Umer Zeeshan Ijaz [Ph.D.Eng.(Inverse Problems), M.Sc.Eng.(Artificial Intelligence), B.Sc.Eng.(Computer Systems)]

Reader in Information Engineering (Civil Engineering*, University of Glasgow)
*Ranked 2nd in the Civil Engineering discipline in the UK according to Complete University Guide 2021 with rankings here

Co-Director, Environmental'Omics Lab (with Dr Ciara Keating), University of Glasgow
PI, Water & Environment Group (James Watt School of Engineering, University of Glasgow)
PI and Co-founder, Bacteria, Immunology, Nutrition, Gastroenterology and OMICS (BINGO) Group (School of Medicine, Dentistry & Nursing, University of Glasgow)
PI, Founder, and Facility Manager, Orion Cluster (James Watt School of Engineering, University of Glasgow)
Consortium Member, A Genetic View into Past Sea Ice Variability in the Arctic (AGENSI) Group (Bergen, Norway)
Consortium Member, Glasgow Water Cluster (University of Glasgow)
Consortium Member, Blackleg Hub (The James Hutton Institute)
Consortium Member, Diversity Group (Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow)
Advisor of Studies - Postgraduate Taught Course (James Watt School of Engineering, University of Glasgow)
Executive Member, Scottish Pakistani Association

Contact

Room 625, Rankine Building
School of Engineering
Oakfield Avenue
University of Glasgow
Glasgow
G12 8LT
Phone (office;direct line): +44(0)141-330-6458
Email: Umer.Ijaz  @  glasgow.ac.uk

Summary Statistics
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
ORCID iD iconorcid.org/0000-0001-5780-8551
ResearchGate
Google Scholar
profile: 292992
Ethnicity: Black, Asian and Minority Ethnic (BAME)
Nationality: Dual [Pakistani (since birth) and British (since 2017)]
21+ years of work experience [since June, 1999 (age 19) with no career breaks; Career profile: here]
40+ research grants (7 UKRI) contributions since 2004
£11.1M+ external grant funding as a PI/Co-I since 2014 (£4.3M+ brought to University of Glasgow)
150+ publications [Full list: PUBLICATIONS.pdf]
20+ scientific software and engineered systems since 2004
135+ supervisions/mentoring (21 completed PhD theses since 2014)


I lead the Environmental 'Omics Lab in Infrastructure & Environment Division, School of Engineering that I established soon after I was awarded the NERC Omics Fellowship in November, 2014. Since 2020, the lab is co-directed with Dr Ciara Keating. We form part of the Water & Environment Group at University of Glasgow:
Tweets by UofGWaterEnv

The purpose of my research is to integrate different sources of 'omics data (metagenomics, metatranscriptomics, metabolomics, and metaproteomics) in environmental science for microbial community analysis. I regularly work on projects where we want to understand the taxonomic and functional diversity of microbial community in the context of metadata often recorded under specific hypotheses. Integrating (N-/P- integration; see figure below) these datasets require a fair deal of multivariate statistical analysis for which I have shared the code on this website.

With Professor Simon Milling, we have then utilised N-integration tool to link host immunology with microbiome profiling, and also developed a toolbox:


Since 2016, I am trying to expand my research to engineering projects that now include: Raman spectroscopy enabled microfluidics; a hardware system for integrating liquid handling, incubation and sensing; and development of artificial intestinal Salmon gut system through bioreactors. My long-term research vision is to develop specialised and bespoke systems (both hardware and software) that can exploit and harness the power of microbial communities (also including statistical tools), and to place Glasgow at the helm of excellence in innovative cutting-edge bioengineering solutions.

One of the recent software projects is on a java-based statistical framework for integration of shotgun metagenomics datasets with other meta'omics technologies, called CViewer, and developed by my former PhD student, Dr Orges Koci. Here are some of the video demos:



Additionally, with the BINGO Group, I am exploring the role of gut microbiota and its interaction with the diet and the immune system in health and disease:
Tweets by BINGO_Group

I also work extensively with NUI Galway, Ireland with Professor Vincent O'Flaherty, Dr Florence Abram, and Dr Gavin Collins in understanding anaerobic digestion processes, sharing multiple PhD students/PDRA staff in the capacity of a co-supervisor. Below is the schematic for one of the completed projects:

Visiting Opportunities

Within the limits of my existence, and the time frames I am not very busy (usually summer and immediately before and after Christmas break), I tend to support talented visiting PDRAs/PhD students in my lab and equip them with the bioinformatics and statistics skills. If you think you have an exciting project that aligns with my research goals, and if there are any mobility/travel schemes that can enable you to visit me, I'd be more than happy to support you in them. In the past five years, I have accommodated over 25 visitors, and they are listed here.

Research Grants

    Medium Scale to Large Scale Grants

  1. With James Hutton Institute, UK, University of Durham, UK, University of Strathclyde, UK, University of Newcastle, UK, and National Institute of Agricultural Botany, UK
    Building a Decision Support Tool for Potato Blackleg Disease (DeS-BL) (2020-2023), BBSRC UKRI Strategic Priorities Fund - Bacterial Plant Diseases BB/T010657/1, [PI:I Toth, R Neilson, P Skelsey, L Dupuy, J Milner, BK Mable, UZ Ijaz, A Sadanandom, M Stalham, A Kleczkowski, G Jones, D Walker, G Saddler, E Anderson, J Wilson, S Alexander, C Lambourne, and M Taylor] ~£2M (To Glasgow: ~£360K)
    The overarching priority of this translational research project is to develop an integrated suite of decision support tools for farmers, agronomists and policy makers to facilitate management of Pectobacterium atrosepticum (Pba), the most economically damaging bacterial plant pathogen in the UK. This causes potato blackleg disease which affects both seed and ware producers across all sectors of the potato industry, e.g. fresh, processed, and salad in an industry of c.a. 3000 growers producing >6M tonnes of potatoes from 120,000 ha of land p.a. The UK's seed potato industry is world renowned and the basis of a highly respected global export market. For the seed industry, blackleg, and therefore the outcomes of this project, affect the whole supply chain from those producing high grade seed, mainly in the north of Scotland,to distributors across the UK and exporters worldwide.

    Industrial Partners

    Media coverage:
  2. With University of Strathclyde, UK and Greater Glasgow and Clyde Health Board
    A novel dietary therapy to control recurrence of gut inflammation in children with Crohn's disease in remission (2020-2023), JP Moulton Charitable Foundation, [PI:K Gerasimidis, R Russell, R Hansen, S Milling, P Henderson, D Wilson, N Rattray, and UZ Ijaz] £520,527

  3. With University of Strathclyde, UK and NHS Greater Glasgow and Clyde Health Board
    Unravelling the dietary triggers of Crohn's disease and their interplay with the microbiome and host (2020-2023), Crohn's & Colitis Foundation, [PI:K Gerasimidis, R Russell, R Hansen, S Milling, UZ Ijaz, and N Rattray] £745,631
    A liquid-only diet, using specialized drinks, is a very effective treatment for active Crohn's disease (CD), in children. Treatment with this liquid-only diet for 6-8 weeks resolves disease symptoms, improves markers of inflammation in blood and feces, and heals the gut. It is probably the best, side-effect free, treatment we can offer to patients with CD. This liquid diet works most likely by altering the bacteria that live within our gut. However, it is a very restrictive and monotonous diet to follow for long-term disease management, particularly in adults. Our recent studies also show that the effect of the liquid-only diet to reduce gut inflammation is lost, in most patients, within just 2 weeks of reintroduction of normal diet. Therefore, in this project we aim to identify the vital dietary ingredients responsible for the triggering of gut inflammation and then study how these interact with our body's immune system and bacteria within our gut. A secondary aim of this study is to test how a new food-based diet for CD, also known as CD-TREAT diet, will control the activation of gut inflammation when patients return to their normal diet, following treatment with the liquid-only diet.
  4. With Moredun Research Institute, UK
    Gill health in scottish farmed salmon (2018-2022), The Scottish Aquaculture Innovation Centre (SAIC), [Lead Commercial Partner: Fish Vet Group; Lead Academic Partner: Scotland's Rural College (SRUC); Other Academic Partners: University of Glasgow School of Engineering (CJ Smith & UZ Ijaz)] £2.3M (To Glasgow: £154,694)
    This project represents an unprecedented industry-wide collaboration of all major salmon producers in Scotland and other key industry stakeholders and academic partners to tackle gill disease that poses a significant challenge to salmon aquaculture globally. It is associated with reduced performance and elevated mortality on affected sites, and can result in difficulties in maintaining effective sea lice control. Since the emergence of a form of gill disease (amoebic gill disease, or AGD) in Scotland in 2011, multifactorial gill conditions, often termed complex gill disease (CGD), have emerged as an even greater challenge. Several pathogens have been implicated in cases of CGD, but our ability to detect them has surpassed our understanding of their clinical significance. Furthermore, the importance of other potential contributors to CGD (for example, environmental factors and management practices) is poorly characterised, and effective means of disease mitigation or prevention remain to be determined. Therefore, the overarching objective of this project is to identify actions and measures that can be used to prevent, reduce, or treat gill disease in farmed salmon by: characterising cases of CGD to develop a consistent definition of the disease; improving our understanding of the factors that drive gill disease via epidemiologic studies; creating evidence-based information and decision support regarding gill disease and fish husbandry; providing knowledge on the gill microbiome, exploring its role in the molecular pathology of gill health, and assessing how it changes under different conditions; and assessing the efficacy of potential treatments for gill disease via treatment trials.

    Outcomes: [P114,P118]
  5. With Asian Institute of Technology, Thailand
    Optimising decentralised low-cost wastewater infrastructure by managing the microbes (2017-2020), EPSRC Global Challenges Research Fund EP/P029329/1. [PI:WT Sloan, T Koottatep, UZ Ijaz, L Cronin, J Reboud, and S Connelly] £1,192,000
    In this project, we aim to innovate biotechnologies enabling low-cost, sustainable decentralised wastewater treatment by characterizing, understanding and ultimately managing the complex microbial communities that underpin treatment in systems innovated by the Asian Institute of Technology in Thailand. To do this we will establish the biological limits of operation of these systems, identify biological predictors of failure in the system and establish robust and effective means of mitigating failure in the field. The research draws on novel application of statistics, bioinformatics, molecular microbial ecology, robotics and machine learning, and low-cost pathogen detection technologies.

    Industrial Partner (Additional Industrial Support: £50K)

    Outcomes: [P72,P81,P83,P91,P103]
  6. With University College Cork, Ireland
    A microbial basis for Atlantic Salmon energetics (2017-2020), BBSRC-Ireland (SFI) joint funding of research BB/P001203/1, [BBSRC PI:M LLewellyn, UZ Ijaz, WT Sloan, N Metcalfe], [Irish PI:P McGinnity, P Connolly, T Reed] (BBSRC: £587,860; SFI: €638,903)
    The overall aim of this project is to establish the microbial basis for different energetic phenotypes in Atlantic salmon. In doing so, we will establish the role of microbiota in influencing host performance, growth and energy economy (energetic phenotype). We will establish the link between salmon energetic phenotype and microbiome diversity a) in a population of wild juvenile salmon that will express natural variation in both traits; and in laboratory-reared fish in simulated aquaculture conditions at the b) freshwater and c) marine life stages. We will also establish the role for intestinal microbiota in driving maladaptive energetic phenotypes in farmed salmon escaped or released into the wild using: a) domesticated farmed fish and b) captive-bred wild fish. Finally, we will establish the basis for microbial energetic differences using ex-vivo and transplantation approaches via a) development of an artificial salmon microbiome system to validate microbial energetic profiles we find in fresh and saltwater settings, and b) transplantation of ex-vivo microbiota into salmon, sequence-based evaluation of transplantation success and energetic phenotype follow-up.

    Industrial Partners (Additional Industrial Support: £300K)

    Media coverage:
    Outcomes: [P104,P111,P118,P119]
  7. Stable Isotope Probing with Resonance Raman Cell Sorting to profile influence of ocean acidification on microbial carbon fixation (2016-2017), NERC NE/P003826/1. [PI:H Yin, M Cusack, UZ Ijaz] £141,110
    The overarching goal of this research is to develop an enabling technology to investigate the influence of environmental factors on microbial communities by linking physiological activities of individual micro-organisms with community diversity and function. To achieve this, we will combine advances in Resonance Raman Activated Cell Sorting and Stable Isotope Probing for rapid screening and sorting of a community, based upon a quantitative measure of specific physiological activities of individual cells. Metagenomic analyses of these functionally sorted cells will further identify the species in each category. As a proof of concept, we aim to develop this technology by interrogating the effect of ocean acidification on marine primary production.

    Outcomes: [P66]
  8. With University of Manchester, UK
    Interactions between the Microbiome, Immunophenotype and Genome in PsA (IMIGPA) (2016-2018). Arthritis Research UK - Microbiome Pathfinder Award.
    [PI:A Barton, I McInnes, C O'Neil, UZ Ijaz, S Milling, S Siebert, I Roberts, A McBain, M Rattray] £298512.50 (To Glasgow: £139,485)
    This research project aims to test whether bacteria living on the skin or in the gut predispose to the risk of developing psoriatic arthritis (PsA) or influence response to treatment in patients with PsA. We will analyse the bacterial communities from the skin and stool samples of patients with PsA, both before and after therapy, and investigate whether the bacterial community composition correlates with the genetic make-up of patients or the immune cells they carry.

    Outcomes: [P33,P40,P60]
  9. With University of Dundee, UK
    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.
    [Co-PI:C Marwick, Co-PI:G Douce, J Coia, D DarkSaddleBrown, UZ Ijaz, P Donnan, J Lindstrom, M Bennie, C Wiuff, P Davey] £366,638 (To Glasgow: £197,734)
    Clostridium difficile remains the major cause of antibiotic associated diarrheal disease, especially for the elderly. Whilst acquisition of the infection continues to be linked to healthcare facilities, increasing numbers of patients are infected in the community. Further, changes to antibiotic prescribing have affected the prevalence of specific ribotypes of the organism. We aim to characterise the molecular epidemiology of C. difficile in community and hospital associated strains in Scotland, especially ribotype 078, now the most common strain in Scottish hospitals. In particular we are developing bioinformatics tools and protocols that will ultimately allow evaluation of the genomic content of clinical strains in real-time. Additionally, we aim to develop a unique electronic resource for C. difficile research in Scotland that will link patient health data and C. difficile whole genome sequencing.

    Partners:

    Outcomes: [P35,P45,P69,P101]
  10. Research Fellowships

  11. Lord Kelvin Adam Smith Leadership Fellow: Understanding microbial communities through in situ environmental 'omic data synthesis (Nov 2014-Oct 2019) [PI:UZ Ijaz] ~£160K
    Acknowledgement: Received salary from November 2017 to October 2019 (2 years)

    Outcomes: [P29,P30,P32,P38,P39,P41,P42,P44,P46,P48,P49,P50,P57,P62,P64,P65,P72,P73,P74,P75,P76,P77,P78,P79,P80,P81,P82,P83,P84,P85,P86,P87,P88,P89,P90,P91,P92,P93,P94,P95,P96,P97,P98,P99,P100,P101,P102,P103,P104,P105]
  12. NERC Independent Research Fellow: Understanding microbial communities through in situ environmental 'omic data synthesis (Nov 2014-Oct 2019), NERC NE/L011956/1. [PI:UZ Ijaz] £425,507
    Acknowledgement: Received salary from November 2014 to October 2017 (3 years)
    The purpose of my fellowship research is to integrate different sources of 'omics data in environmental science for microbial community analysis. The computational based comparative analysis of DNA sequences may provide information about genome structure, gene function, metabolic and regulatory pathways and how microbial genomes evolve. However, to fully delineate microbial activity and its response to environmental factors, it is necessary to include all levels of gene products, mRNA, protein, metabolites, as well as their interactions. I propose to use large-scale whole genome metagenomic sequencing for assessment of taxonomic and functional diversity of microbial communities. The data generated by metagenomic experiments are both enormous and inherently noisy, containing fragmented DNA sequences representing as many as thousands of microbial species. After using pre-filtering steps, including removal of redundant, low quality sequences, the short DNA sequences are assembled together into longer contigs of overlapping reads, and these contigs may then be scaffolded into full genomes in a bottom-up approach. Having obtained the assembled contigs, the obvious next step is to use publically available databases to annotate the coding regions in these contigs. This will tell us WHAT functionality is available and provide information on WHO is there, the metagenomic sequences are binned, i.e., by associating a particular sequence with an organism. This can be done by either searching for phylogenetic markers or by looking for similar sequences in existing public databases. The end result is the community profile of different samples in terms of organismal abundances within each sample.
    Whilst metagenomic analysis gives a profile of the microbial community at a specific place or time, and their potential functional, it does not reveal which genes are actually being transcribed. I thus propose to integrate sequencing-based metatranscriptomics in which total RNA (a proxy for gene activity) is extracted from microbial community, converted to cDNA and sequenced without the need for cloning. This will provide information on the regulation and expression profiles of complex communities by enabling quantitative measurements of dynamic expression of RNA molecules and their variation between different states reflecting the genes that are being actively expressed at any given time. However, the story is still far from complete, as we do not have direct evidence of the metabolism within a cell. To give a more complete picture of living organisms, I will integrate metabolomics which will provide unique chemical fingerprints that are a function of specific cellular activity. In particular, the focus will be on identifying habitat-specific endogenous and exogenous metabolites along distinct geochemical conditions. These metabolites will be detected using two-dimensional gas chromatography coupled with mass spectrometry. They will be related to the expression levels from transcriptomes using information on metabolic pathways readily available from annotating metagenomic sequences. In this way we will integrate all three sources of information, mapping the metatranscriptome onto the assembled annotated metagenomes and reconciling the reconstructed metabolic pathways with observations on metabolite concentrations and fluxes. From this we will be able to predict the metabolic function of the entire community not simply who is there.

    Outcomes: [P29,P30,P32,P38,P39,P41,P42,P44,P46,P48,P49,P50,P57,P62,P64,P65,P72,P73,P74,P75,P76,P77,P78,P79,P80,P81,P82,P83,P84,P85,P86,P87,P88,P89,P90,P91,P92,P93,P94,P95,P96,P97,P98,P99,P100,P101,P102,P103,P104,P105]
  13. 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 my salary from this grant in 2014 before I started my NERC fellowship

    Outcomes: [P27,P34,P36,P43,P48,P54]
  14. With University of Liverpool, UK
    Research Fellow (Infrastructure & Environment): Development of instrumental and bioinformatic pipelines to accelerate commercial applications of metagenomics approaches, Innovate UK (2012-2014). PI: Yvette Visser (Unilever Plc). £2,300,000 (To Glasgow: £284,030)
    Acknowledgement: Received salary from 2012 to 2014 (2.5 years)

    Industrial Partners:

    Outcomes: [P31,P39,P42]
  15. Small Scale Research Projects, Studentships, and Mobility Grants (Primarily Supporting Early Career Researchers)

  16. International Research Support Initiative Program (2019-2020), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2019/8794 [PhD Student: Alam Khan (Quaid-i-Azam University, Islamabad, Pakistan); Foreign supervisor: UZ Ijaz] ~£7K
  17. 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. [Early career researcher and PI:P Salmon; Other co-applicants: UZ Ijaz, K Gerasimidis, and M Lewellyn] £19,800
  18. Use of novel mixomics tools to investigate intestinal fungi in Crohn's disease (2019-2020), Royal Liverpool and Broadgreen University NHS Hospital Trust Afflication for Funding 2019/2020. [Early career researcher and co-investigator: Dr Alessandra Frau (University of Liverpool); PI: Prof Chris Probert (University of Liverpool); Partners: Prof S Allen (Alder Hey), UZ Ijaz] £6,996.83
  19. Analysis pipeline for sea ice reconstructions using ancient environmental DNA (2018), 6 months research visit under Forskerprosjekt-KLIMAFORSK Project No. 273455 [Early career researcher and PI:Dr Jessica L. Ray (NORCE, Norway); Host: UZ Ijaz] NOK 124K (~£12K)
    Outcomes: [P89]
  20. 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. [PI:K Gerasimidis, G Ramage, RK Russell, R Hansen, UZ Ijaz] £9,980
  21. Cabbages, microbes and diversity. Glasgow Polyomics ISSF Consolidator Funding,Wellcome Trust grant 105614/Z/14/Z. [PI: Professor Barbara Mable; PhD Student: Elizabeth Mittel; Co-supervisor: UZ Ijaz] £7,000

    Outcomes: [P112]
  22. Variation in the human pharyngeal microbiome in health and disease (ISSF Catalyst Funding), Welcome Trust [PI: Dr Jan Lindstrom; PhD Student: Asha Ram; Co-supervisor: UZ Ijaz] £20,300
  23. To perform faecal metabolomics and combine with existing whole genome metagenomics. Glasgow Polyomics ISSF Consolidator Funding [PI: Dr Konstantinos Gerasimidis; Named collaborator: UZ Ijaz] £6,995
    Outcomes: [P82]
  24. Kelvin Smith PhD Scholarships 2015/16 - PhD Student: Zihan Dai (~£78,000)

    Outcomes: [P93,P99,P102]
  25. Kelvin Smith PhD Scholarships 2014/15 - PhD Student: Elizabeth Mittell (~£120,000)
    Outcomes: [P112]
  26. Kelvin Smith PhD Scholarships 2012/13 - PhD Student: Asha Rani (~£106,012)
  27. Other National/International Projects as a Participant

  28. 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. [Eary career researcher and investigator: Dr Ozan Gundogdu (LSHTM, London); Other investigators: Prof Nicolae Corcionivoschi (AFBI, Belfast), Prof Nick Dorrell (LSHTM, London); Partner: UZ Ijaz] £50,000

    Industrial Partner

    Outcomes: [P76,P109]
  29. With Norwegian Research Centre (NORCE)
    AGENSI - A Genetic View into Past Sea Ice Variability in the Arctic (2019-2023), ERC, €2.615M
    [PI:Stijn De Schepper; Main participants: Jessica L. Ray, Katrine Sandnes Skaar, Aud Larsen, Dag Inge Blindheim, The Bjerknes Community, Nansen Legacy researchers; International participants: Umer Z. Ijaz, Ruediger Stein, and Sofia Ribeiro]
    Arctic sea ice decline is the exponent of the rapidly transforming Arctic climate. The ensuing local and global implications can be understood by studying past climate transitions, yet few methods are available to examine past Arctic sea ice cover, severely restricting our understanding of sea ice in the climate system. This project develops and apply a novel sea ice proxy that exploits genetic information stored in marine sediments, sedimentary ancient DNA (sedaDNA). This innovation uses the genetic signature of phytoplankton communities from surface waters and sea ice as it gets stored in sediments. This wealth of information has not been explored before for reconstructing sea ice conditions. Preliminary results from my cross-disciplinary team indicate that our unconventional approach can provide a detailed, qualitative account of past sea ice ecosystems and quantitative estimates of sea ice parameters. We will address fundamental questions about past Arctic sea ice variability on different timescales, information essential to provide a framework upon which to assess the ecological and socio-economic consequences of a changing Arctic. This new proxy is not limited to sea ice research and can transform the field of paleoceanography.

    Media coverage: Ancient DNA as a new tool for past climate change, November 29, 2018.
    Outcomes: [P89]
  30. With Norwegian Research Centre (NORCE)
    Environmental ancient DNA as proxy for sea ice reconstructions (aDNAPROX) (2017-2019), Forskerprosjekt-KLIMAFORSK. NOK 8561K
    [Project manager and work package coordinator: Stijn De Schepper; Other work package coordinators: Jorund Stromsoe, Jessica L. Ray; Supporting team: Christofer Troedsson, Katrine Sandnes-Skaar, Henrik Sadatzki, Trond Dokken, Eystein Jansens, Ice2Ice team; International participants: Prof. R. Stein, Kenneth Mertens, Umer Z. Ijaz]
    Sea ice cover is a "canary in the coal mine" for the Arctic and global climate state. Sea ice extent is rapidly decreasing and Arctic summers are predicted to be sea-ice free by 2050. Because sea ice is crucial for sustaining local Arctic communities, international ecosystem services and biological diversity, there is an urgent need to understand variability in sea ice cover over longer time scales. Our best tool to predict future sea ice coverage is to understand past trends. Research activities investigating past natural variability in sea ice extent rely on microfossils and/or organic biomarkers produced by organisms that are associated with sea ice. Both methods have inherent assumptions and limitations, which make sea ice reconstructions non-trivial. To improve our understanding of sea ice history in the recent geological past, with special attention to rapid climate change events (e.g. Daansgaard-Oeschger cycles, Heinrich events), we propose to develop a new proxy for determining past sea ice cover using environmental ancient DNA (aDNA) from Arctic sediments.

    Media coverage: Announcement [Google translated (English)]
    Outcomes: [P89]
  31. With University of Liverpool, UK
    How does the microbiome of the hypochlorhydric stomach promote gastric tumourigenesis? AICR. [PI:M Pritchard, A Varro, N Hall] Collaborator: UZ Ijaz. £199,357
    Gastric cancer is a common and life threatening malignancy and most cases develop as a consequence of chronic Helicobacter pylori infection. Cancers of the stomach arise via a series of premalignant stages, including gastric atrophy. This latter condition is characterised by a loss of acid-secreting parietal cells, which results in elevated gastric pH (hypochlorhydria). Recent murine studies have suggested that additional microorganisms colonise the stomach when acid secretion is impaired and that these bacteria act as cofactors to promote the development of gastric cancer. However, other conditions which are associated with reduced gastric acid secretion, such as longterm acid suppressing drug use are not associated with gastric cancer development in the same way. We therefore hypothesise that specific changes occur in the gastric microbiome in association with H. pylori associated gastric atrophy and that these act as cofactors to promote gastric cancer development in susceptible individuals. We propose to investigate the gastric microbiome using 16S rDNA sequencing in a well established and validated transgenic mouse model in which gastric cancer develops as a result of chronic Helicobacter infection. In addition we will analyse the microbiome present in gastric biopsy samples that have already been collected from well characterised cohorts of human patients who have reduced gastric acid production due to a variety of causes (H. pylori infection, medication or autoimmune). We anticipate that these studies will lead to the development of specific microbial biomarkers that are associated with gastric cancer development. These may have future clinical utility for relatively non-invasive screening of individuals who are susceptible to developing gastric cancer. In addition, we will test the efficacy of one antibiotic and one probiotic strategy (the details of which will be determined by the results of our sequencing studies) for reducing susceptibility to Helicobacter-induced gastric cancer in mice.

    Outcomes: [P58,P108]
  32. With University of Surrey, UK
    Do gut bacteria have a role in the aetiology of type 2 diabetes? European Foundation for the study of Diabetes ISRCTN07813749. PI: Dr Denise Robertson Collaborator: UZ Ijaz.
    The main objectives of this study are to assess whether: colonic microflora, intestinal permeability, and endotoxaemia (plasma levels of lipopolysaccharide) in patients with type 2 diabetes differ from those of matched obese and lean subjects; and manipulation of colonic microflora with prebiotic carbohydrate supplement improves glucose tolerance via improvements in intestinal permeability and endotoxaemia.

    Outcomes: [P51,P52,P68]
  33. With London School of Hygiene & Tropical Medicine, UK
    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. PI: Dr Jeroen Ensink Collaborator: UZ Ijaz. $4,798,496

    Outcomes: [P38]
  34. With Hellenic Centre for Marine Research, Greece
    ENVIRONMENTS: Discovering habitat terms in EOL Contents. Encyclopedia of Life 2013 Rubenstein Research Fellowship. Blog, PI: Dr Evangelos Pafilis International collaborator: UZ Ijaz. $50,000

    Outcomes: [P37]
  35. Previous Research Grants

    (My role is mentioned whether I was involved in the capacity of a Research Fellow, PostDoc or a PhD student)
  36. 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 - Research Fellow
    Provided in-kind support for travel and accommodation for the following events:
    Outcomes: [P28,P49]
  37. At University of Oxford, UK
    IDEAS Factory - Global View, EPSRC EP/I005986/1. Project Page, PI: Dr Nick Jones. £199,342 - Senior PostDoc
    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.
    GlobalView: A software for inferring multiple networks from time series data [Code]
    Software Demo:

  38. At University of Cambridge, UK
    Hybrid Three-Dimensional Ultrasound, EPSRC EP/F016476/1. Project Page, PI: Professor Richard Prager. £385,012 - PostDoc
    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. This has made the data acquisition process easy for clinicians as they can hold the 3D probe with one hand and with other hand can click on the keypad to acquire the volumetric data. The system was then shipped 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. As a proof of concept we have carried out a feasibility study recruiting pregnant women attending for routine obstetric ultrasound scans and have obtained promising results (77% to 83% reliability in clinical trials).
    Developed System:

    Software Demo:

    Partner:

    Outcomes: [P21,P22,P23,P24,P25,P26]
  39. At Jeju National University, South Korea
    The 2nd Phase Brain Korea 21 (BK21) Project - PhD
    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:

    Concentration distribution estimation of fluid using electrical impedance tomography: In this research, the problem of imaging the concentration distribution (by modelling as a stochastic convection-diffusion equation) of a given substance moving in a strong electrolyte in a pipeline is considered.

    Servo track writing error estimation in hard disks: The vibration of disk or head during servo writing proess induces servo track writing error that directly affects the performance of the hard disk drive, especially while writing. We developed an approach to use position error signal and controller output to estimate the servo track writing error and compensate for it in a feed forward manner using Comb filter.

    Adaptive state estimator for Inverse Heat Conduction Problems (IHCP): I developed the adaptive estimator to estimate time-dependent boundary heat flux in two-dimensional heat conduction domain with heated and insulated walls. For the estimation, the algorithm requires only the temperatures measured at the insulated walls. In addition, the estimator also predicts the bias in the measurements. In modeling the system, it is assumed that the input flux and bias sequence dynamics can be modeled by a semi-Markov process. By incorporating the semi-Markovian concept into a Bayesian estimation technique, the estimator consists of a bank of parallel, adaptively weighted, Kalman filters.

    Outcomes: [P3,P5,P9,P17,P18]
  40. At Jeju National University, South Korea
    Korea Science and Engineering Foundation Grant No. R01-2007-000-20155-0 - PhD
    Mammography phantom studies using 3D electrical impedance tomography: In this study, we considered a 3D mammography geometry to detect breast cancer based on the electrical impedance tomography. The finite element method formulation of the forward 3D electrical impedance tomography model with complete electrode model is considered for the rectangular mammography geometry. For the discretization, Galerkin method is adopted on linear tetrahedral elements. The regularized one-step Gauss-Newton method is employed as the inverse solver. A test phantom designed specifically to resemble the shape of compressed breasts is used with the ACT 4 measurement system.

    Tracking moving interfacial boundary in sedimentation process using 3D electrical impedance tomography: The monitoring of solid-fluid suspensions under the influence of gravity is widely used in industrial processes. By considering sedimentation layers with different electrical properties, non-invasive methods such as electrical impedance tomography can be used to estimate the settling curves and velocities.

    Outcomes: [P10,P13,P14,P15,P19,P20]
  41. At Jeju National University, South Korea
    Research Grant of Jeju National University - PhD

    Outcomes: [P19]
  42. At Jeju National University, South Korea
    Korea Research Foundation Grant No. KRF-2005-013-D00075 - PhD
    Moving interfacial boundary estimation in stratified flows of two immiscible liquids using electrical resistance tomography:

    True: Solid; Estimated: Thin lines

    Outcomes: [P12]
  43. At Jeju National University, South Korea
    Hyocheon Research Fund of the Cheju National University Development Foundation - PhD
    Dynamic process monitoring using electrical capacitance tomography:We propose a dynamic Electrical Capacitance Tomography (ECT) image reconstruction algorithm based on the extended Kalman filter (EKF) to estimate the rapidly time-varying changes in the permittivity distribution within the time taken to acquire a full set of independent measurement data. The ECT inverse problem is formulated as a state estimation problem in which the system is modeled with the state equation and the observation equation. Comparison is done with existing modified Newton Raphson (mNR) method to illustrate the superior performance of the EKF approach.

    Outcomes: [P4]
  44. At Jeju National University, South Korea
    Korea Science and Engineering Foundation Grant No. R01-2004-000-0040-0 - PhD

    Outcomes: [P11, P16]
  45. At Jeju National University, South Korea
    2D Electrophoresis Gel Image Processor for Matlab, Ministry of Commerce, Industry and Energy, Korea Grant No. S1005503 - PhD
    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:

    Outcomes: [P1,P2]

Supervision/Mentoring

Bioinformatics

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: Dr Umer Z. Ijaz (for correspondence/issues/usage)
Co-Investigator: Dr Ciara Keating
IT technician and sysadmin: Grant 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
Cost of cluster (to date): ~£180K+:

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)
macalpine.eng.gla.ac.uk (96 hyperthreaded cores)
moore.eng.gla.ac.uk (96 hyperthreaded cores)
howe.eng.gla.ac.uk (96 hyperthreaded cores) [temporarily unaccessible for maintenance purposes]

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 [temporarily unaccessible for maintenance purposes]

Legacy nodes (Old)

quince-srv2.eng.gla.ac.uk (64 cores)
quince-nas.eng.gla.ac.uk
network drive

Profile

Teaching

Recent Invites and Organizations

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
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)
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

Collaborators

Selected Publications

[P120] P Dessi, C Sanchez, S Mills, FG Cocco, M Isipato, UZ Ijaz, G Collins, and PNL Lens
Carboxylic acids production and electrosynthetic microbial community evolution under different CO2 feeding regimens
Bioelectrochemistry, 2020. DOI:10.1016/j.bioelechem.2020.107686
[P119] R Kazlauskaite, B Cheaib, J Humble, C Heys, UZ Ijaz, S Connelly, WT Sloan, J Russell, L Martinez-Rubio, J Sweetman, A Kitts, P McGinnity, P Lyons, and M Llewellyn
Deploying and in vitro gut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-MOS® on the Atlantic salmon (Salmo salar) gut microbiome
bioRxiv, 328427, 2020. DOI:10.1101/2020.10.07.328427
[P118] R Kazlauskaite, B Cheaib, C Heys, UZ Ijaz, S Connelly, WT Sloan, J Russell, L Martinez-Rubio, J Sweetman, A Kitts, P McGinnity, P Lyons, and M Llewellyn
Development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim
bioRxiv, 327858, 2020. DOI:10.1101/2020.10.06.327858
[P117] AC Trego, S O'Sullivan, C Quince, S Mills, UZ 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
[P116] C Keating, M Bolton-Warberg, J Hinchcliffe, R Davies, S Whelan, AHL Wan, RD Fitzgerald, SJ Davies, UZ Ijaz, and CJ Smith
Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae
bioRxiv, 222604, 2020. DOI:10.1101/2020.08.10.222604
[P115] AC Trego, S O'Sullivan, E Porca, S Mills, C Quince, UZ Ijaz, and G Collins
Methanogenic granules are replicated, whole microbial communities with reproducible responses to environmental cues
PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-16883/v1], 2020.
[P114] VB Birlanga, G McCormack, UZ Ijaz, E McCarthy, CJ Smith, and G Collins
Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon
PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-29747/v1], 2020.
[P113] 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, RK Russell, P McGrogan, CA Edwards, UZ Ijaz, and K Gerasimidis
Alterations in intestinal microbiota of children with celiac disease at time of diagnosis and on gluten-free diet
Gastroenterology, accepted for publication (2020).
[P112] E Mittell, CA Cobbold, UZ Ijaz, EA Kilbride, KA Moore, and BK Mable
Feral populations of Brassica oleracea along Atlantic coasts in western Europe
Ecology and Evolution, accepted for publication (2020).
[P111] B Cheaib, P Yang, R Kazlauskaite, E Lindsay, C Heys, M De Noa, P Schaal, T Dwyer, WT Sloan, UZ Ijaz, and M. S. Llewellyn
Unpicking the mysterious symbiosis of Mycoplasma in salmonids
bioRxiv, 209767, 2020. DOI:10.1101/2020.07.17.209767
[P110] K Gkikas, K Gerasimidis, S Milling, UZ Ijaz, R Hansen, and RK 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
[P109] A McKenna*, UZ Ijaz*, C Kelly, M Linton, WT Sloan, BD Green, U Lavery, N Dorrell, BW 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
[P108] S Ciucci, C Duran, A Palladini, UZ Ijaz, FP Sterbini, L Masucci, G Cammarota, G Ianiro, P Spuul, M Schroeder, SW Grill, BN Parsons, M Pritchard, B Posteraro, M Sanguinetti, G Gasbarrini, A Gasbarrini, and CV Cannistraci
Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection
bioRxiv, 005587, 2020. DOI:10.1101/2020.03.24.005587
[P107] F Cholet, UZ Ijaz, and CJ 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
[P106] M Logan, K Gkikas, V Svolos, B Nichols, S Milling, DR Gaya, JP Seenan, J Macdonald, R Hansen, UZ Ijaz, RK 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
[P105] B Cheaib, H Seghouani, UZ 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
[P104] C Heys, B Cheaib, A Busetti, R Kazlauskaite, L Maier, WT Sloan, UZ 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
[P103] S Connelly, T Pussayanavin, R Randle-Boggis, A Wicheansan, S Jampathong, C Keating, UZ Ijaz, WT 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
[P102] Z Dai, M Sevillano, S Calus, QM Bautista-de los Santos, AM Eren, PWJJ van der Wielen, UZ Ijaz, and AJ Pinto
Disinfection exhibits systematic impacts on the drinking water microbiome
Microbiome, 8:42, 2020. DOI:10.1186/s40168-020-00813-0
[P101] CA Jukes, UZ Ijaz, A Buckley, J Spencer, J Irvine, D Candlish, JV Li, JR 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, 2019. DOI:10.1080/19490976.2019.1678996
[P100] AC Stratakos, UZ Ijaz, P Ward, M Linton, C Kelly, L Pinkerton, P Scates, J McBride, I Pet, A Criste, D Stef, JM Couto, WT Sloan, N Dorrell, BW 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
[P99] I Cotto, Z Dai, L Huo, CL Anderson, KJ Vilardi, UZ Ijaz, W Khunjar, C Wilson, H De Clippeleir, K Gilmore, E Bailey, and AJ 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
[P98] M Logan, CM Clark, UZ Ijaz, L Gervais, H Duncan, V Garrick, L Curtis, E Buchanan, T Cardigan, L Armstrong, C Delahunty, DM Flynn, A Barclay, R Tayler, E McDonald, S Milling, R Hansen, K Gerasimidis, and RK Russell
The reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction
Alimentary Pharmacology & Therapeutics, 2019. DOI:10.1111/apt.15425
[P97] T Lynch, G Peirano, T Lloyd, R Read, J Carter, A Chu, JA Shaman, JP Jarvis, E Diamond, UZ 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
[P96] HM Baer, E McDonald, A Ferguson, UZ Ijaz, RJB Nibbs, and SWF Milling
Identification of IBD immunopathotypes [Abstract]
Gut, 68:A69-A70, 2019. DOI:10.1136/gutjnl-2019-BSGAbstracts.134
[P95] A Frau, R Hough, UZ Ijaz, B Campbell, J Kenny, N Hall, J Anson, AC Darby, and CSJ Probert
Metabolomics & Multi-omics analysis of Crohn's disease [Abstract]
Gut, 68:A68, 2019. DOI:10.1136/gutjnl-2019-BSGAbstracts.131
[P94] H Song, E Kang, H Soh, H Chung, J Chun, S Yoon, UZ Ijaz, and Y Koh
Multi-omics approaches to understand gastric mucosa-associated lymphoid tissue (MALT) lymphoma [abstract]
Hematological Oncology, 34:339-340, 2019. DOI:10.1002/hon.2631
[P93] M Sevillano, Z Dai, S Calus, QM Bautista-de los Santos, AM Eren, PWJJ van der Wielen, UZ Ijaz, and AJ Pinto
Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems
Science of the Total Environment, accepted for publication (2020). DOI:10.1101/675561 (bioRxiv 675561, 2019)
[P92] J Plancq, JM Couto, UZ Ijaz, PR Leavitt, and JL 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
[P91] AC Trego, E Galvin, C Sweeney, S Dunning, C Murphy, S Mills, C Nzeteu, C Quince, S Connelly, UZ 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
[P90] A Frau, JG Kenny, L Lenzi, BJ Campbell, UZ Ijaz, CA Duckworth, MD Burkitt, N Hall, J Anson, AC Darby, and CSJ 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
[P89] S De Schepper, JL Ray, KS Skaar, H Sadatzki, UZ 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
[P88] KA Bain, E McDonald, F Moffat, M Tutino, M Castelino, A Barton, J. Cavanagh, UZ Ijaz, S Siebert, IB McInnes, A Astrand, S Homes, and SWF 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, 2019. DOI:10.1111/bjd.18008
[P87] C Gauchotte-Lindsay, TJ Aspray, M Knapp, and UZ 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
[P86] MJ Ormsby, M Logan, SA Johnson, A McIntosh, G Fallata, R Papadopoulou, E Papachristou, R Hansen, UZ Ijaz, RK Russell, K Gerasimidis, and DM 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
[P85] A Frau, UZ Ijaz, R Hough, BJ Campbell, JG Kenny, N Hall, J Anson, AC Darby, and CSJ Probert
Multi-omics analysis suggests an active role of fungi in Crohn's disease [abstract]
Journal of Crohn's and Colitis, 13(suppl 1):S545, 2019. DOI:10.1093/ecco-jcc/jjy222.966
[P84] V Svolos, R Hansen, UZ Ijaz, L Gervais, H Duncan, R Tayler, A Barclay, D Flynn, V Garrick, L Curtis, E Buchanan, T Cardigan, DR Gaya, S Milling, RK Russell, and K Gerasimidis
CD-TREAT a novel dietary therapy of active Crohn's disease using the exclusive enteral nutrition paradigm [abstract]
Journal of Crohn's and Colitis, 13(suppl 1):S416-S417, 2019. DOI:10.1093/ecco-jcc/jjy222.726
[P83] AC Trego, C Morabito, S Mills, S Connelly, I Bourven, G Guibaud, C Quince, UZ 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
[P82] V Svolos, R Hansen, B Nichols, C Quince, UZ Ijaz, RT Papadopoulou, CA Edwards, D Watson, A Alghamdi, A Brejnrod, C Ansalone, H Duncan, J Salmond, D Bolognini, R Klopfleisch, DR Gaya, S Milling, RK Russell, and K Gerasimidis
Treatment of active Crohn's disease with an ordinary food-based diet that replicates exclusive enteral nutrition
Gastroenterology, 2019. DOI:10.1053/j.gastro.2018.12.002
[P81] J De Vrieze, UZ Ijaz, AM 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
[P80] A Kostrytsia, S Papirio, L Morrison, UZ Ijaz, G Collins, PNL 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
[P79] F Cholet, UZ Ijaz, and CJ 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
[P78] I Reich, UZ Ijaz, M Gormally, and CJ 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
[P77] A Frau, UZ Ijaz, B Campbell, A Darby, J Kenny, N Hall, and C Probert
Bacterial and fungal communities in faeces and biopsies in IBD [Abstract]
Gut, 67:A58-A59, 2018. DOI:10.1136/gutjnl-2018-BSGAbstracts.115
[P76] UZ 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
[P75] K Gerasimidis, K Zafeiropoulou, M Mackinder, UZ Ijaz, H Duncan, E Buchanan, T Cardigan, CA Edwards, P McGrogan, and RK 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
[P74] C Keating, D Hughes, T Mahony, D Cysneiros, UZ Ijaz, CJ 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
[P73] O Koci, M Logan, V Svolos, RK Russell, K Gerasimidis, and UZ Ijaz
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights
PeerJ, 6:e5047, 2018. DOI:10.7287/10.7717/peerj.5047
Relevant Software: pyTag
[P72] J De Vrieze, AJ Pinto, WT Sloan, and UZ 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
[P71] A Frau, D Jonkers, J Penders, M Pierik, UZ Ijaz, B Campbell, A Darby, J Kenny, N Hall, and C Probert
Crohn's disease is characterised by a fungal dysbiosis [Abstract]
Journal of Crohn's and Colitis, 12(suppl 1):S550-S551, 2018. DOI:10.1093/ecco-jcc/jjx180.985
[P70] V Svolos, B Nichols, D Bolognini, C Quince, UZ Ijaz, RT Papadopoulou, C Ansalone, J Salmond, R Klopfleisch, DR Gaya, RK Russell, R Hansen, K Gerasimidis, and S Milling
The gut microbiota composition and metabolic activity of HLA-B27 transgenic rats with gut inflammation resembles the dysbiotic characteristics of human inflammatory bowel disease [Abstract]
Journal of Crohn's and Colitis, 12(suppl 1):S549-S550, 2018. DOI:10.1093/ecco-jcc/jjx180.983
[P69] KE Dingle, X Didelot, TP Quan, DW Eyre, N Stoesser, CA Marwick, J Coia, D Brown, S Buchanan, UZ Ijaz, C Goswami, G Douce, WN Fawley, MH Wilcox, TEA Peto, AS Walker, and DW 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
[P68] C Pedersen, UZ Ijaz, E Gallagher, F Horton, RJ Ellis, E Jaiyeola, T Duparck, D Russell-Jones, P Hinton, PD Cani, RM La Ragione, and MD 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
[P67] A Joyce, UZ Ijaz, C Nzeteu, A Vaughan, SL Shirran, CH 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
Code
[P66] X Yuan, Y Song, Y Song, J Xu, Y Wu, A Glidle, M Cusack, UZ 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
[P65] ST Calus, UZ 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
NanoAmpli-Seq - Sample processing and sequence library preparation workflow DOI:10.17504/protocols.io.u26eyhe
NanoAmpli-Seq - Bioinformatics workflow DOI:10.17504/protocols.io.u25eyg6
Code
*Joint corresponding authors
[P64] ND Ritchie, UZ Ijaz, and TJ 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
[P63] M Logan, UZ 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
[P62] AZ Ijaz, T Jeffries, UZ Ijaz, K Hamonts, and BK Singh
Extending SEQenv: A taxa-centric approach to environmental annotations of 16S rDNA sequences
PeerJ, 5:e3827, 2017. DOI:10.7717/peerj.3827
Relevant Software: SEQenv-Ext, TaxaSE System
[P61] SK Cho, KW Jung, DH Kim, JC Kwon, UZ Ijaz, and SG Shin
Bacterial community analysis in upflow multi-layer anaerobic reactor (UMAR) treating high-solids organic wastes
Biotechnology Progress, 2017. DOI:10.1002/btpr.2540
[P60] M Castelino, M Tutino, J Moat, UZ Ijaz, R Parslew, A Al-Sharqi, RB Warren, C Quince, P Ho, M Upton, S Eyre, and A Barton
Comparison of the bacterial stool microbiota in established psoriatic arthritis (PSA) and psoriasis (PSC) - exploratory analysis of pilot data [Abstract]
Annals of the Rheumatic Diseases, 76:1087, 2017. DOI:10.1136/annrheumdis-2017-eular.3404
[P59] V Svolos, R Hansen, UZ Ijaz, C Quince, D Watson, A Alghamdi, A Brejnrod, C Ansalone, R Klopfleisch, S Milling, DR Gaya, RK Russell, and K Gerasimidis
Dietary manipulation of the healthy human and colitic rat gut microbiome by cd-treat diet and exclusive enteral nutrition [Abstract]
Gut, 66:A202, 2017. DOI:10.1136/gutjnl-2017-314472.394
[P58] BN Parsons*, UZ Ijaz*, R D'Amore, M Burkitt, R Eccles, L Lenzi, CA Duckworth, AR Moore, L Tiszlavicz, A Varro, N Hall, and DM 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
[P57] A Ho*, UZ Ijaz*, TKS Janssens, R Ruijs, SY Kim, W de Boer, A Temorshuizen, WH van der Putten, and PLE 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
[P56] S Connelley, SG Shin, RJ Dillon, UZ Ijaz, C Quince, WT Sloan, and G Collins
Bioreactor scalability: laboratory-scale idealisation influences performance, ecology and community physiology in expanded granular sludge bioreactors
Frontiers in Microbiology, 8:664, 2017. DOI:10.3389/fmicb.2017.00664
[P55] V Svolos, R Hansen, UZ Ijaz, C Quince, D Watson, A Alghamdi, A Brejnrod, C Ansalone, S Milling, D Gaya, R Russell, and K Gerasimidis
Dietary manipulation of the healthy human and colitic murine gut microbiome by CD-TREAT diet and exclusive enteral nutrition; a proof of concept study [Abstract]
Journal of Crohn's and Colitis, 11 (suppl 1): S29-S30, 2017. DOI: 10.1093/ecco-jcc/jjx002.045
[P54] UZ Ijaz, C Quince, L Hanske, N Loman, ST Calus, M Bertz, CA Edwards, DR Gaya, R Hansen, P McGrogan, RK 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
[P53] J De Vrieze, ME Christiaens, D Walraedt, A Devooght, UZ 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
[P52] C Pedersen, P Hinton, E Gallagher, F Horton, R Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, GR Gibson, T Duparc, PD Cani, J Wright, D Russell-Jones, RL Ragione, and MD Robertson
Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 Diabetes [Abstract]
Proceedings of the Nutrition Society, 75(OCE3), 2016. DOI:10.1017/S0029665116001191
[P51] C Pedersen, E Gallagher, F Horton, RJ Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, T Duparc, PD Cani, GR Gibson, P Hinton, J Wright, D Russell-Jones, R La Ragione, and MD 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
[P50] JL Ray, J Althammer, KS Skaar, P Simonelli, A Larsen, D Stoecker, A Sazhin, UZ Ijaz, C Quince, JC 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
[P49] L Sinclair*, UZ Ijaz*, LJ Jensen, M Coolen, C Gubry-Rangin, A Chronakova, A Oulas, C Pavloudi, J Schnetzer, A Weimann, AZ 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
Accompanying Software: seqenv
*Joint first authors
[P48] K Gerasimidis, M Bertz, C Quince, K Brunner, A Bruce, E Combet, ST Calus, N Loman, and UZ 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
[P47] V Svolos, R Hansen, K Hughes, UZ Ijaz, C Quince, D Gaya, R Russell, and K Gerasimidis
The impact of 'Crohn's Disease-TReatment-with-EATing' diet (CD-TREAT diet) and exclusive enteral nutrition on healthy gut bacteria metabolism [Abstract]
Journal of Crohn's and Colitis, 10(suppl 1):S14-S15, 2016. DOI:10.1093/ecco-jcc/jjw019.017
[P46] C Varsos, T Patkos, A Oulas, C Pavloudi, A Gougousis, UZ Ijaz, I Filiopoulou, N Pattakos, EV 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
Accompanying Software: RvLab
[P45] N De Souza, G Douce, C Goswami, UZ Ijaz, D SaddleBrown, J Coia, P Donnan, C Wiuff, P Davey, M Bennie, J Lindstrom, and C Marwick
Genetic relatedness among clinical Clostridium difficile strains in one Scottish region
In 26th ECCMID, Amsterdam, Netherlands, 9-12 April, 2016
[P44] QM Bautista-do los Santos, JL Schroeder, MC Sevillano-Rivera, R Sungthong, UZ Ijaz, WT Sloan, and AJ 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
[P43] K Gerasimidis, UZ Ijaz, C Edwards, RK Russell, C Quince, and R Hansen
Response to Kaakoush et al.
American Journal of Gastroenterology, 111(7):1033-1034, 2016.
[P42] M Schirmer, R D'Amore, UZ Ijaz, N Hall, and C Quince
Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing
BMC Bioinformatics, 17:125, 2016. DOI:10.1186/s12859-016-0976-y
Code
[P41] AJ Pinto, DN Marcus, UZ Ijaz, QM Bautista-de los Santos, GJ 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
Data
[P40] M Castelino, S Eyre, M Tutino, J Moat, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, A Barton
Bacterial Skin Microbiome in Psoriatic Arthritis - Pilot Data from Psoriatic Plaques on Dry Skin Sites from Patients with Psoriasis (PsC) and Psoriatic Arthritis (PsA) [abstract]
Arthritis & Rheumatology, 67 (suppl 10), 2015. DOI:10.1002/art.39448
[P39] R D'Amore*, UZ Ijaz*, M Schirmer, J Kenny, R Gregory, AC 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
Code
*Joint first authors
[P38] B Torondel, JHJ Ensink, O Gundogdu, UZ Ijaz, J Parkhill, F Abdelahi, V-A Nguyen, S Sudgen, W Gibson, AW Walker, 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
Code
[P37] E Pafilis, S Frankfield, L Fanini, S Faulwetter, C Pavloudi, J Schnetzer, A Vasileiadou, UZ Ijaz, C Arvanitidis, R Stevenson, and LJ Jensens
Identification of Environmental Ontology terms in text and the annotation of the Encyclopedia of Life
In TDWG 2014 Annual Conference, Jönköping, Sweden, October 27-31, 2014.
[P36] C Quince*, UZ Ijaz*, N Loman, AM Eren, D Saulnier, J Russell, SJ Haig, ST Calus, J Quick, A Barclay, M Bertz, M Blaut, R Hansen, P McGrogan, RK 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
[P35] C Goswami, UZ Ijaz, DJ SaddleBrown, CA Marwick, C Wiuff, A Banks, JE Coia, and GR Douce
Understanding molecular epidemiology of Clostridium Difficile in Scotland
In 5th International Clostridum Difficile Symposium, May 19-21, 2015, Bled, Slovenia.
[P34] MJ Khan, C Quince, V S, UZ Ijaz, N Loman, ST Calus, J Quick, SJ Haig, MG Shaikh, CA 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 [Abstract]
Proceedings of the Nutrition Society, 74(OCE1):E75, 2015.
[P33] M Castelino, S Eyre, J Moat, G Fox, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, and A Barton
The skin microbiome in psoriatic arthritis: methodology development and pilot data [Abstract]
Lancet, 385(Supplement 1):S27, 2015.
[P32] JM Couto, UZ Ijaz, VR Phoenix, M Schirmer, and WT Sloan
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment
Current Microbiology,71(2), 296-302, 2015.
[P31] M Schirmer, UZ Ijaz, R D'Amore, N Hall, WT Sloan, and C Quince
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
Nucleic Acids Research, 2015.
Code
[P30] D Savio, L Sinclair, UZ Ijaz, P Stadler, AP Blaschke, GH Reischer, G Bloeschl, RL Mach, AKT Kirschner, AH Farnleitner, and A Eiler
Bacterial diversity along a 2 600 km river continuum
Environmental Microbiology. doi: 10.1111/1462-2920.12886, 2015.
[P29] K Harris, TL Parsons, UZ 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.
Accompanying Software: NMGS
[P28] J Alneberg, BS Bjarnason, I de Bruijn, M Schirmer, J Quick, UZ Ijaz, L Lahti, NJ Loman, AF Andersson, and C Quince
Binning metagenomic contigs by coverage and composition.
Nature Methods, 2014.
Accompanying Software: CONCOCT, TAXAassign
[P27] K Gerasimidis, N Loman, J Quick, ST Calus, UZ Ijaz, P McGrogan, CA Edwards, C Quince, and R. K. Russell
Metagenomic analysis of the gut microbiome during a course of Exclusive Enteral Nutrition (EEN) provides novel insights on mechanism of EEN action [Abstract]
Journal of Crohn's and Colitis, 8(Supplement 2):S393-S394, 2014.
[P26] UZ Ijaz, RJ Housden, GM Treece, RW Prager, and AH Gee.
Multi-directional scattering models for 3-dimensional ultrasound imaging

Journal of Ultrasound in Medicine, 32(4):699-714, April 2013.
[P25] E Dyer, UZ Ijaz, RJ Housden, RW Prager, AH Gee, and GM Treece.
A clinical system for three-dimensional extended field of view ultrasound
British Journal of Radiology, 85: e919-e924, October 2012. Relevant Software: Stradwin
[P24] UZ Ijaz, RW Prager, AH Gee, and GM Treece
A study of similarity measures for in vivo 3D ultrasound volume registration
Acoustical Imaging, 30:315-323, 2011.
[P23] UZ Ijaz, RW Prager, AH Gee, and GM Treece
Particle swarm optimization for in vivo 3D ultrasound volume registration
Acoustical Imaging, 30:345-354, 2011.
[P22] UZ Ijaz, RW Prager, AH Gee, and GM Treece
Optimisation strategies for ultrasound volume registration
Measurement Science and Technology, 21(8): 085803 (17pp), July 2010.
[P21] RW Prager, UZ Ijaz , AH Gee, and GM Treece
Three-dimensional ultrasound imaging
Proceedings of the Institution of Mechanical Engineers Part H-Journal of Engineering in Medicine, 224(2):193-223, 2010.
[P20] AK Khambampati, UZ Ijaz, JS Lee, S Kim, and KY Kim
Phase boundary estimation in electrical impedance tomography using Hooke and Jeeves pattern search method
Measurement Science and Technology, 21(3):035501 (13pp), March 2010.
[P19] UZ Ijaz, AK Khambampati, JS Lee, S Kim, and KY Kim
Nonstationary phase boundary estimation in electrical impedance tomography using unscented Kalman filter
Journal of Computational Physics , 227(15):7089.7112, July 2008.
[P18] UZ Ijaz, AK Khambampati, MC Kim, S Kim, JS Lee, and KY Kim
Particle swarm optimization technique for elliptic region boundary estimation in electrical impedance tomography
AIP Conference Proceedings, 914:896-901, 2007.
[P17] UZ Ijaz, AK Khambampati, JS Lee, KY Kim, MC Kim, and S Kim
Electrical resistance imaging of two-phase flow through rod bundles
AIP Conference Proceedings, 914:844-849, 2007.
[P16] BS Kim, UZ Ijaz, JH Kim, MC Kim, S Kim, and KY Kim
Nonstationary phase boundary estimation in electrical impedance tomography based on the interacting multiple model scheme
Measurement Science and Technology, 18(1):62-70, January 2007.
[P15] UZ Ijaz
Dynamic phase boundary estimation in electrical impedance tomography
PhD thesis, Cheju National University, Korea, December 2007.
slides [PPT]
[P14] AK Khambampati, A Rashid, UZ Ijaz, S Kim, M Soleimani, and KY 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, August 2009.
[P13] UZ Ijaz, SI Chung, AK Khambampati, KY 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), June 2008.
[P12] S Kim, UZ Ijaz, AK Khambampati, KY Kim, MC Kim, and SI Chung
Moving interfacial boundary estimation in stratified flows of two immiscible liquids using electrical resistance tomography
Measurement Science and Technology, 18(5):1257-1269, May 2007.
[P11] JH Kim, BC Kang, SH Lee, BY Choi, MC Kim, BS Kim, UZ Ijaz, KY 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, October 2006.
[P10] UZ Ijaz, BS Kim, TJ Kao, AK Khambampati, S Kim, MC Kim, JC Newell, D Isaacson, and KY Kim
Mammography phantom studies using 3D electrical impedance tomography with numerical forward solver
In FBIT 2007:379-383.
[P9] UZ Ijaz, JH Kim, AK Khambampati, MC Kim, S Kim, and KY Kim
Concentration distribution estimation of fluid through electrical impedance tomography based on interacting multiple model scheme
Flow Measurement and Instrumentation, 18(1):47-56, March 2007.
[P8] JH Kim, BY Choi, UZ Ijaz, BS Kim, S Kim, and KY Kim
Directional algebraic reconstruction technique for electrical impedance tomography
Journal of The Korean Physical Society, 54(4):1439-1447, April 2009.
[P7] YS Kim, SH Lee, UZ Ijaz, KY Kim, and BY Choi
Sensitivity map generation in electrical capacitance tomography using mixed normalization models
Measurement Science and Technology, 18(7):2092-2102, July 2007.
[P6] FA Khan, UZ Ijaz, KY Kim, MJ Kang, and WC Song
Policy-based management in ad hoc network using geographic routing
Lecture Notes in Computer Science, 3961:237-246, 2006.
[P5] S Kim, UZ Ijaz, AK Khambampati, KY Kim, and MC Kim
Effect of Current Injection Patterns on Dynamic Electrical Resistance Imaging for Fast Transient Processes
In 5th IEEE Conference on Sensors, 2006.
[P4] UZ Ijaz, JH Kim, MC Kim, S Kim, JW Park, and KY Kim
Nondestructive dynamic process monitoring using electrical capacitance tomography
Key Engineering Materials, 321-323(2):1671-1674, 2006.
[P3] UZ Ijaz, AK Khambampati, MC Kim, S Kim, and KY 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, October 2007.
[P2] UZ Ijaz, SU Chaudhary, SM Ahn, BH Lee, and KY Kim
Computational strategies for protein quantitation in 2D electrophoresis gel image processor for Matlab
In FBIT 2007: 129-134.
[P1] UZ Ijaz, SU Chaudhary, SM Ahn, BH Lee, and KY Kim
2D electrophoresis gel image processor for Matlab
In ICHIT 2006, Jeju, Korea, November 9-11, 2006.

Last Updated by Dr Umer Zeeshan Ijaz on October, 2020.