water services resilient to climate change.
    • PI and Co-Founder, Glasgow Geroscience Group (G3) (2024-present; University of Glasgow)
      Significance: Under this group, I am trying to understand and target interventions to mitigate the effects of an advancing ageing process and the resultant "diseasome of ageing".
    • PI and Co-founder, Bacteria, Immunology, Nutrition, Gastroenterology and OMICS (BINGO) Group (2012-present; School of Medicine, Dentistry & Nursing, University of Glasgow)
      Significance: Under this group, I am exploring the role of gut microbiota and its interaction with the diet and the immune system in health and disease. We have two major projects:
      • CD-Treat Diet: A solid food diet using everyday foods for treatment for cases with active Crohn’s Disease (CD). Currently CD-TREAT is used as part of an open-label trial at NHS Greater Glasgow and Clyde in CD patients with active disease, instead of using their standard medical treatment.
      • BIOPIC Diet: The Biologics and Partial Enteral Nutrition in Crohn’s Disease Study (BIOPIC): Combining partial enteral nutrition with biologics to optimise induction and maintenance therapy for adults with active ileocolonic Crohn’s disease. Two of the best treatment options currently available to people with Crohn’s disease are drug injections known as biologics, and a liquid-only diet in the form of specially formulated milkshakes, known as Exclusive Enteral Nutrition (EEN), commonly used as a first line treatment to induce remission in paediatric patients. Here, we are exploring whether replacing part of the diet with the specialised milkshakes, known as Partial Enteral Nutrition (PEN), will improve response to standard treatment with biologics in adults with active Crohn’s disease.
    • PI, Founder, and Facility Manager, Orion Cluster (James Watt School of Engineering, University of Glasgow)
      Significance: I have single-handedly built and managed an HPC facility in James Watt School of Engineering called Orion Cluster. I bought the first server in 2012 through an Innovate UK grant with Unilever (which supported my Research Fellowship between 2012 and 2014) and since then I have religiously pursued my collaborators for in-kind contributions, as well as allocating small equipment budget on every grant I am applying. To date, I have spent £220K on 20 servers. This facility now sits at the heart of all major research groups I am involved with and is envy of many others. One of the reason why I have managed to attract funding and collaborators is through development of bespoke workflows (originating from my research) that I regularly updates and share on my website as well as providing a single place for >500 bioinformatics tools. My cluster and bioinformatics tutorials are of strategic importance as they give me legitimacy and an authority on bioinformatics. Majority of my key collaborators outside Glasgow came about as a result of stumbling on my website/tutorials, sending their students under mobility scheme to get trained on my workflows, and then later inviting me to be an investigator on the research grants. Natural Environment Research Council (NERC) recognizing my potential to lead has in the past funded £23K towards attendance of Cambridge Advanced Leadership Programme in Judge Business School, University of Cambridge in 2016.
  • Academic investigator of major multi-centre research groups (also involving industrial partners, policy makers, and stakeholders)
  • Member (2024-), Internal Peer Review College (PRC), Strategic Research Initiative (SRI), University of Glasgow
  • PGT Advisor of Study (MSc Electronics and Electrical Engineering) (James Watt School of Engineering, University of Glasgow; responsible for academic/pastoral care of 40+ PGT students/year)
  • Advisory Committee Memberships
    • International Advisory Committee Member (2019-), Department of Biosciences, COMSATS University, Islamabad, Pakistan
    • International Advisory Committee Member (2024-), KAM-School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
    • International Advisory Member (2024-), Poultry Diagnostic and Population Dynamics Advisory Committee, Poultry Research Institute, Government of Pakistan
  • Committee chairpersonship within subject-specific society
    • Chairperson of Scottish Pakistani Association (Elected 2023)
      Significance: The Scottish Pakistani Association (SPA) was founded in 1982, led by late Mr Bashir Maan, CBE. Its aim is to develop communications and friendly relations between the Pakistani community and all other people in Scotland and actively engaged in promoting and fostering cultural and social activities, in order to develop a greater understanding at all levels, national and international. The patrons include The High Commissioner of Pakistan to the United Kingdom and His Grace, The Duke of Montrose. The facebook page has over 1K followers.
  • Independent research fellowships
    • Natural Environment Research Council (NERC) Independent Research Fellow (2014-2019; acceptance rate: 8%)
    • Lord Kelvin Adam Smith Leadership Fellow (2014-2019)
    • Research Fellow (Infrastructure & Environment) (2012-2014; Funded through two grants: an Innovate UK grant with Unilever; a small-scale grant with CICRA charity)
  • Past Leadership: Previously, during my studies and on job, I held key leadership and institutional positions
    • President of AIS Badminton Club (2000-2001)
    • President of AIS Entertainment Club (2000-2001)
    • President of Graduate Students Association (representing all PGT/R students in GIKI, Pakistan, 2001-2002)
      Significance: A coveted position, elected via elction of PGT/R students. I liased with university administration to resolve problems faced by post graduate students, and organized cultural events, excursion trips, and get togethers. I also liased with the undergraduate president to involve PGT/R students in their clubs and activities. Additionally, I was incharge of Mess Committee where my role was to set menu items for students residing in local hostels.
    • President of Foreign Students Association (representing >4000 foreign students in JNU, Korea, 2005-2006)
      Significance: I served one-year term, elected via election of foreign student body and worked under Office of Student Affairs, JNU, Korea.
      • I led an English Zone project to increase interaction between Korean students and foreigners (of South Asian descent including Pakistan, India, Bangladesh, and Srilanka); and organized cultural events, excursion trips, and get togethers for foreign students
      • I liased with university administration to resolve problems faced by the foreign students, and was instrumental in building an International Kitchen specifically for those students who have special dietary requirements
      • I organized and coordinated citywide Pakistan Earthquake Relief Fund Campaign (2005) through mass mobilization of foreign students and raised thousands of dollars; The campaign was covered in national media:
        Jeju Sori (16/10/2005)
        Jeju News (15/10/2005)
      • I was also instrumental in growing Pakistani students community at JNU, Korea and was part of numerous committees that recruited Pakistani students. Some notable students that I mentored and who hold key strategic positions in HEIs in Pakistan upon conclusion of their studies include:
        • Safeeullah Chaudhary, Currently Associate Professor, Syed Babar Ali School of Science and Engineering, Lahore University of Management Science, Pakistan (I recruited him on the project which I led as a PI: 2D Electrophoresis Gel Image Processor for Matlab (2005-2006), Ministry of Commerce, Industry and Energy, Korea Grant No. S1005503)
        • Khalid Rehman, Professor and Dean, Faculty of Mechanical Engineering, GIK Institute of Engineering Sciences and Technology, Pakistan
        • Ahmar Rashid, Professor and Former Dean, Faculty of Computer Sciences, GIK Institute of Engineering Sciences and Technology, Pakistan (share co-authorship)
        • Malik Muhammad Nauman, Associate Professor, Faculty of Integrated Technologies, Universiti Brunei Darussalam

Outreach

Recent Invites, Visits, and Organizations

31/03/2025 Invited Talk, Understanding microbial communities through in situ omics data synthesis, Glasgow Computational Biology Community
17/01/2025 K&E-focused engagement with a policy maker; Foreign, Commonwealth & Development Office (FCDO) Round Table Discussion on Pakistan, University of Glasgow
17/09/2024 Invited Talk, Understanding microbial communities through in situ omics data synthesis, The Roslin Institute, University of Edinburgh (c/o Professor Albert Tenesa, Head of Division of Quantitative Biology)
02/08/2024 Invited Talk, Strategies for Improvement, Graduate Students Meeting, Department of Biosciences, COMSATS University, Islamabad, Pakistan
02/08/2024 K&E-focused engagement with a government research institute; Official Visit, Pathogens Genomic Surveillance Center, National Institute of Health, Islamabad, Pakistan (c/o Dr Massab Umair, Head of Virology and Senior Scientific Officer)
02/08/2024 K&E-focused engagement with a higher education institute; Official Visit, FAST National University of Computer and Emerging Sciences, Islamabad, Pakistan (c/o Professor Hammad Majeed, HoD, Department of Computer Science)
01/08/2024 Research Group Collaborative Meeting, Serena Hotel, Islamabad, Pakistan (c/o Professor Syed Muhammad Nurulain, Grand Asian University, Sialkot, Pakistan)
01/08/2024 K&E-focused engagement with a policy maker; Official Visit, Higher Education Commission of Pakistan (HEC), Islamabad, Pakistan (c/o Professor Zia Ul-Qayyum, Executive Director and Acting Chairman (HEC); and Former Vice Chancellor, Allama Iqbal Open University, and University of Gujrat)
30/07/2024 Keynote Speaker and Co-Chair, 1st international symposium on "Applications of OMICS technologies in health and disease" (COMSATS University Islamabad & University of Glasgow).
This event received over 200 registered participants from 12 countries including UK, Germany, Italy, China, South Africa, Thailand, Portugal, Cameroon, Sri Lanka, Malaysia, Tunisia and Pakistan
29/07/2024 K&E-focused engagement with a government research institute; Invited Talk and Official Visit, National Institute for Genomics & Advanced Biotechnology (NIGAB), Government of Pakistan (c/o Dr Ghulam Muhammad Ali, Chairman, Pakistan Agricultural Research Council; and Dr Shoukat Ali, Principal Scientific Officer, and Director NIGAB)
26/07/2024 Invited Online Webinar, Multivariate statistical analysis of shotgun metagenomics and other OMICS datasets with CViewer, DDC Informatics User Group Meeting, Baylor College of Medicine, Texas Medical Center, USA (c/o Dr Numan Oezguen)
26/07/2024 Invited Talk and Official Visit, Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan (c/o Professor Kauser Abdulla Malik (HEC Distinguished Professor, Dean of Postgraduate Studies, and Former Minister of National Food Security and Research, Government of Pakistan))
23/07/2024 Invited Talk and Official Visit, Kohsar University, Murree, Pakistan (c/o Professor Habib Bokhari, Vice Chancellor)
19/07/2024;01/08/2024 K&E-focused engagement with an NGO; Official Visits, Urban Impact Lab (UIL), Research and Development Solutions (RESDEV), Islamabad, Pakistan (c/o Dr Ayesha Khan, CEO Akhter Hameed Khan Foundation; and Dr Adnan Khan, Chief Knowledge Officier RESDEV) [Meeting 1; Meeting 2]
01/07/2024 Invited Speaker, Future of Systems Biology: Roundtable Discussion with Chief Editors of Frontiers in Systems Biology
11-13/06/2024 K&E-focused engagement with an NGO; Organizer and Lecturer, Community Surveys Data Analysis, Online Training Hackathon 1, Urban Impact Lab, Akhter Hameed Khan Foundation, Pakistan [link]
21-22/05/2024 Invited Lecturer, MSc Code & Create Workshop, James Watt School of Engineering, University of Glasgow (c/o Professor Rami Ghannam)
07-08/03/2024 Invited Speaker, Nutrition Sensing and Ageing, A joint workshop of the AGEing and Nutrient Sensing (AGENTs) Network and the Scottish Alliance for Food (SCAF), Advanced Research Centre (ARC), University of Glasgow
04-06/03/2024 K&E-focused engagement; Blog Post: Bac Together in Manchester (Bacterial Plant Diseases UK)
20/02/2024 Invited Speaker, School of Interdisciplinary Engineering & Science (SINES), NUST Islamabad, Pakistan
16/12/2023 Invited Speaker, 3rd International Conference on Research in Biological Sciences, Center to Advance Level Research & Development (SMC-PVT) Ltd, Pakistan
09-11/11/2023 Invited Speaker, Glasgow Geroscience Group Sandpit 2, Meikleour, Scotland (c/o Professor Paul Shiels)
03/08/2023 K&E-focused engagement with a government research institute; Invited Talk and Official Visit, National Institute for Genomics & Advanced Biotechnology (NIGAB), Government of Pakistan (c/o Dr Ghulam Muhammad Ali, Chairman, Pakistan Agricultural Research Council)
02/08/2023 K&E-focused engagement with a government research institute; Official Visit, National Veterinary Laboratory, Ministry of National Food Security and Research, Government of Pakistan (c/o Dr Khurshid Ahmad, Principal Scientific Officer and Director General)
01/08/2023 Invited Talk and Official Visit, Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan (c/o Professor Kauser Abdulla Malik (HEC Distinguished Professor and Dean of Postgraduate Studies), and Professor Samina Mehnaz (Chairperson/Head of School))
31/07/2023 Invited Talk, National University of Science and Technology (NUST), Pakistan (c/o Dr Aneela Javed, Head of the Research Department, NUST Atta ur Rahman School of Biosciences (ASAB) [link]
24/07/2023 K&E-focused engagement with an industry; Official Visit, Alltech Pakistan (c/o Dr Shahzad Naveed Jadoon, Director & CEO)
21/07/2023 K&E-focused engagement with a government research institute; Official Visit, Ecotoxicology Research Institute, Pakistan Agricultural Research Council, Ministry of National Food Security & Research, Government of Pakistan (c/o Dr Farrakh Mehboob, Program Leader and Principal Scientific Officer)
21/07/2023 K&E-focused engagement with a government research institute; Official Visit, Animal Sciences Institute (ASI), Pakistan Agricultural Research Council, Ministry of National Food Security & Research, Government of Pakistan (c/o Dr Hamid Irshad, Principal Scientific Officer)
21/07/2023 K&E-focused engagement with a higher education institute; Official Visit, Health Services Academy, Ministry of National Health Services, Government of Pakistan (c/o Professor Ramesh Kumar, and Dr Tariq Mahmoud Ali (Registrar))
21/07/2023 K&E-focused engagement with a government research institute; Official Visit, National Institute of Health, Islamabad, Pakistan (c/o Dr Massab Umair, Head of Virology and Senior Scientific Officer)
20/07/2023 Official Visit and Round Table Discussion with Faculty and Graduate Students, Department of Biosciences, COMSATS University Islamabad, Pakistan (c/o Professor Qaiser Fatmi, Head of Department of Bioscience)
10/07/2023 Keynote Speaker & Co-Chair, COMSATS University Islamabad and University of Glasgow Online interactive session/seminar on "Pathways to collaborative networking series for Project Investigators: Understanding microbial communities through in situ omics data synthesis – New developments"; Link to Video Lectures Pass Code: B8U2Vb.*
The event was registered by 125 participants from 12 countries including UK, USA, UAE, Germany, Italy, China, Kenya, Cameroon, Sri Lanka, Bangladesh, Iraq and Pakistan.
07/03/2023 K&E activity with industrial partners/stakeholders; To Chlorinate or Not to Chlorinate; Virtual Launch Event
13-14/07/2023 K&E activity with policymakers; Under Pakistan-UK education gateway, a high profile delegate of 20+ Vice Chancellors (VCs) of numerous universities from Pakistan, British Council and Higher Education Commission, Pakistan visited University of Glasgow (Tweet): Three of the VCs: Lt Gen Wasim Alamgir, National University of Medical Sciences; Professor Habib Bokhari, Kohsar University Murree; and Professor Qaisar Abbas, University of Sargodha further visited Environmental'Omics lab in Mazumdar-Shaw Advanced Research Centre (ARC), and were briefed about the ongoing research activities in the Water & Environment Group including the Decentralised Water Technologies Programme Grant in a talk entitled “Understanding microbial communities through in situ omics data synthesis – New developments“. Amongst other things, student projects of visiting PGRs from Pakistan, and further collaborative opportunities were discussed.
08-09/03/2023 K&E-focused engagement; Blog Post: Looking back and looking forwards: BPD Full Team Meeting March 2023 (Bacterial Plant Diseases UK)
19-21/01/2023 Invited Speaker, Geroscience Sandpit, Meikleour, Scotland (c/o Professor Paul Shiels)
08/12/2022 Invited Speaker, Department of Microbiology, Ryan Institute, University of Galway, Ireland
03/11/2022 K&E-focused engagement with stakeholders; Blog Post: Fighting Bac: Making microbes our allies (Stakeholder Workshop) (Bacterial Plant Diseases UK)
13/10/2022 Invited Speaker, Glasgow University Microbiome Initative (GUMI) Symposium 2022, University of Glasgow
26-27/09/2022 Invited Speaker, Urban Microbiome Meeting, University of Glasgow (c/o Dr John Moreau)
27/09/2022 Invited Speaker, University of Sydney and University of Glasgow Virtual Seminar Series: Nutrition, Metabolism and Health
24/05/2022 Invited Speaker, Soil Health & Soil Heritage – Glasgow Workshop: Workshop 2: Enriching Scotland’s soils data – sensing, modelling and interoperability
15-16/03/2022 K&E-focused engagement; Blog Post: Bac Together in Sheffield and Online (Bacterial Plant Diseases UK)
09/03/2022 Invited Speaker, Understanding microbial communities through in situ omics data synthesis, NUI Galway, Ireland (c/o Professor Vincent O'Flaherty)
10/02/2022 Invited Speaker, BBSRC’s EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities, UK
28/01/2022 K&E activity with industrial partners/stakeholders; Blog Post: Decentralised Water Technologies Programme - EPSRC Programme Grant on Off-grid Water Technologies
18/11/2021 K&E activity with industrial partners/stakeholders; Blog Post: Visit to Scottish Water Development Centres
15/11/2021 K&E activity with industrial partners/stakeholders; Blog Post: Bacterial Plant Diseases Programme - Building Bridges to Tackle Blackleg (Bacterial Plant Diseases UK)
05-06/07/2021 Invited Speaker, Single Cell Technology meets Microbiomics 2021, UK
13/02/2020 Keynote Speaker, Data and Society, Oslo Life Science Conference, Norway
05/02/2020 Invited Speaker, NORCE Research, Bergen, Norway
05/12/2018 Invited Speaker, CompLifeSci 3rd Annual Meeting, Biocity Turku, Finland
30/11/2018 Invited Speaker, Microbiome Round Table Discussion with Versus Arthritis and BenevolentAI, London
06-08/06/2018 Host and Co-organizer (with Dr Leo Lahti), Numerical Ecology Workshop, University of Glasgow
17/01/2018 Invited Speaker and centre visit, MRC Centre for Medical Mycology, Aberdeen (c/o Professor Gordon Brown)
28-29/09/2017 Organizer, Pitlatrine Sandpit, University of Glasgow
26/04/2017 Invited Speaker and lab visit, Earlham Institute, Norwich (c/o Professor Neil Hall)
16/09/2016 Lab visit, Center for Microbial Ecology and Technology, Ghent, Belgium (c/o Professor Nico Boon)
12-15/09/2016 Session Chair (Microbial genomics and metagenomics), SETAC/iEOS Joint Focused Topic Meeting, Ghent, Belgium
06-09/08/2015 Session Chair and Invited Speaker (Omics in extreme environments), iEOS2015, St Andrews
22-25/09/2014 Organizer, Hands-on-workshop (hackathon): From signals to environmentally tagged sequences III (SeqEnv III), Hellenic Centre for Marine Research, Crete, Greece
19/06/2014 Invited Speaker, Edinburgh Amplicon Sequencing Group Second Discussion Meeting
07-11/11/2013 Organizer and Participant with Professor Chris Quince, COST ES1103: Extracting strain level variation from shotgun metagenome data, Isaac Newton Institute, Cambridge, UK
24-28/06/2013 Organizer and Participant with Professor Chris Quince, COST ES1103: ProBin: Probabilistic binning for metagenome contigs, Instituto Gulbenkian De CieNcia, Lisbon, Portugal
18-19/06/2013 Led the workshop "Diversity and quantification of microbial communities in terrestrial environments" - the second part focused on interpretation of metagenomic data in microbial ecology. Given approximately 14 hours of lectures at Faculty of Science, in Ceske Budejovice, Czech Republic. These were supplied as part of the resolved project no. CZ.1.07/2.2.00/15.0364 - Molecularisation of biological fields of the Faculty of Science of JU, financed by the European Social Fund and the state budget of the Czech Republic, as part of the Education for Competitiveness Operational Programme (c/o Dr Alica Chronakova)
10-13/06/2013 Organizer and Participant with Professor Chris Quince, COST ES1103: From Signals to Environmentally Tagged Sequences II" (Ref: ECOST-MEETING-ES1103-100613-031037), Hellenic Centre for Marine Research, Crete, Greece
11-14/12/2012 COST training school ES1103: Bioinformatics for Microbial Community Analysis (Tutors: Dr. Christopher Quince, University of Glasgow, UK; Dr. Martin Hartmann, Swiss Federal Research Institute WSL, Agroscope Research Station ART, Switzerland; Dr. Nick Loman, University of Birmingham, UK; Dr. Umer Zeeshan Ijaz, University of Glasgow, UK), University of Liverpool
27-29/09/2012 Organizer and Participant with Professor Chris Quince, COST ES1103: From Signals to Environmentally Tagged Sequences" (Ref: ECOST-MEETING-ES1103-050912-018418), Hellenic Centre for Marine Research, Crete, Greece
06-09/07/2012 Organizer and Participant with Professor Chris Quince, COST ES1103: WGs 1 & 2 Inaugural Hackathon: Resolving uncertainty in microbial metagenomics, University of Glasgow

Publications

My research is both interdisciplinary and transdisciplinary, and has resulted in 240+ publications (ResearchGate; Loop profile: 292992; ORCID iD iconorcid.org/0000-0001-5780-8551) with those that are recently gaining citations can be found at my Google Scholar profile. In terms of total citations in Google Scholar, I am the 3rd most cited researcher in the world in Information Engineering, and the 5th most cited researcher in the world in Numerical Ecology. Note that some of the publications have associated impact in the form of news articles, blogs, wikipedia articles, policy documents, and clinical guidance documents. These publications have associated Altmetric widgets with links as can be seen below. Additionally, some publications are proof-of-concept of a particular technology, with these technologies highlighted in Systems/Products section.

    Journals

  1. F. Cholet, M. Vignola, D. Quinn, U. Z. Ijaz, W. T. Sloan, and C. J. Smith. Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, accepted for publication (2025).
  2. R. V. K. Mellya, J. G. C. Hopcraft, W. Mwakilema, E. Eblate, S. Mduma, B. Mnaya, I. S. Chuma, E. S. Macha, D. Wambura, R. Fyumagwa, E. Kilbride, U. Z. Ijaz, B. K. Mable, and A. Khan. Natural dispersal is better than translocation for reducing risks of inbreading depression in eastern black rhinoceros. Proceedings of the National Academy of Sciences, accepted for publication (2025).
  3. F. Saleem, A. Ameer, F. Afzal, M. Usman, H. Irshad, S. Sattar, U. Z. Ijaz#, and S. Javed#. A Cross-sectional Survey of Poultry Management Systems, Practices and Antimicrobial use in relation to Disease Outbreak in Pakistan. BMC Research Notes, 18:144, 2025. DOI: 10.1186/s13104-025-07220-4
    #Joint corresponding authors
  4. Z. Zainy, M. Z. Hyder, U. Uzma, M. Fayyaz, U. Z. Ijaz#, and S. Farrakh#. Comparative transcriptome analysis of resistant, moderately resistant, and susceptible wheat-near-isogenic lines in response to Puccinia striiformis tritici. Journal of Plant Interactions, 20(1), 2025. DOI: 10.1080/17429145.2025.2481853
    #Joint corresponding authors
  5. A. Trego, C. Morabito, I. Bourven, G. Guibaud, V. O’Flaherty, G. Collins#, and U. Z. Ijaz#. Size matters: Anaerobic granules exhibit distinct ecological and physico-chemical gradients across biofilm size. Environmental Science and Ecotechnology, 100561, 2025. DOI: 10.1016/j.ese.2025.100561
    #Joint corresponding authors
  6. S. Mills, U. Z. Ijaz, and P. N. L. Lens. Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems. npj Biofilms and Microbiomes, 11:54, 2025. DOI: 10.1038/s41522-025-00679-w
  7. A. Badar, R. Aqueel, A. Nawaz, U. Z. Ijaz#, and K. A. Malik#. Microbiota Transplantation for Cotton Leaf Curl Disease Suppression - Core Microbiome and Transcriptome Dynamics. Communications Biology, 8:380, 2025. DOI: 10.1038/s42003-025-07812-7
    #Joint corresponding authors
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  8. A. Khan, R. Carter, C. Mpamhanga, D. Masiga, M. Channumsin, M. Ciosi, O. Manangwa, F. Mramba, U. Z. Ijaz, H. Auty, and B. Mable. Swatting flies: Biting insects as non-invasive samplers for mammalian population genomics. Molecular Ecology, e17661, 2025. DOI: 10.1111/mec.17661
  9. G. M. Pangga, B. Star-Shirko, A. Psifidi, D. Xia, N. Corcionivoschi, C. Kelly, C. Hughes, U. Lavery, A. Richmond, U. Z. Ijaz#, and O. Gundogdu#. Impact of commercial gut health interventions on caecal metagenome and broiler performance. Microbiome, 13:30, 2025. DOI: 10.1186/s40168-024-02012-7
    #Joint corresponding authors
    Video Abstract:

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  10. S. Milling, U. Z. Ijaz, D. Venieri, G. Ε. Christidis, N. J. W. Rattray, I. Gounaki, A. Andrusaite, A. Hareendran, C. W. Knapp, A. X. Jones, and E. Photos-Jones. Beneficial modulation of the gut microbiome by leachates of Penicillium purpurogenum in the presence of clays: a model for the preparation and efficacy of historical Lemnian Earth. PLoS ONE, 19(12):e0313090, 2024. DOI: 10.1371/journal.pone.0313090
    Press Release: Phys.org - Ancient clay remedy may have potential to boost modern gut health
    Press Release: Newsweek - Ancient Pill Secret From 2,500 Years Ago May Improve Gut Health
    Press Release: The Times - Ancient clay remedy 'secret to modern gut health'
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  11. K. J. Katchkin-Stewart, A. S. Boerlage, W. Barr, U. Z. Ijaz, and C. J. Smith. Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea. Animal Microbiome,6:25, 2024. DOI: 10.1186/s42523-024-00347-y
  12. H. Ashraf, P. Dikarlo, A. Masia, I. R. Zarbo, P. Solla, U. Z. Ijaz#, and L. A. Sechi#. Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with Multiple Sclerosis. Scientific Reports, 14:24027, 2024. DOI: 10.1038/s41598-024-74975-4
    #Joint corresponding authors
  13. A. Ameer, F. Saleem, C. Keating, O. Gundogdu, U. Z. Ijaz#, and S. Javed#. Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan. Data in Brief, 57:110957, 2024. DOI: 10.1016/j.dib.2024.110957
    #Joint corresponding authors
  14. S. Martin, C. Smith, K. Stewart, W. Barr, D. Cheslett, I. O'Connor, F. Swords, U. Z. Ijaz, and K. O’Dwyer. The hepatopancreas microbiome of velvet crab, Necora puber. Environmental Microbiology Reports, 16(5):e70014, 2024. DOI: 10.1111/1758-2229.70014
  15. A. Trego, S. O’Sullivan, V. O’Flaherty, G. Collins#, and U. Z. Ijaz#. Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues. Environmental Microbiome, 19:68, 2024. DOI: 10.1186/s40793-024-00615-z
    #Joint corresponding authors
  16. C. Keating#, E. Kilbride, M. Stalham, C. Nellist, J. Milner, S. Humphris, I. Toth, B. K. Mable, and U. Z. Ijaz#. Balancing the scales: Impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities. Microbiome, 12:210, 2024. DOI: 10.1186/s40168-024-01918-6
    #Joint corresponding authors
    Video Abstract:
  17. S. Bibi, C. Kerbiriou, Uzma, S. Mckirdy, A. Kostrytsia, H. Rasheed, S.A.M.A.S. Eqani, K. Gerasimidis, S. M. Nurulain#, and U. Z. Ijaz#. Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan. Ecotoxicology and Environmental Safety, 284:116959, 2024. DOI: 10.1016/j.ecoenv.2024.116959
    #Joint corresponding authors
  18. B. Nichols, R. K. Russell, B. Short, R. Papadopoulou, G. Focht, U. Z. Ijaz, T. D. Walters, M. Sladek, R. Hansen, D. R. Mack, E. Wine, A. M. Griffiths, D. Turner, and K. Gerasimidis. Gut microbial signatures in paediatric Crohn's disease vary according to disease activity measures and are influenced by proxies of gastrointestinal transit time: an ImageKids study. Inflammatory Bowel Diseases, izae199, 2024. DOI: 10.1093/ibd/izae199
  19. T. E. Conley, R. Slater, S. Moss, D. Bulmer, J. de la Revilla Negro, U. Z. Ijaz, D. M. Pritchard, M. Parkes, and C. Probert. Microbiome-driven IBS metabotypes influence response to the low FODMAP diet: Insights from the faecal volatome. EBioMedicine, 107:105282, 2024. DOI: 10.1016/j.ebiom.2024.105282
  20. R. Aqueel, A. Badar, N. Roy, U. Z. Ijaz#, and K. A. Malik#. Disease resistance correlates with core microbiome diversity in cotton. Current Microbiology, 81(9):302, 2024. DOI: 10.1007/s00284-024-03827-1
    #Joint corresponding authors
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  21. A. C. Trego, T. Palmeiro-Sánchez, A. Graham, U. Z. Ijaz#, and V. O'Flaherty. First evidence for temperature influencing the enrichment, assembly and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities. Frontiers in Systems Biology, 4:1375472, 2024. DOI: 10.3389/fsysb.2024.1375472
    #Corresponding author
  22. X. Shi, R. Pereira, Uzma, L. Savage, B. Poursat, D. Quinn, A. Kostritsia, F. Cholet, C. J. Smith, C. Gauchotte-Lindsay, W. T. Sloan, U. Z. Ijaz, and M. Vignola. Microbial stratification and DOM removal in drinking water biofilters: Implications for enhanced performance. Water Research, 262:122053, 2024. DOI: 10.1016/j.watres.2024.122053
  23. H. Ashraf, P. Dikarlo, A. Masia, I. R. Zarbo, P. Solla, U. Z. Ijaz#, and L. A. Sechi#. Network analysis of gut microbial communities reveal key genera for a multiple sclerosis cohort with Mycobacterium avium subspecies paratuberculosis infection. Gut Pathogens, 16:37, 2024. DOI: 10.1186/s13099-024-00627-7
    #Joint corresponding authors
  24. F. Cholet, H. Agogué, U. Z. Ijaz, N. Lachaussée, P. Pineau, and C. J. Smith. Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. Science of the Total Environment, 2024. DOI: 10.1016/j.scitotenv.2024.174312
  25. E. Corbett, U. Z. Ijaz, I. Jackson, and V. R. Phoenix. Stormwater Quality & Microbial Ecology in an Urban Rain Garden System. Frontiers in Water, 6:-, accepted for publication (2024). DOI: 10.3389/frwa.2024.1383382
  26. S. Belnour, R. Slater, K. Tharmaratam, M. K. H. Auth, R. Muhammed, C. Spray, D. Wang, U. Z. Ijaz, C. Probert, and S. Allen. Faecal volatile organic compounds differ according to inflammatory bowel disease sub-type, severity, and response to treatment in paediatric patients. United European Gastroenterology Journal, 1-13, 2024. DOI: 10.1002/ueg2.12603
  27. U. Z. Ijaz#, A. Ameer, F. Saleem, F. Gul, C. Keating, and S. Javed. Speciality Grand Challenge: How can we use integrative approaches to understand microbial community dynamics? Frontiers in Systems Biology, 4:1432791, 2024. DOI: 10.3389/fsysb.2024.1432791
    #Corresponding author
  28. R. Aqueel, A. Badar, U. Z. Ijaz#, and K. A. Malik#. Microbial Influencers and Cotton Leaf Curl Disease (CLCuD) susceptibility: A network perspective. Frontiers in Microbiology, 15:1381883, 2024. DOI: 10.3389/fmicb.2024.1381883
    #Joint corresponding authors
  29. F. Saleem, A. Ameer, B. Star-Shirko, C. Keating, O. Gundogdu, U. Z. Ijaz#, and S. Javed#. Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data in Brief, 110552, 2024. DOI: 10.1016/j.dib.2024.110552
    #Joint corresponding authors
  30. D. M. Grant, K. Steinsland, T. Cordier, U. S. Ninnemann, U. Z. Ijaz, H. Dahle, S. De Schepper, and J. L. Ray. Sedimentary ancient DNA sequences reveal marine ecosystem shifts and indicator taxa for glacial-interglacial sea ice conditions. Quaternary Science Reviews, 339:108619, 2024. DOI: 10.1016/j.quascirev.2024.108619
  31. O. Koci, R. K. Russell, M. G. Sheikh, C. Edwards, K. Gerasimidis, and U. Z. Ijaz#. CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets. Microbiome, 12:117, 2024. DOI: 10.1186/s40168-024-01834-9
    #Corresponding author
    Video Abstract:

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  32. A. Ameer, F. Saleem, C. Keating, O. Gundogdu, U. Z. Ijaz#, and S. Javed#. Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data in Brief, 54:110487, 2024. DOI: 10.1016/j.dib.2024.110487
    #Joint corresponding authors
  33. F. Gul, H. Herrema, M. Davids, C. Keating, A. Nasir, U. Z. Ijaz#, and S. Javed#. Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16(1):5, 2024. DOI: 10.1186/s13099-024-00596-x
    #Joint corresponding authors
  34. B. Nichols, A. Briola, M. Logan, J. Havlik, A. Mascellani, K. Gkikas, S. Milling, U. Z. Ijaz, C. Quince, V. Svolos, R. K. Russell, R. Hansen, and K. Gerasimidis. Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn's disease. American Journal of Clinical Nutrition, 119(4):885-895, 2024. DOI: 10.1016/j.ajcnut.2023.12.027
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  35. A. Ameer, Y. Cheng, F. Saleem, Uzma, A. McKenna, A. Richmond, O. Gundogdu, W. T. Sloan, S. Javed#, and U. Z. Ijaz#. Temporal stability and community assembly mechanisms in healthy broiler cecum. Frontiers in Microbiology, 14:1197838, 2023. DOI: 10.3389/fmicb.2023.1197838
    #Joint corresponding authors
  36. M. Vignola, J. Lenselink, D. Quinn, U. Z. Ijaz, R. Pereira, W. T. Sloan, S. Connelly, G. Moore, C. Gauchotte-Lindsay, and C. J. Smith. Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities. AQUA - Water Infrastructure, Ecosystems and Society, 72(10):1837–1851, 2023. DOI: 10.2166/aqua.2023.036
  37. H. Craven, H. Erlandsson, D. McGuinness, D. H. McGuinness, D. Mafra, U. Z. Ijaz#, P. Bergman, P. G. Shiels#, and P. Stenvinkel#. A normative microbiome is not restored following kidney transplantation. Clinical Science, 137(20): 1563-1575, 2023. DOI: 10.1042/CS20230779
    #Joint corresponding authors
  38. R. Aqueel, A. Badar, N. Roy, Q. Mushtaq, A. F. Ali, A. Bashir, U. Z. Ijaz#, and K. A. Malik#. Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum. npj Biofilms and Microbiomes, 9:100, 2023. DOI: 10.1038/s41522-023-00470-9
    #Joint corresponding authors
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  39. V. O. Okonkwo#, F. Cholet, U. Z. Ijaz#, T. Koottatep, T. Pussayanavin, C. Polpraset, W. T. Sloan, S. Connelly, and C. J. Smith. intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology e01071-23, 2023. DOI: 10.1128/aem.01071-23
    #Joint corresponding authors
  40. S. Mills, T. P. Y. Nguyen, U. Z. Ijaz, and P. N. L. Lens. Process stability in expanded granular sludge bed bioreactors enhances resistance to organic load shocks. Journal of Environmental Management, 342:11827, 2023. DOI: 10.1016/j.jenvman.2023.118271
  41. I. Aziz, Z. Noreen, U. Z. Ijaz#, O. Gundogdu, M. H. Hamid, N. Muhammad, A. Khan, and H. Bokhari#. A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome. Scientific Reports, 13:6802, 2023. DOI: 10.1038/s41598-023-32491-x
    #Joint corresponding authors
  42. S. Singh, C. Keating, U. Z. Ijaz#, and F. Hassard. Molecular insights informing factors affecting low temperature anaerobic applications: diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems. Science of the Total Environment, 2023. DOI: 10.1016/j.scitotenv.2023.162420
    #Corresponding author
  43. P. Dessi, C. Buenano, S. Martinez-Sosa, S. Mills, A. Trego, U. Z. Ijaz, D. Pant, S. Puig, V. O’Flaherty, and P. Farras. Microbial electrosynthesis of acetate from CO2 in three-chamber cells with gas diffusion biocathode under moderate saline conditions. Environmental Science and Ecotechnology, 100261, 2023. DOI: 10.1016/j.ese.2023.100261
  44. L. Bach, A. Ram, U. Z. Ijaz, T. Evans, D. Haydon, and J. Lindström. The effects of smoking on human pharynx microbiota composition and stability. Microbiology Spectrum, 2023. DOI: 10.1128/spectrum.02166-21
  45. M. Batool, C. Keating, S. Javed, A. Nasir, M. Muddassar#, and U. Z. Ijaz#. A cross-sectional study of potential antimicrobial resistance and ecology in gastrointestinal and oral microbial communities of young normoweight Pakistani individuals. Microorganisms, 11(2):279, 2023. DOI: 10.3390/microorganisms11020279
    #Joint corresponding authors
  46. A. Trego, C. Keating, C. Nzeteu, A. Graham, V. O'Flaherty, and U. Z. Ijaz#. Beyond basic diversity estimates - Analytical tools for mechanistic interpretations of amplicon sequencing data. Microorganisms, 10(10):1961, 2022. DOI: 10.3390/microorganisms10101961
    #Corresponding author
  47. S. Mills, P. Dessi, D. Pant, P. Farras, W. T. Sloan, G. Collins#, and U. Z. Ijaz#. A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis. npj Biofilms and Microbiome, 8:73, 2022. DOI: 10.1038/s41522-022-00337-5
    #Joint corresponding authors
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  48. U. Z. Ijaz#, O. Gundogdu, C. Keating, M. van Eekert, W. Gibson, J. Parkhill, F. Abilahi, B. Liseki, V.-A. Nguyen, S. Sudgen, C. Quince, J. H. J. Ensink, B. Torondel, and A. W. Walker. Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with fill-up rate. Frontiers in Microbiology, 13:960747, 2022. DOI: 10.3389/fmicb.2022.960747
    #Corresponding author
  49. K.Bain, B. Nichols, F. Moffat, C. Kerbiriou, U. Z. Ijaz, K. Gerasimidis, I. McInnes, A. Åstrand, S. Holmes, and S. Milling. Stratification of alopecia areata reveals involvement of CD4 T cell populations and altered faecal microbiota. Clinical and Experimental Immunology, 210(2):175-186, 2022. DOI: 10.1093/cei/uxac088
  50. M. F. Carboni, S. Mills, S. Arriaga, G. Collins, U. Z. Ijaz, and P. N. L. Lens. Autotrophic denitrification of nitrate rich wastewater in fluidized bed reactors using pyrite and elemental sulfur as electron donors. Environmental Technology & Innovation, 102878, 2022. DOI: 10.1016/j.eti.2022.102878
  51. J. Yin, X. Chen, X. Li, G. Kang, P. Wang, Y. Song, U. Z. Ijaz, H. Yin, and H. Huang. A droplet-based microfluidic approach to isolating functional bacteria from gut microbiota. Frontiers in Cellular and Infection Microbiology, 12:920986, 2022. DOI: 10.3389/fcimb.2022.920986
  52. F. Cholet, A. Lisik, H. Agogué, U. Z. Ijaz, P. Pineau, N. Lachaussée, and C. J. Smith. Ecological observations based on functional gene sequencing are sensitive to the amplicon processing method. mSphere, e00324-22, 2022. DOI: 10.1128/msphere.00324-22
  53. M. Logan, M. MacKinder, C. M. Clark, A. Kontouri, M. Jere, U. Z. Ijaz, R. Hansen, P. McGrogan, R. K. Russell, and K. Gerasimidis. Intestinal fatty acid binding protein is a disease biomarker in paediatric coeliac disease and Crohn's disease. BMC Gastroenterology, 22:260, 2022. DOI: 10.1186/s12876-022-02334-6
  54. V. B. Birlanga, G. McCormack, U. Z. Ijaz, E. McCarthy, C. J. Smith, and G. Collins. Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon. Scientific Reports, 12:16719, 2022. DOI: 10.1038/s41598-022-17008-2
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  55. R. Kazlauskaite, B. Cheaib, J. Humble, C. Heys, U. Z. Ijaz, S. Connelly, W. T. Sloan, P. McGinnity, J. Russell, L. Martinez-Rubio, J. Sweetman, P. Lyons, A. Kitts, and M. Llewellyn. Deploying an in vitro gut model to assay the impact of the Mannan-Oligosaccharide prebiotic Bio-Mos on the Atlantic Salmon (Salmo salar) gut microbiome. Microbiology Spectrum, 2022. DOI: 10.1128/spectrum.01953-21
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  56. C. Keating, M. Bolton-Warberg, J. Hinchcliffe, R. Davies, S. Whelan, A. H. L. Wan, R. Fitzgerald, S. J. Davies, C. J. Smith, and U. Z. Ijaz#. Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet npj Biofilms and Microbiomes, 8:36, 2022. DOI: 10.1038/s41522-022-00296-x
    #Corresponding author
    Behind the Paper: How do microbial communities assemble in the gut of Atlantic cod in response to diet and novel ingredients?
  57. C. Thom, C. J. Smith, G. Moore, P. Weir, and U. Z. Ijaz. Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap. Water Research, 212:118106, 2022. DOI: 10.1016/j.watres.2022.118106
  58. E. De Pablo-Fernandez, G. G. Gebeyehu, L. Flain, R. Slater, A. Frau, U. Z. Ijaz, T. Warner, and C. Probert. The faecal metabolome and mycobiome in Parkinson's disease. Parkinsonism & Related Disorders, 95:P65-69, 2022. DOI: 10.1016/j.parkreldis.2022.01.005
  59. A. Rashid, S. A. Mirza, C. Keating, U. Z. Ijaz, S. Ali, and L. C. Campos. Machine learning approach to predict quality parameters for bacterial consortium-treating hospital wastewater and phytotoxicity assessment on Radish, Cauliflower, Hot pepper, Rice, and Wheat crops. Water, 14(1):116, 2022. DOI: 10.3390/w14010116
  60. E. Tatti, A. M. Duff, A. Kostrytsia, F. Cholet, U. Z. Ijaz, and C. J. Smith. Potential nitrification activity reflects ammonia oxidising bacteria but not archaea activity across a soil-sediment gradient. Estuarine Coastal and Shelf Science, 264:107666, 2022. DOI: 10.1016/j.ecss.2021.107666
  61. K. Gkikas, M. Logan, B. Nichols, U. Z. Ijaz, C. M. Clark, V. Svolos, L. Gervais, H. Duncan, V. Garrick, L. Curtis, E. Buchanan, T. Cardigan, L. Armstrong, C. Delahunty, D. M. Flynn, A. R. Barclay, R. Tayler, S. Milling, R. Hansen, R. K. Russell, and K. Gerasimidis. Dietary triggers of gut inflammation following exclusive enteral nutrition in children with Crohn’s disease: a pilot study. BMC Gastroenterology, 21:454, 2021. DOI: 10.1186/s12876-021-02029-4
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  62. A. Khan, S. Akbar, V. Okonkwo, C. J. Smith, S. Khan, A. A. Shah, F. Adnan, U. Z. Ijaz, S. Ahmed, and M. Badshah. Enrichment of the hydrogenotrophic methanogens for, in-situ biogas up-gradation by recirculation of gases and supply of hydrogen in methanogenic reactor. Bioresource Technology, 126219, 2021. DOI: 10.1016/j.biortech.2021.126219
  63. S. Mills, A. C. Trego, P. N. L. Lens, U. Z. Ijaz#, and G. Collins#. A Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters. Microbiology Spectrum, 9(3):ee00784-21, 2021. DOI: 10.1128/Spectrum.00784-21
    #Joint corresponding authors
  64. A. Oulas, M. Zachariou, C. T. Chasapis, M. Tomazou, U. Z. Ijaz, G. P. Schmartz, G. Spyrou, and A. Vlamis. Putative antimicrobial peptides within bacterial proteomes affect bacterial predominance: a network analysis perspective. Frontiers in Microbiology, 12:752674, 2021. 10.3389/fmicb.2021.752674
  65. F. Nasher, A. J. Taylor, A. Elmi, B. Lehri, U. Z. Ijaz, D. Baker, R. Goram, S. Lynham, D. Singh, R. Stabler, D. J. Kelly, O. Gundogdu, and B. W. Wren. MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni. Journal of Bacteriology, 2021. DOI: 10.1128/JB.00421-21
  66. P. B. Wright, E. McDonald, A. Bravo-Blas, H. M. Baer, A. Heawood, C. C. Bain, A. M. Mowat, S. L. Clay, E. V. Robertson, F. Morton, J. S. Nijjar, U. Z. Ijaz, S. W. F. Milling, and D. R. Gaya. The mannose receptor (CD206) identifies a population of colonic macrophages in health and inflammatory bowel disease. Scientific Reports, 11:19616, 2021. DOI: 10.1038/s41598-021-98611-7
  67. S. Singh, J. M. Rinta-Kanto, P. N. L. Lens, M. Kokkoa, J. Rintala, V. O'Flaherty, U. Z. Ijaz#, and G. Collins. Microbial community assembly and dynamics in granular, fixed-biofilm and planktonic microbiomes valorizing long-chain fatty acids at 20ºC. Bioresource Technology, 126098, 2021. DOI: 10.1016/j.biortech.2021.126098
    #Corresponding author
  68. C. Nikolova, U. Z. Ijaz#, C. Magill, S. Kleindienst, S. Joy, and T. Gutierrez#. Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants. Microbiome, 9:191, 2021. DOI: 10.1186/s40168-021-01143-5
    #Joint corresponding authors
    Video Abstract:

    Press Release: Phys.org - Oil industry should invest in bio solutions for oil spills
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  69. A. Kostrytsia#, S. Papirio, M. Khozhaev, L. Morrison, G. Collins, P. N. L. Lens, U. Z. Ijaz#, and G. Esposito. Biofilm carrier type affects biogenic sulfur-driven denitrification performance and microbial community dynamics in moving-bed biofilm reactors. Chemosphere, 287(Part 1):131975, 2022. DOI: 10.1016/j.chemosphere.2021.131975
    #Joint corresponding authors
  70. C. Nikolova, U. Z. Ijaz#, and T. Gutierrez#. Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and biosurfactant-assisted oil biodegradation. Ecology and Evolution, 00:1-13, 2021. DOI: 10.1002/ece3.8091
    #Joint corresponding authors
  71. R. Kazlauskaite, B. Cheaib, C. Heys, U. Z. Ijaz, S. Connelly, W. T. Sloan, J. Russell, L. Martinez-Rubio, J. Sweetman, A. Kitts, P. McGinnity, P. Lyons, and M. Llewellyn. SalmoSim: The Development of a Three-Compartment In Vitro Simulator of the Atlantic Salmon GI tract and Associated Microbial Communities. Microbiome, 9(1):1-20, 2021. DOI: 10.1186/s40168-021-01134-6
    Video Abstract:

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  72. A. C. Trego, B. C. Holohan, C Keating, A. Graham, S. O’Connor, M. Gerardo, D. Hughes, U. Z. Ijaz#, and V. O'Flaherty. First proof of concept for full-scale, direct, low-temperature anaerobic treatment of municipal wastewater. Bioresource Technology, 125786, 2021. DOI: 10.1016/j.biortech.2021.125786
    #Corresponding author
  73. H. Craven, D. McGuinness, S. Buchanan, N. Galbraith, D. H. McGuinness, B. Jones, E. Combet, D. Mafra, P. Bergman, A. Ellaway, P. Stenvinkel, U. Z. Ijaz#, and P. G. Shiels#. Socioeconomic position links circulatory microbiota differences with biological age. Scientific Reports, 11:12629, 2021. DOI: 10.1038/s41598-021-92042-0
    #Joint corresponding authors
    Press Release: myScience - Poorer health in most deprived areas may be linked to microbiomes in the gut
    Press Release: The Times - Unfriendly gut bacteria linked to early ageing
    Press Release: MedicalXPress - Earlier onset of disease and aging in the most deprived could be linked to gut health, poor diet
    Press Release: Deadline News - Poorer health in most deprived areas may be linked to microbiomes in the gut
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  74. J. A. Kemp, B. Regis, H. F. dos Santos, H. E. de Jesus, H. Craven, U. Z. Ijaz, P. G. Shiels, and D. Mafra. The impact of enriched resistant starch type-2 cookies on the gut microbiota in hemodialysis patients: A randomized controlled trial. Molecular Nutrition and Food Research, 2100374, 2021. DOI: 10.1002/mnfr.202100374
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  75. A. Mahalhal, A. Frau, M. D. Burkitt, U. Z. Ijaz, C. A. Lamb, J. C. Mansfield, S. Lewis, D. M. Pritchard, and C. S. Probert. Oral ferric maltol does not adversely affect the intestinal microbiome of patients or mice, but ferrous sulphate does. Nutrients, 13(7):2269, 2021. DOI: 10.3390/nu13072269
  76. A. Frau#, U. Z. Ijaz#, R. Slater, D. Jonkers, J. Penders, B. J. Campbell, J. G. Kenny, N. Hall, L. Lenzi, M. D. Burkitt, M. Pierik, A. C. Darby, and C. S. J. Probert. Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach. Gut Microbes, 13:1, 2021. DOI: 10.1080/19490976.2021.1930871
    #Joint corresponding authors
  77. A. C. Trego, P. G. McAteer, C. Nzeteu, T. Mahony, F. Abram, U. Z. Ijaz#, and V. O'Flaherty#. Combined stochastic and deterministic processes drive community assembly of anaerobic microbiomes during granule flotation. Frontiers in Microbiology, 2021. DOI: 10.3389/fmicb.2021.666584
    #Joint corresponding authors
  78. B. Cheaib, P. Yang, R. Kazlauskaite, E. Lindsay, C. Heys, M. De Noa, P. Schaal, T. Dwyer, M. De Noa, P. Schaal, W. T. Sloan, U. Z. Ijaz, and M. S. Llewellyn. Genome erosion and evidence for an intracellular niche - exploring the biology of mycoplasmas in Atlantic Salmon. Aquaculture, 736772, 2021. DOI: 10.1016/j.aquaculture.2021.736772
  79. S. Mills, A. C. Trego, J. Ward, J. Castilla-Archilla, J. Hertel, I. Thiele, P. N. L. Lens, U. Z. Ijaz#, and G. Collins#. Methanogenic granule growth and development is a continual process characterized by distinct morphological features. Journal of Environmental Management, 286:112229, 2021. DOI: 10.1016/j.jenvman.2021.112229
    #Joint corresponding authors
  80. C. Duran, S. Ciucci, A. Palladini, U. Z. Ijaz, A. G. Zippo, F. P. Sterbini, L. Masucci, G. Cammarota, G. Ianiro, P. Spuul, M. Schroeder, S. W. Grill, B. N. Parsons, D. M. Pritchard, B. Posteraro, M. Sanguinetti, G. Gasbarrini, A. Gasbarrini, and C. V. Cannistraci. Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome. Nature Communications, 12:1926, 2021. DOI: 10.1038/s41467-021-22135-x
  81. C. Keating#, M. Bolton-Warberg, J. Hinchcliffe, R. Davies, S. Whelan, A. H. L. Wan, R. D. Fitzgerald, S. J. Davies, U. Z. Ijaz#, and C. J. Smith#. Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae. Animal Microbiome, 3(1):1-21, 2021. DOI: 10.1186/s42523-020-00065-1
    #Joint corresponding authors
  82. P. Dessì, C. Sánchez, S. Mills, F. G. Cocco, M. Isipato, U. Z. Ijaz, G. Collins, and P. N. L. Lens. Carboxylic acids production and electrosynthetic microbial community evolution under different CO2 feeding regimens. Bioelectrochemistry, 137:107686, 2021. DOI: 10.1016/j.bioelechem.2020.107686
  83. L. L. Bach, A. Ram, U. Z. Ijaz, T. J. Evans, and J. Lindstrom. A longitudinal study of the human orophyrnx microbiota over time reveals a common core and significant variations with self-reported disease. Frontiers in Microbiology, 11:573969, 2021. DOI: 10.3389/fmicb.2020.573969
  84. K. Zafeiropoulou, B. Nichols, M. Mackinder, O. Biskou, E. Rizou, A. Karanikolou, C. Clark, E. Buchanan, T. Cadigan, H. Duncan, D. Wands, J. Russell, R. Hansen, R. K. Russell, P. McGrogan, C. A. Edwards, U. Z. Ijaz, and K. Gerasimidis. Alterations in intestinal microbiota of children with celiac disease at time of diagnosis and on gluten-free diet. Gastroenterology, 159(6):2039-2051.e20, 2020. DOI: 10.1053/j.gastro.2020.08.007
    Covering the Cover: Early Age Intestinal Dysbiosis in Patients with Celiac Disease
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  85. A. McKenna*, U. Z. Ijaz*, C. Kelly, M. Linton, W. T. Sloan, B. D. Green, U. Lavery, N. Dorrell, B. W. Wren, A. Richmond, N. Corcionivoschi, and O. Gundogdu. Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter. Microbiome, 8:128, 2020. DOI: 10.1186/s40168-020-00908-8
    *Joint first authors
    Video Abstract:

    Press Release: AGRI-Food & BioSciences Institute - High impact research paper published in Journal of Microbiome
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  86. B. Cheaib, H. Seghouani, U. Z. Ijaz, and N. Derome. Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations. Microbiome, 8:14, 2020. DOI: 10.1186/s40168-020-0789-0
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  87. Z. Dai, M. C. Sevillano-Rivera, S. T. Calus, Q. M. Bautista-de los Santos, A. M. Eren, P. W. J. J. van der Wielen, U. Z. Ijaz, and A. J. Pinto. Disinfection exhibits systematic impacts on the drinking water microbiome. Microbiome, 8:42, 2020. DOI: 10.1186/s40168-020-00813-0
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  88. M. Isipato, P. Dessì, C. Sanchez, S. Mills, U. Z. Ijaz, F. Asunis, D. Spiga, G. De Gioannis, M. Mascia, G. Collins, A. Muntoni, and P. N. L. Lens. Propionate production by bioelectrochemically-assisted lactate fermentation and simultaneous CO2 recycling. Frontiers in Microbiology, 11:599438, 2020. DOI: 10.3389/fmicb.2020.599438
  89. A. C. Trego, S. O'Sullivan, C. Quince, S. Mills, U. Z. Ijaz#, and G. Collins#. Size shapes the active microbiome of methanogenic granules, corroborating a biofilm life-cycle. mSystems, 5(5):e00323-20, 2020. DOI: 10.1128/mSystems.00323-20
    #Joint corresponding authors
    Schematic:

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  90. E. Mittell, C. A. Cobbold, U. Z. Ijaz, E. A. Kilbride, K. A. Moore, and B. K. Mable. Feral populations of Brassica oleracea along Atlantic coasts in western Europe. Ecology and Evolution, 10(20):11810-11825, 2020. DOI: 10.1002/ece3.6821
  91. A. C. Trego, E. Galvin, C. Sweeney, S. Dunning, C. Murphy, S. Mills, C. Nzeteu, C. Quince, S. Connelly, U. Z. Ijaz#, and G. Collins#. Growth and break-up of methanogenic granules suggests mechanisms for biofilm and community development. Frontiers in Microbiology, 11:1126, 2020. DOI: 10.3389/fmicb.2020.01126
    #Joint corresponding authors
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  92. F. Cholet, U. Z. Ijaz, and C. J. Smith. Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts. Environmental Microbiology, 22(6):2383-2402, 2020. DOI: 10.1111/1462-2920.15017
  93. M. C. Sevillano-Rivera, Z. Dai, S. Calus, Q. M. Bautista-de los Santos, A. M. Eren, P. W. J. J. van der Wielen, U. Z. Ijaz, and A. J. Pinto. Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems. Science of the Total Environment, 749:141451, 2020. DOI: 10.1016/j.scitotenv.2020.141451
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  94. M.Logan, K. Gkikas, V. Svolos, B. Nichols, S. Milling, D. R. Gaya, J. P. Seenan, J. Macdonald, R. Hansen, U. Z. Ijaz, R. K. Russell, and K. Gerasimidis. Analysis of 61 exclusive enteral formulas used in management of active Crohn’s disease - new insights on dietary disease triggers. Alimentary Pharmacology & Therapeutics, 51(10):935-947, 2020. DOI: 10.1111/apt.15695
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  95. C. A. Jukes, U. Z. Ijaz, A. Buckley, J. Spencer, J. Irvine, D. Candlish, J. V. Li, J. R. Marchesi, and G. Douce. Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease. Gut Microbes, 11(3): 481-496, 2020. DOI: 10.1080/19490976.2019.1678996
  96. K. Gkikas, K. Gerasimidis, S. Milling, U. Z. Ijaz, R. Hansen, and R. K. Russell. Dietary strategies for maintenance of clinical remission in inflammatory bowel diseases: Are we there yet? Nutrients, 12(7):2018, 2020. DOI: 10.3390/nu12072018
  97. I. Cotto, Z. Dai, L. Huo, C. L. Anderson, K. J. Vilardi, U. Z. Ijaz, W. Khunjar, C. Wilson, H. De Clippeleir, K. Gilmore, E. Bailey, and A. J. Pinto. Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems. Water Research, 169:115268, 2020. DOI: 10.1016/j.watres.2019.115268
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  98. K. A. Bain, E. McDonald, F. Moffat, M. Tutino, M. Castelino, A. Barton, J. Cavanagh, U. Z. Ijaz, S. Siebert, I. B. McInnes, A. Astrand, S. Homes, and S. W. F. Milling. Alopecia areata is characterised by dysregulation in systemic type 17 and type 2 cytokines, which may contribute to disease-associated psychological morbidity. British Journal of Dermatology, 182:130-137, 2020. DOI: 10.1111/bjd.18008
    Plain Language Summary: Specific molecules are found to be increased in people with alopecia areata, and may be associated with an individual's level of depression
  99. C. Heys, B. Cheaib, A. Busetti, R. Kazlauskaite, L. Maier, W. T. Sloan, U. Z. Ijaz, J. Kaufmann, P. McGinnity, and M. Llewellyn. Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar. Applied and Environmental Microbiology, 86:e02283-19, 2020. DOI: 10.1128/AEM.02283-19
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  100. A. C. Stratakos, U. Z. Ijaz, P. Ward, M. Linton, C. Kelly, L. Pinkerton, P. Scates, J. McBride, I. Pet, A. Criste, D. Stef, J. M. Couto, W. T. Sloan, N. Dorrell, B. W. Wren, L. Stef, O. Gundogdu, and N. Corcionivoschi. In vitro and in vivo characterisation of Listeria monocytogenes outbreak isolates. Food Control, 107:106784, 2020. DOI: 10.1016/j.foodcont.2019.106784
  101. K. Gerasimidis, V. Svolos, Ben Nichols, R. Papadopoulou, C. Quince, U. Z. Ijaz, S. Milling, D. R. Gaya, R. K. Russell, and R. Hansen. Reply to GASTRO-D-18-02688. Gastroenterology, 2019. DOI: 10.1053/j.gastro.2019.08.015
  102. M. Logan, C. M. Clark, U. Z. Ijaz, L. Gervais, H. Duncan, V. Garrick, L. Curtis, E. Buchanan, T. Cardigan, L. Armstrong, C. Delahunty, D. M. Flynn, A. Barclay, R. Tayler, E. McDonald, S. Milling, R. Hansen, K. Gerasimidis, and R. K. Russell. The reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction. Alimentary Pharmacology & Therapeutics, 50(6):664-674, 2019. DOI: 10.1111/apt.15425
  103. M. J. Ormsby, M. Logan, S. A. Johnson, A. McIntosh, G. Fallata, R. Papadopoulou, E. Papachristou, R. Hansen, U. Z. Ijaz, R. K. Russell, K. Gerasimidis, and D. M. Wall. Inflammation associated ethanolamine facilitates infection by Crohn’s disease-linked adherent-invasive Escherichia coli. EBioMedicine, 43:325-332, 2019. DOI: 10.1016/j.ebiom.2019.03.071
  104. V. Svolos, R. Hansen, B. Nichols, C. Quince, U. Z. Ijaz, R. T. Papadopoulou, C. A. Edwards, D. Watson, A. Alghamdi, A. Brejnrod, C. Ansalone, H. Duncan, J. Salmond, D. Bolognini, R. Klopfleisch, D. R. Gaya, S. Milling, R. K. Russell, and K. Gerasimidis. Treatment of active Crohn’s disease with an ordinary food-based diet that replicates exclusive enteral nutrition. Gastroenterology, 156(5):P1354-1367.e6, 2019. DOI: 10.1053/j.gastro.2018.12.002
    Video Abstract:

    Press Release: MEDPAGE TODAY - Exclusive Enteral Nutrition Unneeded in Crohn's? Pilot study suggests ordinary whole-foods diet produces same effects in GI tract
    Press Release: MEDPAGE TODAY - Can a Food-based Diet Replace Exclusive Enteral Nutrition for Patients With Crohn’s Disease?
    Press Release: CureCrohn'sColitis - Results are in - CD Treat diet
    Press Release: CureCrohn'sColitis - New TREATment for Crohn’s Disease on the horizon
    FacultyOpinions Recommended
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  105. S. Connelly, T. Pussayanavin, R. Randle-Boggis, A. Wicheansan, S. Jampathong, C. Keating, U. Z. Ijaz, W. T. Sloan, and T. Koottatep. Solar septic tank: next generation sequencing reveals effluent microbial community composition as a useful index of system performance. Water, 11:2660, 2019. DOI: 10.3390/w11122660
  106. T. Lynch, G. Peirano, T. Lloyd, R. Read, J. Carter, A. Chu, J. A. Shaman, J. P. Jarvis, E. Diamond, U. Z. Ijaz, and D. Church. Molecular diagnosis of vaginitis: comparing qPCR and microbiome profiling approaches to current microscopy scoring. Journal of Clinical Microbiology, 57 (9) e00300-19, 2019. DOI: 10.1128/JCM.00300-19
    FacultyOpinions Recommended
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  107. J. Plancq, J. M. Couto, U. Z. Ijaz, P. R. Leavitt, and J. L. Toney. Next generation sequencing to identify lacustrine haptophytes in the canadian prairies: Significance for temperature proxy applications. Journal of Geophysical Research - Biogeosciences, 124, 2019. DOI: 10.1029/2018JG004954
  108. A. Frau, J. G. Kenny, L. Lenzi, B. J. Campbell, U. Z. Ijaz, C. A. Duckworth, M. D. Burkitt, N. Hall, J. Anson, A. C. Darby, and C. S. J. Probert. DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies. Scientific Reports, 9:9328, 2019. DOI: 10.1038/s41598-019-44974-x
  109. S. De Schepper, J. L. Ray, K. S. Skaar, H. Sadatzki, U. Z. Ijaz, R. Stein, and A. Larsen. The potential of sedimentary ancient DNA for reconstructing past sea ice evolution. ISME Journal, 2019. DOI: 10.1038/s41396-019-0457-1
    Behind the Paper: Environmental ancient DNA - a game changer in paleo sea ice research?
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  110. C. Gauchotte-Lindsay, T. J. Aspray, M. Knapp, and U. Z. Ijaz. Systems biology approach to elucidation of contaminants biodegradation in complex samples- integration of high-resolution analytical and molecular tools. Faraday Discussions, 2019. DOI: 10.1039/C9FD00020H
  111. K. E. Dingle, X. Didelot, T. P. Quan, D. W. Eyre, N. Stoesser, C. A. Marwick, J. Coia, D. Brown, S. Buchanan, U. Z. Ijaz, C. Goswami, G. Douce, W. N. Fawley, M. H. Wilcox, T. E. A. Peto, A. S. Walker, and D. W. Crook. A role for tetracycline selection in recent evolution of the agriculture-associated Clostridium difficile PCR-ribotype 078. mBio, 10(2):e02790-18, 2019. DOI: 10.1128/mBio.02790-18
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  112. F. Cholet, U. Z. Ijaz, and C. J. Smith. Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples. Environmental Microbiology, 21(2): 827-844, 2019. DOI: 10.1111/1462-2920.14516
  113. J. De Vrieze, A. J. Pinto, W. T. Sloan, and U. Z. Ijaz#. The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. Microbiome, 6:63, 2018. DOI: 10.1186/s40168-018-0449-9
    #Corresponding author
  114. O. Koci, M. Logan, V. Svolos, R. K. Russell, K. Gerasimidis, and U. Z. Ijaz#. An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights. PeerJ, 6:e5047, 2018. DOI: 10.7717/peerj.5047
    #Corresponding author
  115. K. Gerasimidis, K. Zafeiropoulou, M. Mackinder, U. Z. Ijaz, H. Duncan, E. Buchanan, T. Cardigan, C. A. Edwards, P. McGrogan, and R. K. Russell. Comparison of clinical methods with the faecal gluten immunogenic peptide to assess gluten intake in coeliac disease. Journal of Pediatric Gastroenterology & Nutrition, 67(3):356-360, 2018. DOI: 10.1097/MPG.0000000000002062
  116. J. De Vrieze, U. Z. Ijaz, A. M. Saunders, and S. Theuerl. Terminal restriction fragment length polymorphism as an "old school" but reliable technique for swift microbial community screening in anaerobic digestion. Scientific Reports, 8:16818, 2018. DOI: 10.1038/s41598-018-34921-7
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  117. A. Kostrytsia, S. Papirio, L. Morrison, U. Z. Ijaz, G. Collins, P. N. L. Lens, and G. Esposito. Biokinetics of microbial consortia using biogenic sulfur as a novel electron donor for sustainable denitrification. Bioresource Technology, 270:359-367, 2018. DOI: 10.1016/j.biortech.2018.09.044
  118. I. Reich#, U. Z. Ijaz#, M. Gormally, and C. J. Smith#. 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Scientific Reports, 8:10402, 2018. DOI: 10.1038/s41598-018-28720-3
    #Joint corresponding authors
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  119. U. Z. Ijaz*, L. Sivaloganathan*, A. Mckenna*, A. Richmond, C. Kelly, M. Linton, A. Stratakos, U. Lavery, A. Elmi, B. Wren, N. Dorell, N. Corcionivoschi, and O. Gundogdu. Comprehensive longitudinal microbiome analysis of chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter. Frontiers in Microbiology, 9:2452, 2018. DOI: 10.3389/fmicb.2018.02452
    *Joint first authors
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  120. S. T. Calus, U. Z. Ijaz#, and A. Pinto#. NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. GigaScience, giy140, 2018. DOI: 10.1093/gigascience/giy140
    #Joint corresponding authors
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  121. C. Keating, D. Hughes, T. Mahony, D. Cysneiros, U. Z. Ijaz, C. J. Smith, and V. O’Flaherty. Cold adaptation and replicable microbial community development during long-term low temperature anaerobic digestion of synthetic sewage. FEMS Microbiology Ecology, 94(7):fiy095, 2018. DOI: 10.1093/femsec/fiy095
    Relevant Impact Case Study: NUI Galway - Transforming Sustainable Water Management: Creating Jobs and Saving Energy
  122. X. Yuan, Y. Song, Y. Song, J. Xu, Y. Wu, A. Glidle, M. Cusack, U. Z. Ijaz, J. Cooper, W. Huang, and H. Yin. Effect of laser irradiation on cell function and its implications in Raman spectroscopy. Applied and Environmental Microbiology, 84:e02508-17, 2018. DOI: 10.1128/AEM.02508-17
  123. C. Pedersen, U. Z. Ijaz, E. Gallagher, F. Horton, R. J. Ellis, E. Jaiyeola, T. Duparck, D. Russell-Jones, P. Hinton, P. D. Cani, R. M. La Ragione, and M. D. Robertson. Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans. Physiological Reports, 6(6):e13649, 2018. DOI: 10.14814/phy2.13649
  124. A. Joyce, U. Z. Ijaz, C. Nzeteu, A. Vaughan, S. L. Shirran, C. H. Botting, C. Quince, V. O’Flaherty, and F. Abram. Linking microbial community structure and function during the acidified anaerobic digestion of grass. Frontiers in Microbiology, 9:540, 2018. DOI: 10.3389/fmicb.2018.00540
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  125. U. Z. Ijaz, C. Quince, L. Hanske, N. Loman, S. T. Calus, M. Bertz, C. A. Edwards, D. R. Gaya, R. Hansen, P. McGrogan, R. K. Russell, and K. Gerasimidis. The microbial 'dysbiosis' of Crohn’s disease patients does not occur in their unaffected, genetically linked kindred. PLoS ONE, 12(2):e0172605, 2017. DOI: 10.1371/journal.pone.0172605
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  126. K. Harris, T. L. Parsons, U. Z. Ijaz, L. Lahti, I. Holmes, and C. Quince. Linking statistical and ecological theory: Hubbell’s unified neutral theory of biodiversity as a hierarchical Dirichlet process. Proceedings of the IEEE, 105(3):516-529, 2017. DOI: 10.1109/JPROC.2015.2428213
  127. M. Logan, U. Z. Ijaz, R. Hansen, K. Gerasimidis, and R. Russell. Letter: reproducible evidence shows that exclusive enteral nutrition significantly reduces faecal Calprotectin concentrations in children with active Crohn’s disease. Alimentary Pharmacology & Therapeutics, 46: 1119-1120, 2017. DOI: 10.1111/apt.14351
  128. B. N. Parsons*, U. Z. Ijaz*, R. D'Amore, M. Burkitt, R. Eccles, L. Lenzi, C. A. Duckworth, A. R. Moore, L. Tiszlavicz, A. Varro, N. Hall, and D. M. Pritchard. Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use. PLoS Pathogens, 13(11): e1006653, 2017. DOI: 10.1371/journal.ppat.1006653
    *Joint first authors
    Press Release: PLOS - Shifting bacterial communities in the stomach may influence cancer risk
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  129. N. D. Ritchie, U. Z. Ijaz, and T. J. Evans. IL-17 signalling restructures the nasal microbiome and drives dynamic changes following Streptococcus pneumoniae colonization. BMC Genomics, 18:807, 2017. DOI: 10.1186/s12864-017-4215-3
  130. J. De Vrieze, M. E. Christiaens, D. Walraedt, A. Devooght, U. Z. Ijaz, and N. Boon. Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure. Water Research, 111:109-117, 2017. DOI: 10.1016/j.watres.2016.12.042
  131. A. Z. Ijaz, T. Jeffries, U. Z. Ijaz, K. Hamonts, and B. K. Singh. Extending SEQenv: A taxa-centric approach to environmental annotations of 16S rDNA sequences. PeerJ, 5:e3827, 2017. DOI: 10.7717/peerj.3827
  132. S. -K. Cho, K. -W. Jung, D. -H. Kim, J. -C. Kwon, U. Z. Ijaz, and S. G. Shin. Bacterial community analysis in upflow multi-layer anaerobic reactor (UMAR) treating high-solids organic wastes. Biotechnology Progress, 2017. DOI: 10.1002/btpr.2540
  133. S. Connelley, S. G. Shin, R. J. Dillon, U. Z. Ijaz, C. Quince, W. T. Sloan, and G. Collins. Bioreactor scalability: laboratory-scale idealisation influences performance, ecology and community physiology in expanded sludge bioreactors. Frontiers in Microbiology, 8:664, 2017. DOI: 10.3389/fmicb.2017.00664
  134. A. Ho*, U. Z. Ijaz*, T. K. S. Janssens, R. Ruijs, S. Y. Kim, W. de Boer, A. Temorshuizen, W. H. van der Putten, and P. L. E. Bodelier. Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition. Global Change Biology Bioenergy, 2017. DOI: 10.1111/gcbb.12457
    *Joint first authors
  135. K. Gerasimidis, M. Bertz, C. Quince, K. Brunner, A. Bruce, E. Combet, S. T. Calus, N. Loman, and U. Z. Ijaz#. The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes, 9:365, 2016. DOI: 10.1186/s13104-016-2171-7
    #Corresponding author
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  136. M. Schirmer, R. D'Amore, U. Z. Ijaz, N. Hall, and C. Quince. Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17:125, 2016. DOI: 10.1186/s12859-016-0976-y
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  137. R. D'Amore*, U. Z. Ijaz*, M. Schirmer, J. Kenny, R. Gregory, A. C. Darby, M. Shakya, M. Podar, C. Quince, and N. Hall. A comprehensive benchmarking study of next-generation sequencing platforms for 16S rRNA community profiling. BMC Genomics, 17:55, 2016. DOI: 10.1186/s12864-015-2194-9
    *Joint first authors
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  138. K. Gerasimidis, U. Z. Ijaz, C. Edwards, R. K. Russell, C. Quince, and R. Hansen. Response to Kaakoush et al. American Journal of Gastroenterology, 111(7):1033-1034, 2016. DOI: 10.1038/ajg.2016.169
  139. J. L. Ray, J. Althammer, K. S. Skaar, P. Simonelli, A. Larsen, D. Stoecker, A. Sazhin, U. Z. Ijaz, C. Quince, J. C. Nejstgaard, M. Frischer, G. Pohnert, and C. Troedsson. Metabarcoding and metabolome analysis of copepod grazing reveals feeding preference and linkage to metabolite classes in dynamic microbial plankton communities. Molecular Ecology, 2016. DOI: 10.1111/mec.13844
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  140. L. Sinclair*, U. Z. Ijaz*, L. J. Jensen, M. Coolen, C. Gubry-Rangin, A. Chronakova, A. Oulas, C. Pavloudi, J. Schnetzer, A. Weimann, A. Z. Ijaz, A. Eiler, C. Quince, and E. Pafilis. Seqenv: linking microbes to environments through text mining. PeerJ, 4:e2690, 2016. DOI: 10.7717/peerj.2690
    *Joint first authors
  141. C. Pedersen, E. Gallagher, F. Horton, R. J. Ellis, U. Z. Ijaz, H. Wu, E. Jaiyeola, O. Diribe, T. Duparc, P. D. Cani, G. R. Gibson, P. Hinton, J. Wright, D. Russell-Jones, R. La Ragione, and M. D. Robertson. Host-microbiome interactions in human type 2 diabetes following prebiotic dietary fibre (galacto-oligosaccharide) intake. British Journal of Nutrition, 116(11):1869-1877, 2016. DOI: 10.1017/S0007114516004086
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  142. C. Varsos, T. Patkos, A. Oulas, C. Pavloudi, A. Gougousis, U. Z. Ijaz, I. Filiopoulou, N. Pattakos, E. V. Berghe, A. Fernandez-Guerra, S. Faulwetter, E. Chatzinikolaou, E. Pafilis, C. Beikiari, M. Doerr, and C. Arvantidis. Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab). Biodiversity Data Journal, 4: e8357, 2016. DOI: 10.3897/BDJ.4.e8357
    Schematic:

  143. Q. M. Bautista-do los Santos, J. L. Schroeder, M. C. Sevillano-Rivera, R. Sungthong, U. Z. Ijaz, W. T. Sloan, and A. J. Pinto. Microbial communities in full-scale drinking water distribution systems – A meta-analysis. Environmental Science-Water Research & Technology, 2:631-644, 2016. DOI: 10.1039/C6EW00030D
  144. B. Torondel, J. H. J. Ensink, O. Gundogdu, U. Z. Ijaz, A. W. Walker, J. Parkhill, F. Abdelahi, V. –A. Nguyen, S. Sudgen, W. Gibson, and C. Quince. Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microbial Biotechnology, 9(2):209-223, 2016. DOI: 10.1111/1751-7915.12334
    Custom-made Oggy Bottom Latrine Sampler:

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  145. C. Quince*, U. Z. Ijaz*, N. Loman, A. D. Eren, D. Saulnier, J. Russell, S. J. Haig, S. T. Calus, J. Quick, A. Barclay, M. Bertz, M. Blaut, R. Hansen, P. McGrogan, R. K. Russell, C. Edwards, and K. Gerasimidis. Extensive modulation of the fecal metagenome in children with Crohn’s disease during exclusive enteral nutrition. American Journal of Gastroenterology, 110:1718–1729, 2015. DOI: 10.1038/ajg.2015.357
    *Joint first authors
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  146. M. Schirmer, U. Z. Ijaz, L. D’Amore, N. Hall, W. T. Sloan, and C. Quince. Insights into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research, 43(6):pp.e37, 2015. DOI: 10.1093/nar/gku1341
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  147. A. J. Pinto, D. N. Marcus, U. Z. Ijaz, Q. M. de los Santos Bautista, G. J. Dick, and L. Raskin. Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in drinking water system. mSphere, 1 (1): e00054-15, 2015. DOI: 10.1128/mSphere.00054-15
    Press Release: Engineering and Physical Sciences Research Council - Chance find has big implications for water treatment's costs and carbon footprint
  148. J. M. Couto, U. Z. Ijaz, V. R. Phoenix, M. Schirmer, and W. T. Sloan. Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment. Current Microbiology, 71:296-302, 2015. DOI: 10.1007/s00284-015-0846-2
  149. D. Savio, S. Lucas, U. Z. Ijaz, A. P. Blaschke, G. H. Reischer, G. Bloschl, R. L. Mach, A. K. T. Kirschner, A. H. Farnleitner, and A. Eiler. Bacterial diversity along a 2600 km river continuum. Environmental Microbiology, 17:4994-5007, 2015. DOI: 10.1111/1462-2920.12886
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  150. J. Alneberg, B.S. Bjarnason, I. de Bruijn, M. Schirmer, J. Quick, U. Z. Ijaz, L. Lahti, N. J. Loman, A. F. Andersson, and C. Quince. Binning metagenomic contigs by coverage and composition. Nature Methods, 11:1144-1146, 2014. DOI: 10.1038/nmeth.3103
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  151. U. Z. Ijaz, R. J. Housden, G. M. Treece, R. W. Prager, and A. H. Gee. Multi-directional scattering models for 3-Dimensional ultrasound imaging. Journal of Ultrasound in Medicine, 32(4):699-714, April 2013. DOI: 10.7863/ultra.32.4.699
  152. E. Dyer, U. Z. Ijaz, R. J. Housden, R. W. Prager, A. H. Gee, and G. M. Treece. A clinical system for three-dimensional extended field of view ultrasound. British Journal of Radiology, 85:e919-e924, 2012. DOI: 10.1259/bjr/46007369
    System:

  153. R. W. Prager, U. Z. Ijaz, A. H. Gee, and G. M. Treece. Three-dimensional ultrasound imaging. Proceedings of the Institution of Mechanical Engineers Part H-Journal of Engineering in Medicine, 224(2):193-223, 2010. DOI: 10.1243/09544119JEIM586
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  154. U. Z. Ijaz, R. W. Prager, A. H. Gee, and G. M. Treece. Optimisation strategies for ultrasound volume registration. Measurement Science and Technology, 21(8): 085803 (17pp), 2010. DOI: 10.1088/0957-0233/21/8/085803
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  155. A. K. Khambampati, U. Z. Ijaz, J. S. Lee, S. Kim, and K. Y. Kim. Phase boundary estimation in electrical impedance tomography using Hooke and Jeeves pattern search method. Measurement Science and Technology, 21(3):035501 (13pp), 2010. DOI: 10.1088/0957-0233/21/3/035501
  156. A. K. Khambampati, A. Rashid, U. Z. Ijaz, S. Kim, M. Soleimani, and K. Y. Kim. Unscented Kalman filter approach to tracking a moving interfacial boundary in sedimentation process using three-dimensional electrical impedance tomography. Philosophical Transactions of The Royal Society A - Mathematical Physical and Engineering Sciences, 367:3095-3120, 2009. DOI: 10.1098/rsta.2009.0081
  157. J. H. Kim, B. Y. Choi, U. Z. Ijaz, B. S. Kim, S. Kim, and K. Y. Kim. Directional algebraic reconstruction technique for electrical impedance tomography. Journal of The Korean Physical Society, 54(4):1439-1447, April 2009. DOI: 10.3938/jkps.54.1439
  158. U. Z. Ijaz, S. I. Chung, A. K. Khambampati, K. Y. Kim, and S. Kim. Electrical resistance imaging of time-varying interface in stratified flows using unscented Kalman filter. Measurement Science and Technology, 19(6) 065501 (11pp), 2008. DOI: 10.1088/0957-0233/19/6/065501
  159. U. Z. Ijaz, A. K. Khambampati, J. S. Lee, S. Kim, and K. Y. Kim. Nonstationary phase boundary estimation in electrical impedance tomography using unscented Kalman filter. Journal of Computational Physics, 227(15):7089–7112, 2008. DOI: 10.1016/j.jcp.2007.12.025
    System:
  160. U. Z. Ijaz, A. K. Khambampati, M. C. Kim, S. Kim, and K. Y. Kim. Estimation of time-dependent heat flux and measurement bias in two-dimensional heat conduction problems. International Journal of Heat and Mass Transfer, 50(21-22):4117-4130, 2007. DOI: 10.1016/j.ijheatmasstransfer.2007.02.037
  161. Y. S. Kim, S. H. Lee, U. Z. Ijaz, K. Y. Kim, and B. Y. Choi. Sensitivity map generation in electrical capacitance tomography using mixed normalization models. Measurement Science and Technology, 18(7):2092-2102, 2007. DOI: 10.1088/0957-0233/18/7/040
  162. S. Kim, U. Z. Ijaz, A. K. Khambampati, K. Y. Kim, M. C. Kim, and S. I. Chung. Moving interfacial boundary estimation in stratified flows of two immiscible liquids using electrical resistance tomography. Measurement Science and Technology, 18(5):1257-1269, 2007. DOI: 10.1088/0957-0233/18/5/012
  163. U. Z. Ijaz, J. H. Kim, A. K. Khambampati, M. C. Kim, S. Kim, and K. Y. Kim. Concentration distribution estimation of fluid through electrical impedance tomography based on interacting multiple model scheme. Flow Measurement and Instrumentation, 18(1):47-56, 2007. DOI: 10.1016/j.flowmeasinst.2006.12.005
  164. B. S. Kim, U. Z. Ijaz, J. H. Kim, M. C. Kim, S. Kim, and K. Y. Kim. Nonstationary phase boundary estimation in electrical impedance tomography based on the interacting multiple model scheme. Measurement Science and Technology, 18(1):62-70, 2007. DOI: 10.1088/0957-0233/18/1/008
  165. J. H. Kim, B. C. Kang, S. H. Lee, B. Y. Choi, M. C. Kim, B. S. Kim, U. Z. Ijaz, K. Y. Kim, and S. Kim. Phase boundary estimation in electrical resistance tomography with weighted multi-layered neural networks and front point approach. Measurement Science and Technology, 17(10):2731-2739, 2006. DOI: 10.1088/0957-0233/17/10/02
  166. U. Z. Ijaz, J. H. Kim, M. C. Kim, S. Kim, J. W. Park, and K. Y. Kim. Nondestructive dynamic process monitoring using electrical capacitance tomography. Key Engineering Materials, 321-323(2):1671-1674, 2006. DOI: 10.4028/www.scientific.net/KEM.321-323.1671
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  167. F. A. Khan, U. Z. Ijaz, K. Y. Kim, M. J. Kang, and W. C. Song. Policy-based management in ad hoc network using geographic routing. Lecture Notes in Computer Science, 3961:237-246, 2006. DOI: 10.1007/11919568_24
  168. U. Z. Ijaz, and K. Y. Kim. Kinematic models for non-stationary elliptic region boundaries in electrical impedance tomography. Cheju Nat’l Univ. Res. Inst. Adv. Tech. Jour., 17(2):25-32, 2006.
  169. U. Z. Ijaz, and K. Y. Kim. Dynamic estimation in GPS through a covariance compensation extended Kalman filter. Cheju Nat’l Univ. Res. Inst. Adv. Tech. Jour., 16(2):111-119, 2005.

  170. Book Chapters

  171. U. Z. Ijaz, R. W. Prager, A. H. Gee, and G. M. Treece. A study of similarity measures for in vivo 3D ultrasound volume registration. Acoustical Imaging, 30:315-323, 2011. DOI: 10.1007/978-90-481-3255-3_36
  172. U. Z. Ijaz, R. W. Prager, A. H. Gee, and G. M. Treece. Particle swarm optimization for in vivo 3D ultrasound volume registration. Acoustical Imaging, 30:345-354, 2011. DOI: 10.1007/978-90-481-3255-3_39
  173. U. Z. Ijaz, A. K. Khambampati, M. C. Kim, S. Kim, J. S. Lee, and K. Y. Kim. Particle swarm optimization technique for elliptic region boundary estimation in electrical impedance tomography. AIP Conf. Proc., 914:896-901, 2007. DOI: 10.1063/1.2747529
  174. U. Z. Ijaz, A. K. Khambampati, J. S. Lee, K. Y. Kim, M. C. Kim, and S. Kim. Electrical resistance imaging of two-phase flow through rod bundles. AIP Conf. Proc., 914:844-849, 2007. DOI: 10.1063/1.2747522

  175. Preprints (Not Published as Journal Papers)

  176. M. Castelino*, U. Z. Ijaz*, M. Tutino, E. McDonald, G. Fragoulis, P. Ho, D. Mewar, G. Chelliah, A. McBain, C. O'Neill, S. Siebert, A. Barton, and S. Milling. The stool microbiome in patients with psoriatic arthritis is altered but, unlike the skin microbiome, does not change following treatment: evidence for an underlying inflammatory drive from the intestine. medRxiv, 2023.05.18.23289979, 2023. DOI: 10.1101/2023.05.18.23289979
    *Joint first authors
  177. C. Keating, A. C. Trego, W. T. Sloan, V. O’Flaherty#, U. Z. Ijaz#. Circular economy of anaerobic biofilm microbiomes: A meta-analysis framework for re-exploration of amplicon sequencing data. bioRxiv, 2020.12.23.424166, 2020. DOI: 10.1101/2020.12.23.424166
    #Joint corresponding authors
  178. A. C. Trego, C. Morabito, S. Mills, S. Connelly, I. Bourven, G. Guibaud, C. Quince, U. Z. Ijaz#, and G. Collins#. Diversity converges during community assembly in methanogenic granules, suggesting a biofilm life-cycle. bioRxiv, 484642, 2018. DOI: 10.1101/484642
    #Joint corresponding authors

  179. Proceedings

  180. V. Phoenix, E. Corbett, E., and U. Z. Ijaz. Impact of hydraulic conductivity on water quality and microbial ecology of rain garden. In EGU General Assembly 2024, Vienna, Austria, April 14-19, 2024. DOI: 10.5194/egusphere-egu24-214
  181. T. Conley, R. Slater, D. Bulmer, S. Moss, J. De La Revilla Negro, U. Z. Ijaz, T. Lawley, D. M. Pritchard, M Parkes, and C. Probert. O64 Microbiome-driven metabotypes influence response to the low FODMAP diet in IBS and implicate short chain fatty acids. Gut, 73:A40-A41, 2024. DOI: 10.1136/gutjnl-2024-BSG.64
  182. K. Gkikas, M. Lima, S. McKirdy, L. Gervais, C. Kerbiriou, B. Nichols, G. Smith, L. Armstrong, T. Jordan, I. Chalmers, H. Barlow, G. Al Hourani, R. Muhammed, D. Wands, P. Narula, M. Patel, U. Z. Ijaz, S. Milling, M. Gasparetto, P. Henderson, D. C. Wilson, R. Hansen, R. K. Russell, and K. Gerasimidis. OC1 High faecal pH and low total microbial load associate with normalisation of faecal calprotectin in children with Crohn’s disease treated with exclusive enteral nutrition; results from iPENS, a multicentre, prospective study. Frontline Gastroenterology, 15:A1, 2024. DOI: 10.1136/flgastro-2024-bspghan.1
  183. K. Gkikas, M. Lima, S. McKirdy, L. Gervais, C. Kerbiriou, B. Nichols, L. Armstrong, T. Jordan, G. Smith, I. Chalmers, H. Barlow, G. Al Hourani, R. Muhammed, D. Wands, P. Narula, M. Patel, U. Z. Ijaz, S. Milling, M. Gasparetto, P. Henderson, D. C. Wilson, R. Hansen, R. K. Russell, and K. Gerasimidis. OC2 Cereal intake and diet-related microbial metabolites in faeces associate with recurrence of gut inflammation during food reintroduction in children with Crohn’s disease treated with exclusive enteral nutrition; iPENS a multicentre, prospective study. Frontline Gastroenterology, 15:A2, 2024. DOI: 10.1136/flgastro-2024-bspghan.2
  184. R. Slater, A. Frau, S. Belnour, U. Z. Ijaz, S. Allen, and C. Probert. P136 Faecal volatile organic compounds (VOCs) are correlated with bacterial taxa and functional genes in paediatric Crohn’s disease. Gut, 73:A134-A135, 2024. DOI: 10.1136/gutjnl-2024-BSG.218
  185. K. Gkikas, M. Lima, S. McKirdy, L. Gervais, G. Smith, C. Kerbiriou, B. Nichols, F. Zille, L. Armstrong, T. Jordan, I. Chalmers, H. Barlow, G. Al Hourani, R. Muhammed, D. Wands, P. Narula, M. Patel, U. Z. Ijaz, S. Milling, M. Gasparetto, P. Henderson, D. C. Wilson, R. Hansen, R. K. Russell, and K. Gerasimidis. P056 Cereal intake and diet-related microbial metabolites in faeces associate with recurrence of gut inflammation during food reintroduction in children with Crohn’s disease treated with exclusive enteral nutrition; iPENS a multicentre, prospective study. Journal of Crohn's and Colitis, 18(Suppl1):i323–i324, 2024. DOI: 10.1093/ecco-jcc/jjad212.0186
  186. K. Gkikas, M. Lima, S. McKirdy, B. Nichols, C. Kerbiriou, L. Gervais, G. Smith, L. Armstrong, T. Jordan, I. Chalmers, H. Barlow, G. Al Hourani, R. Muhammed, D. Wands, P. Narula, M. Patel, U. Z. Ijaz, S. Milling, M. Gasparetto, P. Henderson, D. C. Wilson, R. Hansen, R. K. Russell, and K. Gerasimidis. P080 High faecal pH and low total microbial load associate with normalisation of faecal calprotectin in children with Crohn’s disease treated with exclusive enteral nutrition; results from iPENS, a multicentre, prospective study. Journal of Crohn's and Colitis, 18(Suppl1):i353–i354, 2024. DOI: 10.1093/ecco-jcc/jjad212.0210
  187. K. Gerasimidis, B. Nichols, A. Briola, J. Havlik, A. Mascellani, S. Milling, U. Z. Ijaz, C. Quince, V. Svolos, R. K. Russell, and R. Hansen. DOP31 Gut metabolomic and compositional signatures predict response to treatment with exclusive enteral nutrition in children with active Crohn’s disease. Journal of Crohn's and Colitis, 17(suppl1):i96, 2023. DOI: 10.1093/ecco-jcc/jjac190.0071
  188. V. Svolos, R. Hansen, R. K. Russell, D. R. Gaya, J. P. Seenan, J. Macdonald, D. Wilson, P. Henderson, S. Din, G. T. Ho, C. Quince, U. Z. Ijaz, S. Milling, B. Nichols, R. Papadopoulou, S. McKirdy, L. Gervais, S. Shields, and K. Gerasimidis. P380 Changes in faecal microbiome and metabolome are more pronounced in Crohn’s disease patients who adhered to the CD-TREAT diet and responded by calprotectin. Journal of Crohn's and Colitis, 17(suppl1):i513-i515, 2023. DOI: 10.1093/ecco-jcc/jjac190.0510
  189. K. Gerasimidis, B. Nichols, R. Papadopoulou, U. Z. Ijaz, R. Rajendran, C. Quince, R. K. Russell, R. Hansen. DOP52 The faecal bacterial and fungal microbiome of newly-diagnosed, treatment naïve children with Crohn’s disease and the modifying effects of exclusive enteral nutrition and re-introduction of habitual diet. Journal of Crohn's and Colitis, 17(suppl1):i122-i124, 2023. DOI: 10.1093/ecco-jcc/jjac190.0092
  190. V. Svolos, R. Hansen, R. Russell, D. R. Gaya, S. J. Paul, J. Macdonald, B. Nichols, R. Papadopoulou, M. Logan, S. Mckirdy, R. Gervais, U. Z. Ijaz, S. Milling, S. Shields, D. Wilson, P. Henderson, S. Din, G. T. Ho, and K. Gerasimidis. DOP68 CD-TREAT diet induces remission and improves quality of life in an open label trial in children and adults with active Crohn’s Disease. Journal of Crohn's and Colitis, 16(suppl1):i112, 2022. DOI: 10.1093/ecco-jcc/jjab232.107
  191. K. Bain, B. Nichols, R. Papadopoulou, F. Moffat, I. McInnes, U. Z. Ijaz, K. Gerasimidis, A. Astrand, S. Holmes, and S. Milling. Alopecia areata pathotypes are associated with distinct immune and intestinal microbiome signatures. British Journal of Dermatology, 187(1):E3-E4, 2022. DOI: 10.1111/bjd.20477
  192. D. Grant, K. Steinsland, S. Mugu, K. S. Skaar, U. Z. Ijaz, U. Ninneman, J. L. Ray, and S. De Schepper. The last interglacial in the Labrador sea: a sedimentary ancient DNA investigation. In EGU General Assembly 2021, April 19-30, 2021. DOI: 10.5194/egusphere-egu21-3587
  193. G. G. Gebeyehu, L. Flain, R. Slater, A. Frau, C. Probert, U. Z. Ijaz, E. De Pablo-Fernandez, and T. Warner. OWE-1 Investigation of the metabolome and mycobiome in Parkinson’s disease. Gut, 70(suppl 4):A18, 2021. DOI: 10.1136/gutjnl-2021-BSG.32
  194. K. Gkikas, M. Logan, S. Milling, U. Z. Ijaz, R. Hansen, R. K. Russell, and K. Gerasimidis. DOP27 The fibre fermentative capacity of the gut microbiota is diminished in children with Crohn’s Disease and it is independent of disease activity or treatment with exclusive enteral nutrition. Journal of Crohn’s and Colitis, 15(suppl 1):S065-S066, 2021. DOI: 10.1093/ecco-jcc/jjab073.066
  195. M. Pidoux, M. Logan, S. Milling, U. Z. Ijaz, R. Hansen, R. K. Russell, and K. Gerasimidis. DOP66 The effect of exclusive enteral nutrition on circulating inflammatory protein levels in paediatric patients with Crohn’s Disease. Journal of Crohn’s and Colitis, 15(suppl 1):S100-S101, 2021. DOI: 10.1093/ecco-jcc/jjab073.105
  196. H. M. Baer, E. McDonald, A. N. Ferguson, A. Scott, M. I. Khan, K. A. Bain, U. Z. Ijaz, J. J. Cole, M. Ramanujam, R. J. B. Nibbs, D. R. Gaya, and S. W. F. Milling. P83 Understanding differences in serum and mucosal immunopathotypes in Crohn’s disease. Gut, 70(suppl 1):A83, 2021. DOI: 10.1136/gutjnl-2020-bsgcampus.158
  197. M. Logan, K. Gkikas, V. Svolos, B. Nichols, S. Milling, U. Z. Ijaz, J. Macdonald, J. Macdonald, J. P. Seenan, R. Hansen, R. K. Russell, and K. Gerasimidis. P275 Analysis of exclusive enteral nutrition formulas in Crohn’s disease – new insights into dietary triggers. Gut, 70(suppl 1):A183-A184, 2021. DOI: 10.1136/gutjnl-2020-bsgcampus.349
  198. M. Logan, C. M. Clark, B. N. Nichols, U. Z. Ijaz, S. Milling, R. Hansen, R. K. Rusell, and K. Gerasimidis. O12 Reversion to baseline microbiome following successful course of exclusive enteral nutrition in paediatric Crohn’s disease. Gut, 70(suppl 1):A6-A7, 2021. DOI: 10.1136/gutjnl-2020-bsgcampus.12
  199. K. Gkikas, M. Logan, B. Nichols, C. M. Clark, U. Z. Ijaz, L. Gervais, H. Duncan, V. Garrick, L. Curtis, E. Buchanan, T. Cardigan, L. Armstrong, C. Delahunty, D. M. Flynn, A. R. Barclay, R. Tayler, R. Hansen, R. K. Russell, and K. Gerasimidis. O49 Dietary triggers of colonic inflammation following exclusive enteral nutrition treatment in children with Crohn’s disease. Gut, 70(suppl 1):A27-A28, 2021. DOI: 10.1136/gutjnl-2020-bsgcampus.49
  200. S. De Schepper, J. L. Ray, L. Griem, N. V. Nieuwenhove, D. M. Grant, K. Steinsland, K. S. Skaar, and U. Z. Ijaz. A sedimentary ancient DNA approach to elucidate the Labrador Sea paleoceanography over the last ~130,000 years. In EGU General Assembly 2020, May 4-8, 2020. DOI: 10.5194/egusphere-egu2020-10928
  201. M. Logan, K. Gkikas, V. Svolos, B. Nichols, S. Milling, U. Z. Ijaz, R. Hansen, R. K. Russell, and K. Gerasimidis. P050 Analysis of 61 exclusive enteral nutrition formulas used for induction of remission in Crohn’s disease: new insights on dietary disease triggers. Journal of Crohn's and Colitis, 14(suppl 1):S157–S158, 2020. DOI: 10.1093/ecco-jcc/jjz203.179
  202. H. M. Baer, E. MacDonald, A. Ferguson, A. M. Scott, M. I. Khan, K. A. Bain, U. Z. Ijaz, J. Cole, M. Ramanujam, R. J. B. Nibbs, D. R. Gaya, S. W. F. Milling. P014 Identification of Crohn’s disease immunopathotypes. Journal of Crohn's and Colitis, 14(suppl 1):S137, 2020. DOI: 10.1093/ecco-jcc/jjz203.143
  203. K. Gkikas, M. Logan, B. Nichols, C. M. Clark, U. Z. Ijaz, L. Gervais, H. Duncan, V. Garrick, L. Curtis, E. Buchanan, T. Cardigan, L. Armstrong, C. Delahunty, D. M. Flynn, A. R. Barclay, R. Tayler, R. Hansen, R. K. Russell, and K. Gerasimidis. P091 Dietary triggers of colonic inflammation following treatment with exclusive enteral nutrition in children with Crohn’s disease. Journal of Crohn's and Colitis, 14(supp 1):S180–S181, 2020. DOI: 10.1093/ecco-jcc/jjz203.220
  204. A. Frau, R. Hough, U. Z. Ijaz, B. Campbell, J. Kenny, N. Hall, J. Anson, A. C. Darby, and C. S. J. Probert. ATH-09 Metabolomics & Multi-omics analysis of Crohn’s disease. Gut, 68:A68, 2019. DOI: 10.1136/gutjnl-2019-BSGAbstracts.131
  205. H. M. Baer, E. McDonald, A. Ferguson, U. Z. Ijaz, R. J. B. Nibbs, and S. W. F. Milling. PTH-075 Identification of IBD immunopathotypes. Gut, 68:A69-A70, 2019. DOI: 10.1136/gutjnl-2019-BSGAbstracts.134
  206. H. Song, E. Kang, H. Soh, H. Chung, J. Chun, S. Yoon, U. Z. Ijaz, and Y. Koh. Multi-omics approaches to understand gastric mucosa-associated lymphoid tissue (MALT) lymphoma. Hematological Oncology, 34:339-340, 2019. DOI: 10.1002/hon.2631
  207. A. Frau, U. Z. Ijaz, R. Hough, B. J. Campbell, J. G. Kenny, N. Hall, J. Anson, A. C. Darby, and C. S. J. Probert. P842 Multi-omics analysis suggests an active role of fungi in Crohn’s disease. Journal of Crohn’s and Colitis, 13(suppl 1):S545, 2019. DOI: 10.1093/ecco-jcc/jjy222.966
  208. V. Svolos, R. Hansen, U. Z. Ijaz, L. Gervais, H. Duncan, R. Tayler, A. Barclay, D. Flynn, V. Garrick, L. Curtis, E. Buchanan, T. Cardigan, D. R. Gaya, S. Milling, R. K. Russell, and K. Gerasimidis. P602 CD-TREAT a novel dietary therapy of active Crohn’s disease using the exclusive enteral nutrition paradigm. Journal of Crohn’s and Colitis, 13(suppl 1):S416-S417, 2019. DOI: 10.1093/ecco-jcc/jjy222.726
  209. A. Stratakos, M. Linton, P. Ward, U. Z. Ijaz, P. Scates, J. McBride, O. Gundogdu, and N. Corcionivoschi. Integrated phenotypic and genomics analysis to elucidate differences in stress resistance and virulence of Listeria monocytogenes strains. Access Microbiology, 1(1A), 2019. DOI: 10.1099/acmi.ac2019.po0264
  210. M. J. Ormsby, M. Logan, S. A. Johnson, A. McIntosh, R. Hansen, U. Z. Ijaz, R. K. Russell, K. Gerasimidis, and D. M. Wall. Inflammation associated ethanolamine facilitates infection by Crohn’s disease-linked adherent-invasive Escherichia coli. Access Microbiology, 1(1A), 2019. DOI: 10.1099/acmi.ac2019.po0096
  211. A. Frau, U. Z. Ijaz, B. Campbell, A. Darby, J. Kenny, N. Hall, and C. Probert. OWE-010 Bacterial and fungal communities in faeces and biopsies in IBD. Gut, 67:A58-A59, 2018. DOI: 10.1136/gutjnl-2018-BSGAbstracts.115
  212. A. Frau, D. Jonkers, J. Penders, M. Pierik, U. Z. Ijaz, B. Campbell, A. Darby, J. Kenny, N. Hall, and C. Probert. P858 Crohn’s disease is characterised by a fungal dysbiosis. Journal of Crohn's and Colitis, 12(suppl 1):S550-S551, 2018. DOI: 10.1093/ecco-jcc/jjx180.985
  213. V. Svolos, B. Nichols, D. Bolognini, C. Quince, U. Z. Ijaz, R. T. Papadopoulou, C. Ansalone, J. Salmond, R. Klopfleisch, D. R. Gaya, R. K. Russell, R. Hansen, K. Gerasimidis, and S. Milling. P856 The gut microbiota composition and metabolic activity of HLA-B27 transgenic rats with gut inflammation resembles the dysbiotic characteristics of human inflammatory bowel disease. Journal of Crohn's and Colitis, 12(suppl 1):S549–S550, 2018. DOI: 10.1093/ecco-jcc/jjx180.983
  214. V. Svolos, R. Hansen, U. Z. Ijaz, C. Quince, D. Watson, A. Alghamdi, A. Brejnrod, C. Ansalone, R. Klopfleisch, S. Milling, D.R. Gaya, R. K. Russell, and K. Gerasimidis. AODTH-007 Dietary manipulation of the healthy human and colitic rat gut microbiome by cd-treat diet and exclusive enteral nutrition; a proof of concept study. Gut, 66:A202, 2017. DOI: 10.1136/gutjnl-2017-314472.394
  215. M. Castelino, M. Tutino, J. Moat, U. Z. Ijaz, R. Parslew, A. Al-Sharqi, R. B. Warren, C. Quince, P. Ho, M. Upton, S. Eyre, and A. Barton. AB0115 Comparison of the bacterial stool microbiota in established psoriatic arthritis (PSA) and psoriasis (PSC) - exploratory analysis of pilot data. Annals of the Rheumatic Diseases, 76:1087, 2017. DOI: 10.1136/annrheumdis-2017-eular.3404
  216. V. Svolos, R. Hansen, U. Z. Ijaz, C. Quince, D. Watson, A. Alghamdi, A. Brejnrod, C. Ansalone, S. Milling, D. Gaya, R. Russell, and K. Gerasimidis. DOP008 Dietary manipulation of the healthy human and colitic murine gut microbiome by CD-TREAT diet and exclusive enteral nutrition; a proof of concept study. Journal of Crohn’s and Colitis, 11 (suppl 1): S29-S30, 2017. DOI: 10.1093/ecco-jcc/jjx002.045
  217. C. Pedersen, P. Hinton, E. Gallagher, F. Horton, R. Ellis, U. Z. Ijaz, H. Wu, E. Jaiyeola, O. Diribe, G. R. Gibson, T. Duparc, P. D. Cani, J. Wright, D. Russell-Jones, R. L. Ragione, and M. D. Robertson. Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 Diabetes. Proceedings of the Nutrition Society, 75(OCE3), 2016. DOI: 10.1017/S0029665116001191
  218. V. Svolos, R. Hansen, K. Hughes, U. Z. Ijaz, C. Quince, D. Gaya, R. Russell, and K. Gerasimidis. OP18 - The impact of 'Crohn's Disease-TReatment-with-EATing' diet (CD-TREAT diet) and exclusive enteral nutrition on healthy gut bacteria metabolism. Journal of Crohn’s and Colitis, 10(suppl 1):S14-S15, 2016. DOI: 10.1093/ecco-jcc/jjw019.01
  219. M. Castelino, S. Eyre, M. Tutino, J. Moat, P. Martin, U. Z. Ijaz, C. Quince, P. Ho, M. Upton, and A. Barton. Bacterial Skin Microbiome in Psoriatic Arthritis- Pilot Data from Psoriatic Plaques on Dry Skin Sites from Patients with Both Psoriasis (PsC) and Psoriatic Arthritis (PsA). Arthritis & Rheumatology, 67 (suppl 10), 2015. DOI: 10.1002/art.39448
  220. M. J. Khan, C. Quince, V. S, U. Z. Ijaz, N. Loman, S. T. Calus, J. Quick, S. J. Haig, M. G. Shaikh, C. A. Edwards, and K. Gerasimidis. A detailed analysis of the gut microbial diversity and metabolic activity in children with obesity of different aetiology and lean controls. Proceedings of the Nutrition Society, 74(OCE1):E75, 2015. DOI: 10.1017/S0029665115000907
  221. M. Castelino, S. Eyre, J. Moat, G. Fox, P. Martin, U. Z. Ijaz, C. Quince, P. Ho, M. Upton, A. Barton. The skin microbiome in psoriatic arthritis: methodology development and pilot data. The Lancet, 385(suppl 1):S27, 2015. DOI: 10.1016/S0140-6736(15)60342-7
  222. K. Gerasimidis, N. Loman, J. Quick, S. T. Calus, U. Z. Ijaz, P. McGrogan, C. A. Edwards, C. Quince, R. K. Russell. O-05: Metagenomic analysis of the gut microbiome during a course of Exclusive Enteral Nutrition (EEN) provides novel insights on mechanism of EEN action. Journal of Crohn’s and Colitis, 8(suppl 2):S393-S394, 2014. DOI: 10.1016/S1873-9946(14)50003-7
  223. U. Z. Ijaz, B. S. Kim, T. -J. Kao, A. K. Khambampati, M. C. Kim, J. C. Newell, D. Isaacson, and K. Y. Kim. Mammography phantom studies using 3D electrical impedance tomography with numerical forward solver. In Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies 2007 (FBIT 2007), IEEE CS Press, Jeju, Korea, October 11-13, 2007. DOI: 10.1109/FBIT.2007.93
  224. U. Z. Ijaz, S. U. Chaudhary, M. S. Don, and K. Y. Kim. Computational strategies for protein quantitation in 2D electrophoresis gel image processor for matlab. In Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies 2007 (FBIT 2007), IEEE CS Press, Jeju, Korea, October 11-13, 2007. DOI: 10.1109/FBIT.2007.95
  225. S. I. Chung, J. S. Lee, U. Z. Ijaz, A. K. Khambampati, S. Kim, and K. Y. Kim. Dynamic estimation of interfacial boundary in a stratified flow with electrical impedance tomography. In Proceedings of the Korea Society for Energy Engineering Meeting, pages 101-105, Seoul, Korea, November 9, 2007. UCI: G300-cX919241.vn0p100
  226. J. S. Lee, S. I. Chung, U. Z. Ijaz, A. K. Khambampati, S. Kim, and K. Y. Kim. Image reconstruction using unscented Kalman filter in electrical impedance tomography. In Proceedings of the Korea Society for Energy Engineering Meeting, pages 106-111, Seoul, Korea, November 9, 2007. UCI: G300-cX919242.vn0p106
  227. S. Kim, U. Z. Ijaz, A. K. Khambampati, K. Y. Kim, and M. C. Kim. Effect of Current Injection Patterns on Dynamic Electrical Resistance Imaging for Fast Transient Processes. In Proceedings of the 5th IEEE Conference on Sensors (IEEE-SENSORS 2006), Daeku, Korea, October 22-25, 2006. DOI: 10.1109/ICSENS.2007.355516
  228. U. Z. Ijaz, S. U. Chaudhary, S. M. Ahn, B. H. Lee, and K. Y. Kim. 2D electrophoresis gel image processor for Matlab. In Proceedings of the 2006 International Conference on Hybrid Information Technology (ICHIT 2006), Jeju, Korea, November 9-11, 2006.
  229. U. Z. Ijaz, J. H. Kim, A. K. Khambampati, M. C. Kim, S. Kim, and K. Y. Kim. Process tomography-EIT application with interacting multiple model scheme. In Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2006), Chiang Mai, Thailand, volume 3, pages 369-372, July 10-13, 2006.
  230. A. K. Khambampati, U. Z. Ijaz, K. Y. Kim, and C. I. Kang. Compensation of servo track writing error in high track density disk drives. In Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2006), Chiang Mai, Thailand, volume 3, pages 373-376, July 10-13, 2006.
  231. B. S. Kim, U. Z. Ijaz, J. H. Kim, M. C. Kim, S. Kim, and K. Y. Kim. Nonstationary boundary estimation in electrical impedance tomography based on the IMM scheme. In Proceedings of the 5th International Conference on Inverse Problems in Engineering: Theory and Practice (ICIPE), Cambridge, England, pages K06 1-10, July 11-15, 2005.
  232. U. Z. Ijaz, J. H. Kim, and K. Y. Kim. Application of dependency constrained genetic algorithm on traveling salesman problem. In Proceedings of the 20th International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2005), Jeju, Korea, volume 1, pages 21-22, July 4-7, 2005.
  233. U. Z. Ijaz, J. H. Kim, F. A. Khan, W. C. Song, Y. B. Choi, and K. Y. Kim. Dynamic estimation in GPS through covariance compensation extended Kalman filter. In Proceedings of the 20th International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2005), Jeju, Korea, volume 2, pages 571-572, July 4-7, 2005.
  234. U. Z. Ijaz, J. H. Kim, B. S. Kim, S. Kim, M. C. Kim, and K. Y. Kim. Improvement of electrical impedance tomography images for the binary mixture system through image transform filter. In Proceedings of the 20th International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2005), Jeju, Korea, volume 2, pages 703-704, July 4-7, 2005.
  235. J. H. Kim, U. Z. Ijaz, B. S. Kim, M. C. Kim, S. Kim, and K. Y. Kim. Nonlinearity-compensation extended Kalman filter for handling unexpected measurement uncertainty in process tomography. In Proceedings of the International Conference on Control, Automation and Systems (ICCAS 2005), Gyeong Gi, Korea, pages 1897-1902, June 2-5, 2005.

  236. Datasets

  237. A. Badar, R. Aqueel, A. Nawaz, K. A. Malik, and U. Z. Ijaz. Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics (1.0). Zenodo, 2025. DOI: 10.5281/zenodo.14912809
  238. S. Mills, U. Z. Ijaz, and P. N. L. Lens. Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems. Zenodo, 2025. DOI: 10.5281/zenodo.14845121
  239. H. Sadatzki, S. De Schepper, J. L. Ray, K. S. Skaar, U. Z. Ijaz, R. Stein, and A. Larsen. Biomarkers of sediment cores from site GS15-198-38. PANGAEA - Data Publisher for Earth & Environmental Science, 2019. DOI: 10.1594/PANGAEA.900720
  240. S. De Schepper, J. L. Ray, K. S. Skaar, H. Sadatzki, U. Z. Ijaz, R. Stein, and A. Larsen. Palynology of sediment cores from site GS15-198-38. PANGAEA - Data Publisher for Earth & Environmental Science, 2019. DOI: 10.1594/PANGAEA.900715
  241. S. De Schepper, J. L. Ray, K. S. Skaar, H. Sadatzki, U. Z. Ijaz, R. Stein, and A. Larsen. Palynology, biomarkers and droplet digital PCR data from the Late Quaternary of Site GS15-198-38, Greenland Sea. PANGAEA - Data Publisher for Earth & Environmental Science, 2019. DOI: 10.1594/PANGAEA.900724
  242. J. L. Ray, K. S. Skaar, S. De Schepper, H. Sadatzki, U. Z. Ijaz, R. Stein, and A. Larsen. Polarella glacialis droplet digital PCR data from sediment cores from site GS15-198-38. PANGAEA - Data Publisher for Earth & Environmental Science, 2019. DOI: 10.1594/PANGAEA.900723
  243. S. T. Calus, U. Z. Ijaz, and A. Pinto. NanoAmpli-Seq - Bioinformatics Workflow v1 (protocols.io.u25eyg6). protocols.io, 2018. DOI: 10.17504/protocols.io.u25eyg6
  244. S. T. Calus, U. Z. Ijaz, and A. Pinto. Sample processing and sequencing library preparation workflow v1 (protocols.io.u26eyhe). protocols.io, 2018. DOI: 10.17504/protocols.io.u26eyhe

  245. Technical Reports & Theses

  246. U. Z. Ijaz, R. J. Housden, G. M. Treece, R. W. Prager, and A. H. Gee. Multi-directional scattering models for 3D ultrasound. Technical Report CUED/F-INFENG/TR 661, Cambridge University Department of Engineering, January 2011.
  247. U. Z. Ijaz, R. W. Prager, A. H. Gee, and G. M. Treece. Rapid hybrid ultrasound volume registration. Technical Report CUED/F-INFENG/TR 644, Cambridge University Department of Engineering, March 2010.
  248. U. Z. Ijaz, R. W. Prager, A. H. Gee, and G. M. Treece. Optimisation strategies for ultrasound volume registration. Technical Report CUED/F-INFENG/TR 635, Cambridge University Department of Engineering, August 2009.
  249. U. Z. Ijaz. Dynamic phase boundary estimation using electrical impedance tomography. Ph.D. thesis, Cheju National University, Korea, December 2007. DOI: 10.13140/RG.2.2.31090.71366

Systems & Products

  • Products

    • CD-TREAT Diet: A liquid-only diet (without any of a patient’s normal food or drink) for 8 weeks, called Exclusive Enteral Nutrition (EEN), is the best initial treatment for cases with active Crohn’s Disease (CD). In the BINGO Group, we have shown previously that this liquid-only diet works by changing the bacteria (germs) in the gut. This liquid-only diet is however very restrictive, and patients can find it difficult to stick to it for a long time, particularly if they are adults. Therefore, there is a lot of interest and enthusiasm to develop new diets that work as well as the liquid-only diet, but do not involve stopping all solid food. Such a solid food diet is more acceptable to most patients than a liquid-only diet. Our main product from the BINGO group is a recently developed solid food diet using everyday foods (called CD-TREAT), which we hope will work as well as the liquid-only diet. We have shown that CD-TREAT changes the gut bacteria of healthy people in a similar way to the liquid-only diet. The solid diet also improved gut inflammation in animal experiments. For, further details, see the Project Page.


      Publication: [DOI:10.1053/j.gastro.2018.12.002]

  • Systems

    • NanoAmpli-Seq: Amplicon sequencing, particularly sequencing of the small subunit rRNA (SSU rRNA) gene and internal transcribed spacer regions, is widely used for profiling of microbial community structure and membership. The introduction of single-molecule sequencing platforms, such as Pacific Bioscience's (PacBio's) single-molecule real-time sequencing (SMRT) and single-molecule sensing technologies on the Oxford Nanopore Technologies (ONT) MinION platform, has opened the possibility of obtaining ultra-long reads. MinION is a hand-held DNA sequencer, and has been heralded as revolutionary in bringing real-time sequencing closer to fruition. We have developed both sample processing and sequencing library preparation workflow as well as the software tools.

      Publication: [DOI:10.1093/gigascience/giy140]
    • Full-scale Hybrid EGSB Reactor (to operate at low temperatures): We demonstrated for the first time, direct, high-rate, low-temperature anaerobic digestion (AD) of low-strength municipal wastewater at full-scale. An 88 m hybrid reactor was installed at the municipal wastewater treatment plant in Builth Wells, UK and operated for 290 days. Ambient temperatures ranged from 2 to 18 ᵒC, but remained below 15 ᵒC for > 100 days. Influent BOD fluctuated between 2 and 200 mg L-1. However, BOD removal often reached > 85%. 16S rRNA amplicon sequencing of DNA from the biomass revealed a highly adaptable core microbiome. The combination of data and analysis from this study provides strong evidence in favour of treating dilute municipal wastewater directly and at low ambient temperatures using AD technology. Given the immense quantities of municipal wastewater produced daily around the world, and the energy and land requirement for conventional treatment, a low-temperature anaerobic solution could have an enormous positive environmental impact - especially for temperate climates. Our data suggest that the biologically-mediated processes underpinning AD are possible under these conditions. Moreover, the microbial community is adaptable and resilient to the nutrient limitations and low temperatures that have been generally considered unfavourable with respect to municipal wastewater treatment. This full-scale modular demonstration provides game-changing possibilities for the treatment of municipal wastewater.

      Impact case study arising from publications (DOI:10.1016/j.biortech.2021.125786; DOI:10.1093/femsec/fiy095): NUI Galway - Transforming Sustainable Water Management: Creating Jobs and Saving Energy
    • Solar Septic Tank: The Solar Septic Tank (SST) is a novel septic tank design that uses passive heat from the sun to raise in-tank temperatures and improves solids degradation, resulting in a cleaner effluent. Treatment has been shown to exceed conventional systems, however, the underlying biology driving treatment in the system is poorly understood. With Professor William T. Sloan (through EPSRC EP/P029329/1 grant), Dr Stephanie Connelly, and colleagues at Asian Institute of Technology Thailand (technology inventors), we have used next generation sequencing (Illumina Miseq (San Diego, CA, USA), V4 region 16S DNA) to monitor the microbiology in the sludge and effluent of two mature systems, a conventional septic tank and an SST, during four months of routine operation in Bangkok, Thailand, and evaluated the ecology against a suite of operating and performance data collected during the same time period. We have shown that there are significant differences in the microbial communities between conventional septic tanks and solar septic tanks with the key species that make up the differences can be used to index enhance degradation of waste and hence will inform management strategies. The solar septic tank technology that we are working on, with colleagues in Thailand, has been installed in a School in Bangalore India as part of a Scottish Government initiative.

      Publication: [DOI: 10.3390/w11122660]
    • Smart Raman Activated Cell Sorting System: With MPhil student (Yuchen Fu) and Professor Huabing Yin (through NERC NE/P003826/1 grant), we have developed a smart Raman activated cell sorting system (thesis: Smart Raman Activated Cell Sorting System) where using microfluidics, stable isotopes, and machine learning algorithm (probabilistic LDA), we have been able to sort microbes based on function.
    • microbiomeSeq (designed with Alfred Ssekagiri): An R Package for multivarite statistical analysis of microbial community analysis in an environmental context.
    • RvLab (with collaborators at HCMR, Greece): This website makes use of R which is a statistical processing environment widely used by scientists working in many biodiversity related disciplines. It supports an integrated and optimized (in respect to computational speed-up and data manipulation) online R environment. This vLab tackles common problems faced by R users, such as severe computational power deficit. Many of the routines operating under the R environment, such as the calculation of several biodiversity indices and the running of the multivariate analyses, are often of high computational demand and cannot deliver a result when the respective datasets are in the form of large matrices.

      Publications: [DOI:10.3897/BDJ.4.e8357]
    • seqenv: Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. The software carry out precisely such a task by performing similarity searches of short sequences against publicly available online repository (NCBI) and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the relevant fields, a text mining algorithm is run to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples.

      Publications: [DOI:10.7717/peerj.2690]
    • SeqEnv-Ext (designed by Ali Z. Ijaz): A taxa-centric extension to seqenv pipeline, which consisted of two parts, each providing environmental annotations under different context, with first part providing taxon abundance on a per term basis while the second part lists environmental term abundance under a per taxon context. A separately developed program that required the use of the original seqenv pipeline, this enabled two different methods of viewing environmental annotations, which significantly augments the analysis capability of the pipeline.
      Code: SEQenv-Ext, TaxaSE System

      Publication: [DOI:10.7717/peerj.3827]
    • CONCOCT: A software for binning metagenomic contigs with coverage and composition.

      Publication: [DOI:10.1038/nmeth.3103]
    • CViewer (designed with Orges Koci): The past few years have seen an increased utility of shotgun metagenomics for microbial community surveys over traditional amplicon sequencing. This is made possible by the technological advancement in methods development that enables us now to assemble short sequence reads into longer contiguous regions that can be binned together to identify species they are part of, e.g., through CONCOCT. The advantage of shotgun metagenomics is that coding regions of these contigs can further be annotated against public databases to give an assessment of the functional diversity. With integrated solutions gaining importance by complementing metagenomics with other meta’omics technologies (e.g., metabolomics), there is a need to have a single platform to consolidate all these realisations on the same sample space. Thus, we have developed CViewer, a Java-based statistical framework to integrate all levels of gene products, mRNA, protein, metabolites for microbial communities and allows exploration of their response to environmental factors through multivariate statistical analysis.
    • pyTag (designed with Orges Koci): With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, through our pyTag workflow, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis.

      Publication: [DOI:10.7287/10.7717/peerj.5047]
    • NMGS: Neutral models which assume ecological equivalence between microbial species provide null models for community assembly. In Hubbell's Unified Neutral Theory of Biodiversity (UNTB), the microbial communities are modelled as many local communities connected to a single metacommunity through differing immigration rates. The software is an efficient Bayesian fitting strategy for the multi-site UNTB.

      Publication: [DOI:10.1109/JPROC.2015.2428213]
    • GlobalView: At University of Oxford (2011-2012), I worked on a project that investigated methods to infer time-varying networks from multiple time signals (slides). The time signals pertain to Google trends, Twitter feeds, stock prices, exchange rates, commodity prices, weather statistics and transport statistics. My responsibilities were: established a template of usage requirements from relevant stakeholders in UK government and other beneficiaries; worked on housing datasets in collaboration with Institute of Public Policy Research and Rightmove; identification of unusual behaviour in single signals, in particular weak signal changes that are distributed across many variables but causing global changes in network topology; detrending the data to remove seasonal or periodic components, and irregular fluctuation; forecasting of future values of individual signals using Gaussian Processes based regression; constructed a hierarchy of increasingly sophisticated methods for network inference; it is particularly important that we establish which of the wide range of available methods is most appropriate for the data we have and that we infer plausible networks of relations. I considered simple correlations with sliding windows; a range of causal methods such as Dynamic Bayesian Networks and Granger Causality; those that are based on Markov Random Field (Eric Xing's work at Carnegie Mellon), and some that are based on State-Space Models (Zoubin Ghahramani's work at Cambridge); and identification of high trending keywords from Google Trends Datasets using residual time series obtained from the difference between the linearly interpolated values and original values and by using various outlier detection methods; and developed a cross-platform prototype software tool GlobalView in C++ for dynamic network inference [Code; Project Page]
    • Hybrid 3D Ultrasonic Imaging System: At University of Cambridge (2008-2011), I developed a Hybrid 3D Ultrasonic Imaging System. The project focused on: tracking the trajectory of a 3D ultrasound probe based on the image-based registration of acquired data and the output of an inertial position sensor; calibration of the hybrid system; correction of artifacts in the data caused by variations of the pressure from the probe during the scan; differentiation of backscatter into diffuse and directional components using the overlap data from multiple scans; and development and evaluation of software tools to enable the system to be used effectively in a Hospital environment. The system was implemented in Stradwin software (written in C++ and using wxWidgets to provide cross-platform compatibility and OpenGL for 3D visualisation). The software was then modified to run on a mobile ultrasound machine Ultrasonix Sonix RP; and to communicate with the inertial sensor through it's serial port. The software was also modified to provide a calibration protocol to compensate for the orientation in which the sensor, Intersense Inertia Cube 3, was mounted on the ultrasound probe. Additionally, the keypad controls for the ultrasound machine were fully integrated with the developed software.
      Developed System:

      Publication: [DOI:10.1259/bjr/46007369]
    • Dynamic Electrical Impedance Tomography System: During my PhD (2004-2008), I focused primarily on the development of static and dynamic algorithms for inverse problems that arise in a variety of engineering applications including but not limited to electrical impedance tomography (EIT). I developed novel tomographic imaging methods using EIT to manipulate measurement data from electrodes attached to the surface of a pipeline in order to estimate the multidimensional distribution of physical parameters inside. As compared to the traditional EIT, those scenarios were considered in which the object to be imaged is changing very rapidly during the data acquisition; necessitating a desire for reasonable spatio-temporal resolution. Rather than considering the inverse problem as a traditional tomography reconstruction problem, the problem was formulated as a state estimation problem utilising different kinematic evolution models for the physical parameters along with an observation model based on finite element analysis (FEM). In particular, the Kalman-type inverse algorithms were developed for estimation of time-varying interfacial boundary in stratified flows of immiscible liquids (targeting liquid hydrocarbon transportation in pipelines that often contain free water).
      Developed System:

      Publication: [DOI:10.1016/j.jcp.2007.12.025]
    • 2D Electrophoresis Gel Image Processor for Matlab: During my PhD (2004-2008), I worked on a joint project with the Systems Biology Group, JNU and developed a software, 2D electrophoresis Gel Image Processor for Matlab. This software is useful for the analysis of bio-markers by quantifying individual proteins, showing the separation between one or more protein "spots" on a scanned image of a 2D gel, and measuring running differences between gels. The salient features of the software include but not limited to:
      Software Demo:


      Publication: [DOI:10.1109/FBIT.2007.95]
    • SalmoSim: A device with series of bioreactors innoculated with microbes and applied with biofluids originating from the salmon's gastro-intestinal tract. This is aimed at understanding the relationship between aquaproducts, nutrient bioaccessibility and gut microbes in order to improve the productivity and sustainability of farmed salmon. Aquafeed is fermented in our system, physiological parameters are carefully regulated and bioaccessible nutrients are dialysed. Samples are taken throughout to analyse microbial life, nutrients and biochemical properties.

      Publications: [DOI:10.1101/2020.10.07.328427; DOI:10.1101/2020.10.06.327858 ]
    • AmpliPyth (designed by David Meltzer): Python-based pipeline that processes metagenomic amplicons (16S rRNA/18S rRNA and Fungal ITS) and generates an HTML report.
    • SNPCallPHYLO (designed by Cosmika Goswami): Python-based SNPs calling pipeline that processes whole genome shotgun sequencing data from single genome isolates and generates an HTML report.
    • AMPLImock: A python based pipeline for analyzing 16s rRNA amplicons generated from mock communities [Code, Usage]
      To collate statistics and frequencies from multiple samples, use collateResults.pl
      To generate transition probabilities from alignment files, use usearch_aln_transition_prob.py
    • AMPLICONprocessing: A bash based pipeline for generating taxonomic profiles for Illumina paired-end reads using CREST and RDP classifiers [Usage]
    • METAmock: A python based pipeline for analyzing Whole-Genome Shotgun sequences generated from mock communities [Code, Usage]
    • TAXAenv: A website useful for multivariate statistical analysis of microbial community structure (abundance tables) in an environmental context (metadata).
    • TAXAassign: A bash based pipeline for generating taxonomic prifles using NCBI's Taxonomy.
    • CLUSThack: A python package that has an embarassingly-parallel (multithreaded + utilises streaming SIMD extensions) implemention for qgram-based edit distance measurement and is useful for hierarchical clustering of 16S rRNA sequences.
      Package: CLUSThack_v0.2.tar.gz
      Test files: hclust.py, test.fasta, test.pdf.
      Usage: $ time ./hclust.py -f test.fasta -t 32
    • Interactive tools for visualising abundance tables from metagenomic surveys:
      • PHYLOmap: A software for drawing heatmaps with phylogenetic trees from metagenomic surveys based on Interactive Tree of Life (ITOL) API.
      • HEATcloud: Web-based interactive heatmap viewer (programmed using javascript and jQuery) for abundance tables.
      • SUMMARIZEplot: Web-based interactive stacked barplot viewer (programmed using D3.js) for abundance tables.
      • PHYLObar: Web-based interactive viewer (programmed using D3.js) for trees in Newick format.
    • clust_validity.R: This script takes a CSV file of N D-dimensional features, performs K-means or dp-means clustering and chooses the optimum number of clusters based on either of the implemented internal clustering validation indices. Additionally, if the csv file contains a column titled "True_Clusters" containing true clusters membership for each object, you can use it to validate clustering performance using several external clustering indices.
      Code: clust_validity.R (Tutorial, Reference slides (maths), Example datasets)
    • GraphicalLasso.tar.gz: Generates network of associations between OTUs as a DOT file which can then be visualised in GraphViz.
    • Faster blastn searches using GNUparallel: For an Illumina dataset with 6 million reads, blastn_parallel.sh took 2.5 minutes on 45 cores as compared to blastn.sh which took 86 minutes.
    • Extracting representative sequences from OTU clusters generated in AmpliconNoise. extract_clust_seqs_fasta.pl is an extension of AmpliconNoise's Typical.pl and can give the most abundant sequence, consensus sequence, first sequence, and the longest sequence of each cluster as representative OTU.
    • remove_colinear_terms.R: An R script to iteratively remove colinear variables by calculating step-wise Variance Inflation Factor (VIF) of terms (columns) in a CSV file.
    • convIDs.pl : This script takes a (TAB/COMMA) delimited file and converts words in a particular column to those provided by a COMMA delimited IDs list.
    • collate_CSV.R: This R script takes two frequency tables in CSV format and collates them together by either taking union or intersection of columns. Furthermore it inserts "F1_" and "F2_" as prefixes to rownames of both CSV files, respectively.
    • collateResults.pl: This script is useful for combining CSV files generated by TAXAassign, AMPLICONprocessing or any software that produces two-column CSV files without header information. It takes as an input the path to a main folder where subfolders contain CSV files, each matching a particular pattern in their names.
    • collateGCMSResults.pl: This script is useful for collating data generated from GC-MS machines.
    • Google Colaboratory Workflows: Google Colaboratory allows one to write and execute Python in web browser (whether running on smart phones or laptop) and requires just a valid google account to run python notebooks (which have .ipynb extensions). With ~30GB DISK and 12GB RAM "FREELY" available on Colaboratory associated with Google accounts, the following workflows serves as modular streams for microbial informatics in the absence of any dedicated computing cluster. These are highly reusable, customisable, and serve to communicate research findings to funders/external collaborators as well as software outputs for the grants (Research Fish etc.). The run time for these workflows is ~3 to 4 hours on mediocre datasets.
      • conda_qiime2.ipynb: A proof-of-concept that QIIME2 can be run on Google Colab, and can process a proper 16S rRNA amplicons study
        Inputs: Paired-end Illumina FASTQ files (successfully tested with 97 samples comprising 7.7M reads).
        Outputs: Abundance Table of Amplicon Sequence Variants (ASVs) with Taxonomy (feature_w_tax.biom); Phylogenetic Tree (tree.nwk).
        Usefulness: Can use the workflow for current experiments as well as existing samples (meta-analysis studies).
      • conda_pangenome.ipynb: Prokaryotic pan genome analysis with Prokka and Roary
        Inputs: Prokaryotic Strains/Draft Assemblies in FASTA format (successfully tested on 12 strains of Peptobacterium atrosepticum).
        Outputs: Fully Annotated Genomes (*.GFF/*.GBK files); Phylogenetic Tree of Strains; Core/Accessory Genes.
        Usefulness: Can analyse functional gain/loss in prokaryotic strains of interest in intervention/case-control studies.

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