Intro

Bioinformatics is becoming a vital component of a wide variety of disciplines, from engineering to medicine and ecology, and from drug delivery (pharmacogenomics) to medicinal chemistry. With theoretical foundations in Information Engineering (Discrete Mathematics, Control Theory, System Theory, Information Theory, and Statistics), my research has delivered a suite of systems and products that has allowed me to carve out a niche within an extensive collaborative network (>200 academics).

This is as a result of leading the Environmental'Omics Lab in Infrastructure & Environment Division, James Watt 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.
The purpose of my research is to integrate different sources of 'omics data (e.g., metagenomics, metatranscriptomics, metabolomics, and metaproteomics) in environmental and medical science for microbial community analysis. I particularly work on the informatics side of Microbial Ecology field, and within it, whole-genome shotgun metagenomics is a new field that came about as a consequence of advancement in next generation sequencing platforms in the past decade. CONCOCT software, originating from Glasgow in a collaborative venture, was one of the first international attempts at separating microbial genomes from mixed communities which created several opportunities to map out not only taxonomy (which species are there) but their function (what they are doing) also. With a PhD student (Dr Orges Koci), as a followup to CONCOCT, we have developed a java-based statistical framework for integration of shotgun metagenomics datasets with other meta'omics technologies, called CViewer. Here are some of the video demos:

Side by side, hand-held DNA sequencers such as Oxford MinIon were introduced and our NanoAmpli-Seq technology was then one of the first attempts at reducing the sequencing errors to tag microbial species based on sequence similarities.
The impact was materialised soon after (in the past few years) when we started using these new tools in clinical as well as in environmental sciences. These have affected and benefited both academic and non-academic audiences, the latter one as a result of the software used in analysing the datasets and then leading on to the development of products e. g. CD-Treat Diet developed in 2019 which, is increasingly emphasizing the importance of modulation of gut microbiome to improve health, and is currently being evaluated in NHS as an alternative Dietary Intervention to manage and control Crohn's disease. My software tools enables us to sift through thousands of features (from multi-omics modalities), identify what changes differentially in response to treatments e.g., with University of Liverpool we have identified changes in stomach microbiome with different risk levels of gastric tumor; with MoyPark (Largest poultry producer in Ireland), we have studied their production systems (dietary feeds) and highlighted microbial ecology and mechanistic understanding of diets supplemented with Omega-3 associated with increased weight production of the poultry.
In Climate and Environmental Science, reconstructing sea ice change is one of the most challenging topics in paleoceanography. By applying techniques from molecular ecology on marine sediments, supported through a massive sampling campaign in the Arctic and the Greenland Sea, my analytical tools have been instrumental in finding diverse DNA signatures and paleodiversity shifts back to circa 100,000 years ago.
As the technology is new, it is also affecting stakeholders such as policy-makers (e.g. on how to go about microbial community surveys in built environment, National Academies of Sciences, Engineering, and Medicine. 2017). In Aquaculture, with Professor Sloan and colleagues at Institute of Biodiversity, Animal Health & Comparative Medicine, I am involved in SalmoSim Gut Simulator project which, is a bespoke gut simulation machine for research on aquafeed nutrition, veterinary pharmaceuticals and microbiome health of Atlantic Salmon, and which, has recently led to a start-up and has won silicon-valley contract with Calysta. In Agriculture, with colleagues at College of Medical, Veterinary & Life Sciences, since 2020, I am part of a Bacterial Plant Diseases UK consortium to counter diseases that threaten crop production, forestry, horticulture, woodlands and wider biodiversity, and cause severe economic, environmental and social impact.
In Water & Waste Water Treatment, with Professor Sloan, I am part of a recently funded EPSRC programme grant to deliver decentralised technologies to rural Scotland. This has its roots in an EPSRC grant where through solar septic tank technology (invented by colleagues at Thailand), enhances degradation of waste and informs management strategies in LMIC. This technology has been installed in a School in Bangalore India as part of a Scottish Government initiative. Furthermore, in collaboration with Welsh Water and NVP Energy Ltd and colleagues at O'Flaherty Lab (NUI Galway, Ireland), we designed, commissioned and monitored a full-scale (88 m3) high-rate anaerobic reactor directly treating municipal wastewater at ambient temperatures in Wales, UK. This is a new technological advancement which could provide more sustainable treatment options for municipal wastewater at low temperatures. Lastly, using my software, we accidently discovered a bacteria that could fundamentally re-shape efforts to cut the huge amount of electricity consumed during wastewater clean-up and upended century old thinking resulting in a press release by EPSRC.
With collaborators, we 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 also trying to involve engineering in my projects that now include: Raman spectroscopy enabled microfluidics; and a hardware system for integrating liquid handling, incubation and sensing. 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.

I also work with our sister group at NUI Galway, Ireland, particularly with Professor Vincent O'Flaherty, Dr Florence Abram, and Dr Gavin Collins on 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:

Note: With Dr Ciara Keating, I am editing a special issue on "Drinking Water Microbiome" in Microorganisms (Impact Factor: 4.152). Deadline for manuscript submission is 30 September 2021. Submit the manuscripts here.

Grants

I am involved in £18M+ grant money funded as a Principal Investigator(PI)/Co-Investigator(Co-I)/International Participant (with £10,323,746 brought to University of Glasgow since 2014 that includes £8,706,880 funding from UK Research and Innovation (UKRI) through BBSRC, 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 82 publications listed here. Overall, the grant fundings have resulted in 180+ publications as per my ORCID iD iconorcid.org/0000-0001-5780-8551 record.

    Medium Scale to Large Scale Grants

  1. 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:
  2. A novel dietary therapy to control recurrence of gut inflammation in children with Crohn's disease in remission (2020-2023), JP Moulton Charitable Foundation £520,527
    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
  3. Unravelling the dietary triggers of Crohn's disease and their interplay with the microbiome and host (2020-2023), Crohn's & Colitis Foundation $745,631
    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
  4. 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
  5. 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)
  6. 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
  7. 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:
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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.
  13. 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)]

  14. Research Fellowships

  15. 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)
  16. 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)
  17. 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
  18. 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
  19. 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
  20. 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

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

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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 £6,996.83
    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
  31. 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
  32. 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
  33. Leadership Training Bursaries for NERC fellows (2016) £23,100 FEC
    Note: Tuition fee for Cambridge Advanced Leadership Programme (Judge Business School, University of Cambridge, UK)
  34. 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
  35. 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
  36. 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
  37. Kelvin Smith PhD Scholarships 2015/16 (~£78,000)
    PhD student: Zihan Dai
    Supervisors: U. Z. Ijaz (lead), and A. J. Pinto
  38. Kelvin Smith PhD Scholarships 2014/15 (~£120,000)
    PhD student: Elizabeth Mittell
    Supervisors: B. K. Mable (lead), U. Z. Ijaz, and C. Cobbold
  39. Kelvin Smith PhD Scholarships 2012/13 (~£106,012)
    PhD student: Asha Ram
    Supervisors: J. Lindstrom (lead), U. Z. Ijaz, and T. Evans
  40. 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
  41. 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
  42. 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)
  43. 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
  44. Send-A-Newbie Award (YAPC::EU 2012) ~£600

  45. Other Grants

  46. 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
  47. 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
  48. 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)
  49. 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)
  50. 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
  51. Korea Science and Engineering Foundation Grant No. R01-2007-000-20155-0 (2007-2008)
    PhD student and PI: U. Z. Ijaz
  52. Research Grant of Jeju National University (2007)
    PhD student and PI: U. Z. Ijaz
  53. Korea Research Foundation Grant No. KRF-2005-013-D00075 (2005)
    PhD student and PI: U. Z. Ijaz
  54. Hyocheon Research Fund of the Cheju National University Development Foundation (2005)
    PhD student and PI: U. Z. Ijaz
  55. Korea Science and Engineering Foundation Grant No. R01-2004-000-0040-0 (2004)
    PhD student and PI: U. Z. Ijaz
  56. 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
  57. Korean Government IT Scholarship (2004-2008), Institute of Information Technology Assessment, Korea ₩56,000,000 (~$56,000)
  58. JNU Category-A Scholarship (2004-2006)
    Note: Full tuition fee waiver during PhD coursework
  59. GIKI Merit Scholarship (2001-2003)
    Note: Awarded after standing 2nd in the entrance exam for MS; Full tuition fee waiver during MS coursework and received a monthly stipend of PKR 5000/month

Supervisions

To date, with my involvement, 28 PhD students have successfully defended their theses, some 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 (utilising the Orion cluster). In majority of the cases, I have conceded support on bioinformatics and statistical analyses.

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 40 visitors, and they are listed here.

PhD Opportunities

Please note that I am looking to recruit talented students with computational/statistical background on the following projects, all involving microbial informatics and numerical ecology:
PhD Project 1: Phylogeny-aware metrics for microbial community assembly driven by ecological and evolutionary principles
PhD Project 2: Improving network inference in complex microbial communities: test case using soil bacteria associated with crops
PhD Project 3: Null Models to delineate microbial community assembly
PhD Project 4: Development of meta-analyses framework for microbial community data

To apply for the above projects, please visit this link. Please find below the list of staff/students I have mentored/or am mentoring:

    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.
  1. Dr Ciara Keating (University of Glasgow, UK)
    Mentors (2020-): 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]
  2. Dr Anubhab Khan (University of Glasgow, UK)
    Hosted on Orion Cluster (2021-)
    Mentors (2021-): B. K. Mable (lead), and U. Z. Ijaz [Grant: What can you learn from a fly? Biting insects as noninvasive samplers, Leverhulme Trust]
  3. 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]
  4. 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]
  5. Dr Tarah Lynch (University of Calgary, Canada)
    Virtual visitor to Environmental'Omics Lab (2019-)
    Mentor (2019-): U. Z. Ijaz
  6. 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]
  7. Dr Ben Nichols (University of Glasgow, UK)
    Hosted on Orion Cluster (2020-)
    Mentors (2018-): K. Gerasimidis (lead), and U. Z. Ijaz [Grant: Supported by grants to BINGO Group]
  8. 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]
  9. 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]
  10. 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]
  11. Dr Adrian Ho (Leibniz University, Germany)
    Mentor (2015-): U. Z. Ijaz [Adrian's work is supported by Wissenschaftliche Mitarbeiter since 2017]
  12. 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]
  13. Dr Julien Plancq (University of Glasgow, UK)
    Mentors (2017-2019): J. Toney (lead), and U. Z. Ijaz [Grant: Project: ALKENoNE, ERC Starting Grant]
  14. 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]
  15. 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)]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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)]
  22. 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]
  23. 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]
  24. Dr Fabien Cholet (University of Glasgow, UK)
    Mentors (2020-): C. J. Smith (lead), and U. Z. Ijaz [Grant: Biofiltration by biological design, Royal Academy of Engineering-Scottish Water Senior Reserach Fellowship]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. Dr Ozan Gundogdu (London School of Hygiene & Tropical Medicine, UK)
    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]
  31. 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]
  32. 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]
  33. 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)]
  34. 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]
  35. 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]

  36. Current PhD Students

  37. Yuchen Fu (University of Glasgow, UK)
    Supervisors: H. Yin (lead), U. Z. Ijaz, and A. Glidle
  38. Yecang Chen (University of Glasgow, UK)
    Supervisors: H. Yin (lead), and U. Z. Ijaz
  39. Kelly Stewart (University of Glasgow, UK)
    Supervisors: C. J. Smith (lead), and U. Z. Ijaz
  40. Caroline Kerbiriou (University of Glasgow, UK)
    Supervisors: K. Gerasimidis (lead), S. Milling, G. Raptis, and U. Z. Ijaz
  41. Konstantinos Gkikas (University of Glasgow, UK)
    Supervisors: K. Gerasimidis (lead), S. Milling, R. K. Russell, and U. Z. Ijaz

  42. Past PhD Theses

  43. 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)
  44. 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)
  45. 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)
  46. 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)
  47. 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
  48. 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)
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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)
  57. 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
  58. 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
  59. 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)
  60. 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)
  61. 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
  62. 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)
  63. 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
  64. 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
  65. 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
  66. 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)
  67. 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)
  68. 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)
  69. 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)
  70. 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

  71. Past MSc Theses

  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. Liu Kai (University of Glasgow, UK)
    MSc Engineering Project, 2020
    Project: Snakemake workflows for metagenomics data
    Supervisor: U. Z. Ijaz (lead)
  82. Wang Chen (University of Glasgow, UK)
    MSc Engineering Project, 2020
    Project: Phylogeny-aware metrics for microbial community surveys
    Supervisor: U. Z. Ijaz (lead)
  83. 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)
  84. 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)
  85. 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
  86. 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
  87. 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
  88. 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
  89. 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)
  90. 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
  91. 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
  92. 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
  93. 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
  94. 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
  95. 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
  96. Orges Koci (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2015
    Project: Metagenomic Contigs Visualisation Tool
    Supervisor: U. Z. Ijaz (lead)
  97. 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)

  98. Summer Placement Students

  99. 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
  100. 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

  101. Other MSc Theses in James Watt School of Engineering, Glasgow

  102. 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)
  103. Ann-Cathrin Reissmann
    Project: Analysis of Intermodal Interactions at Side Street Junctions (2021)
    Supervisors: A. McCay (1st), and U. Z. Ijaz(2nd)
  104. Lewen Qi
    Project: Comparing the finite element method to peridynnamics (2020)
    Supervisors: A. McBride (1st), and U. Z. Ijaz(2nd)
  105. 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)
  106. Jinxin Chen
    Project: How will the 5G technology change the geotechnical engineering practice? (2020)
    Supervisors: Z. Gao (1st), and U. Z. Ijaz(2nd)
  107. 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)
  108. Jinliang Wang
    Project: The effect of dilation angle on slope stability analysis (2019)
    Supervisors: Z. Gao (1st), and U. Z. Ijaz(2nd)
  109. Fernando Ardavin
    Project: Feasibility Study of the Mayan Train in Mexico's Yucatan Peninsula (2019)
    Supervisors: K. Ampountolas (1st), and U. Z. Ijaz(2nd)
  110. Xiaoqian Wang
    Project: Modelling creep and rate effects in soils (2019)
    Supervisors: S. Wheeler (1st), and U. Z. Ijaz(2nd)
  111. 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)
  112. 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)
  113. 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)
  114. Chao Zhou
    Project: Computational Modelling of Granular Systems (2018)
    Supervisors: A. McBride (1st), and U. Z. Ijaz(2nd)
  115. 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)
  116. 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)
  117. 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)

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

  119. 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)
  120. 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)
  121. 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)
  122. Yeoh Ya Yun
    Individual Project 4S (SIT4017P) (2019-2020)
    Project: Depression Analysis: Spectrogram Deep Learning
    Supervisors: H. Nguyen (1st), and U. Z. Ijaz (2nd)
  123. 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)
  124. 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)
  125. 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)

  126. Informatics Support (including external visitors)

  127. Valentine Okonkwo (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019-
  128. Claire Thom (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019-
  129. Dominic Quin (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2020-
  130. Alison Graham (O'Flaherty Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab 2020-
  131. Jasmine Connolly (O'Flaherty Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab 2020-
  132. Victor Birlanga (Collins Lab, NUI Galway, Ireland)
    Visitor to Environmental'Omics Lab 2017, 2018
    Virtual visitor to Environmental'Omics Lab 2019-
  133. Ali Z. Ijaz (Hawkesbury Institute for the Environment, Australia)
    Visitor to Environmental'Omics Lab 2015
  134. Marco Kreuzer (University of Reading, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2015
  135. Dr Hussain Jaffery (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2017
  136. Dr Kathryn Jane Gray (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019
  137. Kym Bain (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2020
  138. Hannah Baer (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2020
  139. Anabelle Ferguson (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018; Undergraduate summer 2018 intern
  140. Hannah Craven (Institute of Cancer Sciences, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2021
  141. Dr Lydia Bach (Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2020-2021
  142. Hyojin Song (Seoul National University, South Korea)
    Visitor to Environmental'Omics Lab 2019 (5 months) [Mobility grant: Seoul National University]
    Foreign supervisor: U. Z. Ijaz
  143. Alam Khan (Quaid-i-Azam University, Islamabad, Pakistan)
    Visitor to Environmental'Omics Lab 2019-2020 (6 months) [Grant: International Research Support Initiative Program under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2019/8794]
    Foreign supervisor: U. Z. Ijaz
  144. 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
  145. Dr Ranjith Rajendran (Dental School, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2017
  146. Christopher Delaney (Dental School, University of Glasgow, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2017
  147. Mauro Tutino (University of Manchester, UK)
    Visitor to Environmental'Omics Lab 2017
  148. Cadi Davies (London School of Hygiene & Tropical Medicine)
    Virtual visitor to Environmental'Omics Lab 2019
  149. Maria Catalina Sevillano Rivera (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2015-2020)
  150. Irmarie Cotto (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  151. Solize Vosloo (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  152. Katie Vilardi (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  153. Sadia Khan (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)

Teaching

  • In University of Glasgow:
    • ENG5322: Engineering Skills M (2018-)
    • ENG2079: Civil Engineering Skills 2 (2018-)
    • ENG4110P: Individual Project 4 (2018-)
    • ENG5041P: Individual Project 5 (2020-)
    • ENG5059P: MSc Projects (2019-)
    • BIOL 5173P: MSc Bioinformatics Projects (2018-)
    • BIOL5172: Metagenomics (2015-2017)
    • EU's ES1103 COST action hackathons (organization and teaching)
      • 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
    • Teaching in foreign institutes: 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)
  • 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, GIKI Institute of Engineering Sciences and Technology (GIKI), 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: British Pakistani
21+ years of work experience since June 1999 with no career breaks


Appointments


Recent Invites and Organizations

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
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

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
Cost of cluster (to date): ~£211K+:
  • 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

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

About

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Publications

My research is both interdisciplinary and transdisciplinary, and has resulted in 180+ publications (PUBLICATIONS.pdf; ORCID iD iconorcid.org/0000-0001-5780-8551) with those that are recently gaining citations can be found at my Google Scholar profile. Summary statistics of publications (n=35) in high impact academic journals (top 5% of journals have impact factors (IF) approximately equal to or greater than 6 as per discussion here) along with their rankings is given below with the annotated list of publications given afterwards.

Summary Statistics

Journal Name Journal Metrics (JCR 2020) Number of Publications
Nature Methods IF: 28.547, Ranking: 1/77 (Biochemical Research Methods) 1
DOI:10.1038/nmeth.3103
Gastroenterology IF: 22.682, Ranking: 4/92 (Gastroenterology & Hepatology) 2
DOI:10.1053/j.gastro.2020.08.007
DOI:10.1053/j.gastro.2018.12.002
Nucleic Acids Research IF: 16.971, Ranking: 8/298 (Biochemistry & Molecular Biology) 1
DOI:10.1093/nar/gku1341
Nature Communications IF: 14.919, Ranking: 4/73 (Multidisciplinary Sciences) 1
DOI:10.1038/s41467-021-22135-x
Microbiome IF: 14.650, Ranking: 8/137 (Microbiology) 6
DOI:10.1186/s40168-020-00908-8
DOI:10.1186/s40168-020-00813-0
DOI:10.1186/s40168-020-0789-0
DOI:10.1186/s40168-018-0449-9
DOI:10.1186/s40168-021-01134-6
DOI:10.1186/s40168-021-01143-5
Water Research IF: 11.236, Ranking: 2/98 (Water Resources) 2
DOI:j.watres.2019.115268
DOI:j.watres.2016.12.042
Proceedings of the IEEE IF: 10.961, Ranking: 8/273 (Engineering, Electrical & Electronic) 1
DOI:10.1109/JPROC.2015.2428213
American Journal of Gastroenterology IF: 10.864, Ranking: 9/92 (Gastroenterology & Hepatology) 1
DOI:10.1038/ajg.2015.357
ISME Journal IF: 10.302, Ranking: 7/166 (Ecology) 1
DOI:10.1038/s41396-019-0457-1
Gut Microbes IF: 10.245, Ranking: 10/92 (Gastroenterology & Hepatology) 2
DOI:10.1080/19490976.2021.1930871
DOI:10.1080/19490976.2019.1678996
Bioresource Technology IF: 9.642, Ranking: 1/14 (Agricultural Engineering) 3
DOI:10.1016/j.biortech.2018.09.044
DOI:10.1016/j.biortech.2021.125786
DOI:10.1016/j.biortech.2021.126098
British Journal of Dermatology IF: 9.302, Ranking: 3/68 (Dermatology) 1
DOI:10.1111/bjd.18008
Alimentary Pharmacology & Therapeutics IF: 8.171, Ranking: 13/275 (Pharmacology & Pharmacy) 3
DOI:10.1111/apt.15695
DOI:10.1111/apt.14351
DOI:10.1111/apt.15425
EBiomedicine IF: 8.143, Ranking: 17/140 (Medicine, Research & Experimental) 1
DOI:10.1016/j.ebiom.2019.03.071
Science of the Total Environment IF: 7.963, Ranking: 25/274 (Environmental Sciences) 1
DOI:10.1016/j.scitotenv.2020.141451
mBio IF: 7.867, Ranking: 15/137 (Microbiology) 1
DOI:10.1128/mBio.02790-18
Microbiology Spectrum IF: 7.171, Ranking: 18/137 (Microbiology) 1
Mills et al. 2021 (in press)
Chemosphere IF: 7.086, Ranking: 30/274 (Environmental Sciences) 1
DOI:10.1016/j.chemosphere.2021.131975
PLoS Pathogens IF: 6.823, Ranking: 3/38 (Parasitology) 1
DOI:10.1371/journal.ppat.1006653
Journal of Environmental Management IF: 6.789, Ranking: 34/274 (Environmental Sciences) 1
DOI:10.1016/j.jenvman.2021.112229
GigaScience IF: 6.524, Ranking: 10/73 (Multidisciplinary Sciences) 1
DOI:10.1093/gigascience/giy140
mSystems IF: 6.492, Ranking: 21/137 (Microbiology) 1
DOI:10.1128/mSystems.00323-20
Molecular Ecology IF: 6.185, Ranking: 7/50 (Evolutionary Biology) 1
DOI:10.1111/mec.13844

Annotated List of Selected Publications

  1. 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, accepted for publication (2021).
    #Joint corresponding authors
    Schematic:
  2. 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
    Graphical Abstract:
  3. 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:
  4. 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:
  5. 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, accepted for publication (2021).
    Schematic:
  6. 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
    Schematic:
  7. 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
    Graphical Abstract:

    Relevant Impact Case Study: NUI Galway - Transforming Sustainable Water Management: Creating Jobs and Saving Energy
  8. 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
    Graphical abstract:
  9. 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
    Community assembly approaches:
  10. 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

  11. 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
    Schematic:
  12. 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
    Sneak Peek:
  13. 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
    Sneak Peek:
  14. 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
    Schematic:
  15. 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
    Sneak Peek:
  16. 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
    Schematic:
  17. 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
    Schematic:
  18. 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
    Graphical Abstract:
  19. 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
    Sneak Peek:

  20. 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
    Graphical Abstract:
  21. 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
  22. C. Thom, C. J. Smith, G. Moore, P. Weir, and U. Z. Ijaz. Microbiome in drinking water treatment and distribution: a critical review and meta-analysis from source to tap. bioRxiv 457654, 2021. DOI: 10.1101/2021.08.30.457654
    Graphical Abstract:
  23. 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#. Key Drivers of Ecological Assembly in the Hindgut of Atlantic Cod (Gadus morhua) when Fed with a Macroalgal Supplemented diet - How Robust Is the Gut to Taxonomic Perturbation? bioRxiv 457479, 2021. DOI: 10.1101/2021.08.24.457479
    #Corresponding author
  24. 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. PREPRINT (Version 1) available at Research Square [http://dx.doi.org/10.21203/rs.3.rs-646699/v1], 2021. DOI: 10.21203/rs.3.rs-646699/v1
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
    Graphical Abstract:

    Covering the Cover: Early Age Intestinal Dysbiosis in Patients with Celiac Disease
  33. 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
  34. 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
    Video Abstract:
  35. 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
    Video Abstract:
  36. 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
    Schematic:

  37. 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:
  38. 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
    Schematic:
  39. 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
    Schematic:

  40. 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
    Schematic:

  41. 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
    Graphical Abstract:
  42. 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
  43. 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
    Schematic:
  44. 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
  45. 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
    Graphical Abstract:
  46. 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
  47. 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
  48. 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
  49. 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
  50. C. Keating, A. C. Trego, W. T. Sloan, V. O'Flaherty#, and U. Z. Ijaz#. Circular economy of anaerobic biofilm microbiomes: A meta-analysis framework for re-exploration of amplicon sequencing data. bioRxiv 424166, 2020. DOI: 10.1101/2020.12.23.424166
    #Joint corresponding authors
    Graphical Abstract:

  51. R. Kazlauskaite, B. Cheaib, J. Humble, 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. 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
  52. V. B. Birlanga, G. McCormack, U. Z. Ijaz, E. McCarthy, C. J. 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. DOI: 10.21203/rs.3.rs-29747/v1
    Schematic:

  53. A. C. Trego, S. O’Sullivan, E. Porca, S. Mills, C. Quince, U. Z. 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. DOI:10.21203/rs.3.rs-16883/v1
    #Joint corresponding authors
    Schematic:

  54. 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
  55. 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
  56. 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
  57. 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, 157(4):P1161-1162, 2019. DOI: 10.1053/j.gastro.2019.08.015
  58. 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
  59. 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
  60. 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
  61. 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
    Schematic:

  62. 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
  63. 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
  64. 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
  65. 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
    Schematic:

    Behind the Paper: Environmental ancient DNA - a game changer in paleo sea ice research?
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
    Schematic:
  72. 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
    Schematic:
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
    Schematic:

  82. 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
  83. 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
  84. 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
    Graphical Abstract:
  85. 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
  86. 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
    Schematic:
  87. 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
    Schematic:
  88. 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
  89. 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
  90. 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
  91. 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
    Schematic:

  92. 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
  93. 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
  94. 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
    Schematic:

  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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
  101. 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
    Schematic:

    Press Release: PLOS - Shifting bacterial communities in the stomach may influence cancer risk
  102. 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
  103. 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
    Graphical Abstract:
  104. 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
    Schematic:

  105. 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
    Schematic:

  106. 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
    Schematic:

  107. 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
  108. 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
  109. 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
  110. 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
  111. 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
  112. 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
  113. 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
    Schematic:

  114. 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
  115. 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
  116. 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
    Schematic:

  117. 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
  118. 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:

  119. 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
  120. 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:
  121. 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
  122. 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
  123. 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
  124. 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
  125. 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
  126. 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
  127. 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
    Schematic:
  128. 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
  129. 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
  130. 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
  131. 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
    Schematic:
  132. 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
  133. 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
  134. 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:

  135. 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
  136. U. Z. Ijaz, R. W. Prager, A. H. Gee, and Graham 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
  137. 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
    Schematic:

  138. 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
    Schematic:

  139. 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
  140. 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
  141. 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
  142. 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
    Schematic:

  143. 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:
  144. 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
  145. 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
  146. 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
  147. 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
    Schematic:
  148. U. Z. Ijaz, B. S. Kim, T. J. Kao, A. K. Khambampati, S. Kim, 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 FBIT 2007, 379-383, 2007. DOI: 10.1109/FBIT.2007.93
    Schematic:

  149. 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
  150. 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
  151. 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
    Schematic:

  152. 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
  153. 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
  154. 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
  155. 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
  156. J. S. Lee, S. I. Chung, U. Z. Ijaz, A. K. Khambampati, K. Y. Kim, and S. Kim. Electrical resistance imaging of bubble boundary in annular two-phase flows using unscented Kalman filter. In Transactions of the Korean Nuclear Society Annual Meeting, Pyeong Chang, Korea, October 25-26, 2007.
  157. S. I. Chung, U. Z. Ijaz, A. K. Khambampati, S. Kim, K. Y. Kim, and M. C. Kim. Effect of current patterns for stratified flow estimation in electrical impedance tomography. In Proceeding of the Fourth National Congress on Fluids Engineering, Kyungju, Korea, August 23-25, 2006.
  158. 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.
    Schematic:

  159. 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.
  160. 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
    Schematic:
  161. 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
    Schematic:

  162. 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
  163. 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.
  164. 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.
    Software Demo:
  165. 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.
  166. 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.
  167. 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.
  168. 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.
  169. 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.
  170. 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.

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]
    • 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. 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) [Project Page].
      Developed System:

      Software Demo:

      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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