Intro

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

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

Since 2016, I am trying to expand my research to engineering projects that now include: Raman spectroscopy enabled microfluidics; a hardware system for integrating liquid handling, incubation and sensing; and development of artificial intestinal Salmon gut system through bioreactors. My long-term research vision is to develop specialised and bespoke systems (both hardware and software) that can exploit and harness the power of microbial communities (also including statistical tools), and to place Glasgow at the helm of excellence in innovative cutting-edge bioengineering solutions.
One of the recently completed software projects is on a java-based statistical framework for integration of shotgun metagenomics datasets with other meta'omics technologies, called CViewer, and developed by my former PhD student, Dr Orges Koci. Here are some of the video demos:

Additionally, with the BINGO Group, I am exploring the role of gut microbiota and its interaction with the diet and the immune system in health and disease. I also work extensively with colleagues at NUI Galway, Ireland, particularly 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:


Visiting Opportunities

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

PhD Opportunities

Please note that I am trying 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.

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

    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. Research Fellowships

  12. 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)
  13. 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)
  14. 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
  15. 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
  16. 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
  17. 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

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

  19. 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
  20. 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
  21. 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
  22. International Research Support Initiative Program (2021-2022), 6 months research visit under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2020/10901 ~£7K
    PhD student: Habiba Tariq (COMSATS University, Islamabad, Pakistan)
    Foreign supervisor: U. Z. Ijaz
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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)
  29. 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
  30. 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
  31. 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
  32. Kelvin Smith PhD Scholarships 2015/16 (~£78,000)
    PhD student: Zihan Dai
    Supervisors: U. Z. Ijaz (lead), and A. J. Pinto
  33. Kelvin Smith PhD Scholarships 2014/15 (~£120,000)
    PhD student: Elizabeth Mittell
    Supervisors: B. K. Mable (lead), U. Z. Ijaz, and C. Cobbold
  34. Kelvin Smith PhD Scholarships 2012/13 (~£106,012)
    PhD student: Asha Ram
    Supervisors: J. Lindstrom (lead), U. Z. Ijaz, and T. Evans
  35. 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
  36. 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
  37. 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)
  38. 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
  39. Send-A-Newbie Award (YAPC::EU 2012) ~£600

  40. Other National/International Grants as a Participant

  41. 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.
  42. Environmental ancient DNA as proxy for sea ice reconstructions (aDNAPROX) (2017-2019), Forskerprosjekt-KLIMAFORSK NOK 8561K
    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)]
  43. 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
  44. 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
  45. 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)
  46. 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)
  47. 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
  48. Korea Science and Engineering Foundation Grant No. R01-2007-000-20155-0 (2007-2008)
    PhD student and PI: U. Z. Ijaz
  49. Research Grant of Jeju National University (2007)
    PhD student and PI: U. Z. Ijaz
  50. Korea Research Foundation Grant No. KRF-2005-013-D00075 (2005)
    PhD student and PI: U. Z. Ijaz
  51. Hyocheon Research Fund of the Cheju National University Development Foundation (2005)
    PhD student and PI: U. Z. Ijaz
  52. Korea Science and Engineering Foundation Grant No. R01-2004-000-0040-0 (2004)
    PhD student and PI: U. Z. Ijaz
  53. 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
  54. Korean Government IT Scholarship (2004-2008), Institute of Information Technology Assessment, Korea ₩56,000,000 (~$56,000)
  55. JNU Category-A Scholarship (2004-2006)
    Note: Full tuition fee waiver during PhD coursework
  56. 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

    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 Students

  43. 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)
  44. Dr Christina Nikolova (Heriot-Watt University, UK)
    PhD thesis: Characterisation and effectiveness evaluation of microbial biosurfactants for their use in oil spill response (2021)
    Supervisor: T. Gutierrez
    Host and tutor: U. Z. Ijaz (Environmental'Omics Lab 2019-2020)
  45. 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
  46. 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)
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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)
  55. 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
  56. 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
  57. 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)
  58. 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)
  59. 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
  60. 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)
  61. 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
  62. 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
  63. 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
  64. 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)
  65. 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)
  66. 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)
  67. 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)
  68. 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

  69. Past MSc Students

  70. Liu Kai (University of Glasgow, UK)
    MSc Engineering Project, 2020
    Project: Snakemake workflows for metagenomics data
    Supervisor: U. Z. Ijaz
  71. Wang Chen (University of Glasgow, UK)
    MSc Engineering Project, 2020
    Project: Phylogeny-aware metrics for microbial community surveys
    Supervisor: U. Z. Ijaz
  72. Chuanfei Tang (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2020
    Project: Development of a mobile app to give summary statistics of micronutrients and group comparisons
    Supervisor: U. Z. Ijaz
  73. 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
  74. Rachal 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, and B. K. Mable
  75. 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, and C. Keating
  76. 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, and C. Keating
  77. 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, and C. Keating
  78. 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
  79. 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, and U. Z. Ijaz
  80. 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, and U. Z. Ijaz
  81. 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, C. A. Edwards, and U. Z. Ijaz
  82. Alfred Ssekagiri (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2017
    Project: An R package for microbial community analysis in an environmental context
    Supervisors: U. Z. Ijaz, and W. T. Sloan
  83. 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, and U. Z. Ijaz
  84. 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, and U. Z. Ijaz
  85. Orges Koci (University of Glasgow, UK)
    MSc Bioinformatics, Polyomics and Systems Biology Project, 2015
    Project: Metagenomic Contigs Visualisation Tool
    Supervisor: U. Z. Ijaz
  86. 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

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

  88. 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)
  89. Ann-Cathrin Reissmann
    Project: Analysis of Intermodal Interactions at Side Street Junctions (2021)
    Supervisors: A. McCay (1st), and U. Z. Ijaz(2nd)
  90. Lewen Qi
    Project: Comparing the finite element method to peridynnamics (2020)
    Supervisors: A. McBride (1st), and U. Z. Ijaz(2nd)
  91. 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)
  92. Jinxin Chen
    Project: How will the 5G technology change the geotechnical engineering practice? (2020)
    Supervisors: Z. Gao (1st), and U. Z. Ijaz(2nd)
  93. 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)
  94. Jinliang Wang
    Project: The effect of dilation angle on slope stability analysis (2019)
    Supervisors: Z. Gao (1st), and U. Z. Ijaz(2nd)
  95. Fernando Ardavin
    Project: Feasibility Study of the Mayan Train in Mexico's Yucatan Peninsula (2019)
    Supervisors: K. Ampountolas (1st), and U. Z. Ijaz(2nd)
  96. Xiaoqian Wang
    Project: Modelling creep and rate effects in soils (2019)
    Supervisors: S. Wheeler (1st), and U. Z. Ijaz(2nd)
  97. 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)
  98. 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)
  99. 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)
  100. Chao Zhou
    Project: Computational Modelling of Granular Systems (2018)
    Supervisors: A. McBride (1st), and U. Z. Ijaz(2nd)
  101. 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)
  102. 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)
  103. 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)

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

  105. 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)
  106. 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)
  107. Yeoh Ya Yun
    Individual Project 4S (SIT4017P) (2019-2020)
    Project: Depression Analysis: Spectrogram Deep Learning
    Supervisors: H. Nguyen (1st), and U. Z. Ijaz (2nd)
  108. 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)
  109. 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)
  110. 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)

  111. Informatics Support (including external visitors)

  112. Valentine Okonkwo (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019-
  113. Claire Thom (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019-
  114. Dominic Quin (University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2020-
  115. Alison Graham (O'Flaherty Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab 2020-
  116. Jasmine Connolly (O'Flaherty Lab, NUI Galway, Ireland)
    Virtual visitor to Environmental'Omics Lab 2020-
  117. Victor Birlanga (Collins Lab, NUI Galway, Ireland)
    Visitor to Environmental'Omics Lab 2017, 2018
    Virtual visitor to Environmental'Omics Lab 2019-
  118. Ali Z. Ijaz (Hawkesbury Institute for the Environment, Australia)
    Visitor to Environmental'Omics Lab 2015
  119. Marco Kreuzer (University of Reading, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2015
  120. Dr Hussain Jaffery (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2017
  121. Dr Kathryn Jane Gray (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2019
  122. Kym Bain (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2020
  123. Hannah Baer (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2020
  124. Anabelle Ferguson (Milling Lab, Institute of Infection, Immunity, and Inflammation, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018; Undergraduate summer 2018 intern
  125. Hannah Craven (Institute of Cancer Sciences, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2018-2021
  126. Dr Lydia Bach (Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2020-2021
  127. 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
  128. 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
  129. 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
  130. Dr Ranjith Rajendran (Dental School, University of Glasgow, UK)
    Visitor to Environmental'Omics Lab 2017
  131. Christopher Delaney (Dental School, University of Glasgow, UK)
    Attended BIOL5172: Metagenomics (Course leader: U. Z. Ijaz) 2017
  132. Mauro Tutino (University of Manchester, UK)
    Visitor to Environmental'Omics Lab 2017
  133. Cadi Davies (London School of Hygiene & Tropical Medicine)
    Virtual visitor to Environmental'Omics Lab 2019
  134. Aaron McKenna (Moy Park, Belfast, UK)
    Visitor to Environmental'Omics Lab 2019; On his PhD thesis (2015 - Present) entitled "Efficient prevention of Campylobacter spp. entrance in broiler houses improves flock performance at slaughter"
  135. Maria Catalina Sevillano Rivera (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2015-2020)
  136. Irmarie Cotto (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  137. Solize Vosloo (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  138. Katie Vilardi (Pinto Lab, Northeastern University, USA)
    Hosted on Orion Cluster (2018-2020)
  139. 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: Dual [Pakistani (since birth) and British (since 2017)]
21+ years of work experience since June 1999 with no career breaks
£10M+ external grant funding brought to University of Glasgow as a PI/Co-I since 2014 (including £8,706,880 funding from UK Research and Innovation (UKRI) from BBSRC, EPSRC, and NERC with details available on Gateway to Research (GtR) portal)

Appointments


Recent Invites and Organizations

13/02/2020 Keynote Speaker, Data and Society, Oslo Life Science Conference, Norway
05/02/2020 Invited Speaker, NORCE Research, Bergen, Norway
05/12/2018 Invited Speaker, CompLifeSci 3rd Annual Meeting, Biocity Turku, Finland
30/11/2018 Invited Speaker, Microbiome Round Table Discussion with Versus Arthritis and BenevolentAI, London
06-08/06/2018 Host and Co-organizer (with Dr Leo Lahti), Numerical Ecology Workshop, University of Glasgow
17/01/2018 Invited Speaker and centre visit, MRC Centre for Medical Mycology, Aberdeen (c/o Professor Gordon Brown)
28-29/09/2017 Organizer, Pitlatrine Sandpit, University of Glasgow
26/04/2017 Invited Speaker and lab visit, Earlham Institute, Norwich (c/o Professor Neil Hall)
16/09/2016 Lab visit, Center for Microbial Ecology and Technology, Ghent, Belgium (c/o Professor Nico Boon)
12-15/09/2016 Session Chair (Microbial genomics and metagenomics), SETAC/iEOS Joint Focused Topic Meeting, Ghent, Belgium
06-09/08/2015 Session Chair and Invited Speaker (Omics in extreme environments), iEOS2015, St Andrews
22-25/09/2014 Organizer, Hands-on-workshop (hackathon): From signals to environmentally tagged sequences III (SeqEnv III), Hellenic Centre for Marine Research, Crete, Greece
19/06/2014 Invited Speaker, Edinburgh Amplicon Sequencing Group Second Discussion Meeting
18-19/06/2013 Led the workshop "Diversity and quantification of microbial communities in terrestrial environments" - the second part focused on interpretation of metagenomic data in microbial ecology. Given approximately 14 hours of lectures at Faculty of Science, in Ceske Budejovice, Czech Republic. These were supplied as part of the resolved project no. CZ.1.07/2.2.00/15.0364 - Molecularisation of biological fields of the Faculty of Science of JU, financed by the European Social Fund and the state budget of the Czech Republic, as part of the Education for Competitiveness Operational Programme (c/o Dr Alica Chronakova)
11-14/12/2012 COST training school ES1103: Bioinformatics for Microbial Community Analysis (Tutors: Dr. Christopher Quince, University of Glasgow, UK; Dr. Martin Hartmann, Swiss Federal Research Institute WSL, Agroscope Research Station ART, Switzerland; Dr. Nick Loman, University of Birmingham, UK; Dr. Umer Zeeshan Ijaz, University of Glasgow, UK), University of Liverpool

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)
Co-Investigator: C. Keating
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): ~£180K+:
  • 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": £9,500
  • EPSRC project entitled "Sythetic biology applications to the water industry": £60,000
  • SAIC project entitled "Gill health in scottish farmed salmon": £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

    Peer-reviewed, Supplementary & Working Articles (Pre-prints)

    [ ORCID iD iconorcid.org/0000-0001-5780-8551 | ResearchGate | Google Scholar | Loop profile: 292992 | Citing patents: lens.org ]
  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. C. Nikolova, U. Z. Ijaz#, and T. Gutierrez. Use of null models to compare the assembly of northeast Atlantic bacterial community in the presence of crude oil with either chemical dispersant or biosurfactant. bioRxiv 424141, 2020. DOI: 10.1101/2020.12.23.424141
    #Corresponding author
  30. 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
  31. 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. bioRxiv 423525, 2020. DOI: 10.1101/2020.12.18.423525
  32. 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
  33. 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. Development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim. bioRxiv 327858, 2020. DOI: 10.1101/2020.10.06.327858
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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
  93. 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
  94. 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
  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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
  101. 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
  102. 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
  103. 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
  104. 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
  105. 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
  106. 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
  107. 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
  108. 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
  109. 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
  110. 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
  111. 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
  112. 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
  113. 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
  114. 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
  115. 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
  116. 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
  117. 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
  118. 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
  119. 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
  120. 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
  121. 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
  122. 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
  123. 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
  124. 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
  125. 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
  126. 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
  127. 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
  128. 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
  129. 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
  130. 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.
  131. 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.
For complete list of publications, see PUBLICATIONS.pdf

Systems (Software/Hardware) & 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 87 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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