Umer Zeeshan Ijaz [Ph.D., M.Sc.Eng., B.Sc.Eng.]

NERC Independent Research Fellow & Lord Kelvin Adam Smith Leadership Fellow
Group Leader, Environmental 'Omics Lab
Co-Investigator, Water and Environment Group, School of Engineering, University of Glasgow
Co-Investigator, Bacteria Immunology Nutrition Gastroenterology Omics (BINGO) Group, School of Medicine, University of Glasgow
Co-Investigator, Diversity Group,The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow
Co-Investigator, Clostridium difficile ~ patients pathways pathogenesis (C3P) Group, University of Dundee


School of Engineering
Oakfield Avenue
University of Glasgow
G12 8LT
Email: Umer.Ijaz  @
Twitter: @umer_z_ijaz

Research Grants
Selected Publications
Key Collaborators


I lead the Environmental 'Omics Lab in Infrastructure & Environment Division, School of Engineering that I established soon after I was awarded the NERC Independent Research Fellowship back in November, 2014. The purpose of my research is to integrate different sources of 'omics data (metagenomics, metatranscriptomics, metabolomics, and metaproteomics) in environmental science for microbial community analysis. The computational based comparative analysis of DNA sequences may provide information about genome structure, gene function, metabolic and regulatory pathways, how microbial genomes evolve, how they exist in a community and how they compete for resources whether they work together in a symbiosis or otherwise.

At the heart of my research lab is a newly-launched bioinformatics cluster called Orion (I own a total of 8 servers all running CentOS) 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. Below is the university-wide usage (November 2015) of my cluster with brown boxes representing the research groups from College of Medical, Veterinary and Life Sciences, blue box representing the research group from College of Science & Engineering, along with emoticons for both PhD students and PostDocs:

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 these datasets require a fair deal of multivariate statistical analysis for which I have shared the code on this website. Those who are new to metagenomics may find my online tutorials listed under Bioinformatics useful.

The following infographics shows some of the applications I am currently involved in:


At the moment, I have no PhD studentships/PostDoc opportunities available, however:
*potential international applicants (bioinformatics/engineering/computational/statistical background) from Commonwealth nations (Developed, Developing) wanting to do their PhD under my supervision can apply for a Commonwealth Scholarship by naming me as a UK supervisor for the application [Requirements: (a) Your research proposal revolves around my research interests; and (b) You have my consent to supervise you. Attach research proposal + CV in your first correspondence].
*potential international applicants who have already secured partial funding through external sources [say their monthly stipend] and want to do their PhD under my supervision can apply for College of Science & Engineering Scholarships to cover their tuition fee [Note: These will only support exceptional students].


Research Grants - Total funding (excluding PhD studentships) generated as PI/Co-I since 2014: ~£3.0M

This section excludes the PhD studentships mentioned in the "Supervisions" section.


Note: Names are in brown where I'm the 1st supervisor.



Selected Publications

For the full list of publications, please see PUBLICATIONS.pdf
[P53] S Connelly, SG Shin, RJ Dillon, UZ Ijaz, C Quince, WT Sloan, and G Collins
The disparity of scale: lab-scale idealization influences performance, ecology and community physiology in expanded granular sludge bed bioreactors
Submitted for publication (2016).
[P52] UZ Ijaz, C Quince, L Hanske, N Loman, ST Calus, M Bertz, CA Edwards, DR Gaya, R Hansen, P McGrogan, RK Russell, and K Gerasimidis
The microbial 'dysbiosis' of Crohn's disease patients does not occur in their unaffected, genetically linked kindred
Submitted for publication (2016).
[P51] C Pedersen, E Gallagher, F Horton, RJ Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, T Duparc, PD Cani, GR Gibson, P Hinton, J Wright, D Russell-Jones, R La Ragione, and MD Robertson
Host-microbiome interactions in human type 2 diabetes following prebiotic intake
Submitted for publication (2016).
[P50] JL Ray, J Althammer, KS Skaar, P Simonelli, A Larsen, D Stoecker, A Sazhin, UZ Ijaz, C Quince, JC Nejstgaard, M Frischer, G Pohnert, and C Troedsson
Metabarcoding and metabolome analysis of copepod grazing reveals feeding preference and linkage to metabolite classes in dynamic microbial plankton communities
Molecular Ecology, Accepted for publication (2016). DOI:10.1111/mec.13844
[P49] L Sinclair*, UZ Ijaz*, LJ Jensen, M Coolen, C Gubry-Rangin, A Chronakova, A Oulas, C Pavloudi, J Schnetzer, A Weimann, AZ Ijaz, A Eiler, C Quince, and E Pafilis
Seqenv: linking microbes to environments through text mining
PeerJ Preprints, 4:e2317v1, 2016. DOI:10.7287/peerj.preprints.2317v1
Accompanying Software: seqenv
*Joint first authors
[P48] K Gerasimidis, M Bertz, C Quince, K Brunner, A Bruce, E Combet, ST Calus, N Loman, and UZ Ijaz
The effect of DNA extraction methodology on gut microbiota research applications
BMC Research Notes, 9:365, 2016. DOI:10.1186/s13104-016-2171-7
[P47] V Svolos*, R Hansen, K Hughes, UZ Ijaz, C Quince, D Gaya, R Russell, and K Gerasimidis
The impact of 'Crohn's Disease-TReatment-with-EATing' diet (CD-TREAT diet) and exclusive enteral nutrition on healthy gut bacteria metabolism
Journal of Crohn's and Colitis, 10(suppl 1):S14-S15, 2016. DOI:10.1093/ecco-jcc/jjw019.017
*Winner of Best investigator-initiated study (IIS) Award at the 11th Congress of ECCO
[P46] C Varsos, T Patkos, A Oulas, C Pavloudi, A Gougousis, UZ Ijaz, I Filiopoulou, N Pattakos, EV Berghe, A Fernandez-Guerra, S Faulwetter, E Chatzinikolaou, E Pafilis, C Beikiari, M Doerr, and C Arvantidis
Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)
Biodiversity Data Journal, Accepted for publication (2016).
Accompanying Software: RvLab
[P45] N De Souza, G Douce, C Goswami, UZ Ijaz, D Brown, J Coia, P Donnan, C Wiuff, P Davey, M Bennie, J Lindstrom, and C Marwick
Genetic relatedness among clinical Clostridium difficile strains in one Scottish region
In 26th ECCMID, Amsterdam, Netherlands, 9-12 April, 2016
[P44] QM Bautista-do los Santos, JL Schroeder, MC Sevillano-Rivera, R Sungthong, UZ Ijaz, WT Sloan, and AJ Pinto
Microbial communities in full-scale drinking water distribution systems - A meta-analysis
Environmental Science: Water Research & Technology, 2:631-644, 2016. DOI:10.1039/C6EW00030D
[P43] K Gerasimidis, UZ Ijaz, C Edwards, RK Russell, C Quince, and R Hansen
Response to Kaakoush et al.
American Journal of Gastroenterology, 111(7):1033-1034, 2016.
[P42] M Schirmer, R D'Amore, UZ Ijaz, N Hall, and C Quince
Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing
BMC Bioinformatics, 17:125, 2016. DOI:10.1186/s12859-016-0976-y
[P41] AJ Pinto, DN Marcus, UZ Ijaz, QM Bautista-de los Santos, GJ Dick, and L Raskin
Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in drinking water system
mSphere, 1 (1): e00054-15, 2015. DOI:10.1128/mSphere.00054-15
[P40] M Castelino, S Eyre, M Tutino, J Moat, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, A Barton
Bacterial Skin Microbiome in Psoriatic Arthritis - Pilot Data from Psoriatic Plaques on Dry Skin Sites from Patients with Psoriasis (PsC) and Psoriatic Arthritis (PsA) [abstract]
Arthritis & Rheumatology, 67 (suppl 10), 2015. DOI:10.1002/art.39448
[P39] R D'Amore*, UZ Ijaz*, M Schirmer, J Kenny, R Gregory, AC Darby, M Shakya, M Podar, C Quince, and N Hall
A comprehensive benchmarking study of next-generation sequencing platforms for 16S rRNA community profiling
BMC Genomics, 17:55, 2016. DOI:10.1186/s12864-015-2194-9
*Joint first authors
[P38] B Torondel, JHJ Ensink, O Gundogdu, UZ Ijaz, J Parkhill, F Abdelahi, V-A Nguyen, S Sudgen, W Gibson, AW Walker, and C Quince.
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
Microbial Biotechnology, 9(2):209-223, 2016. DOI:10.1111/1751-7915.12334
[P37] E Pafilis, S Frankfield, L Fanini, S Faulwetter, C Pavloudi, J Schnetzer, A Vasileiadou, UZ Ijaz, C Arvanitidis, R Stevenson, and LJ Jensens
Identification of Environmental Ontology terms in text and the annotation of the Encyclopedia of Life
In TDWG 2014 Annual Conference, Jönköping, Sweden, October 27-31, 2014.
[P36] C Quince*, UZ Ijaz*, N Loman, AM Eren, D Saulnier, J Russell, SJ Haig, ST Calus, J Quick, A Barclay, M Bertz, M Blaut, R Hansen, P McGrogan, RK Russell, C Edwards, and K Gerasimidis
Extensive modulation of the fecal metagenome in children with Crohn's disease during exclusive enteral nutrition
American Journal of Gastroenterology, 110:1718-1729, 2015. DOI:10.1038/ajg.2015.357
*Joint first authors
[P35] C Goswami, UZ Ijaz, DJ Brown, CA Marwick, C Wiuff, A Banks, JE Coia, and GR Douce
Understanding molecular epidemiology of Clostridum Difficile in Scotland
In 5th International Clostridum Difficile Symposium, May 19-21, 2015, Bled, Slovenia.
[P34] MJ Khan, C Quince, V S, UZ Ijaz, N Loman, ST Calus, J Quick, SJ Haig, MG Shaikh, CA Edwards, and K Gerasimidis
A detailed analysis of the gut microbial diversity and metabolic activity in children with obesity of different aetiology and lean controls
Proceedings of the Nutrition Society, 74(OCE1):E75, 2015.
[P33] M Castelino, S Eyre, J Moat, G Fox, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, and A Barton
The skin microbiome in psoriatic arthritis: methodology development and pilot data
Lancet, 385(Supplement 1):S27, 2015.
[P32] JM Couto, UZ Ijaz, VR Phoenix, M Schirmer, and WT Sloan
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment
Current Microbiology,71(2), 296-302, 2015.
[P31] M Schirmer, UZ Ijaz, R D'Amore, N Hall, WT Sloan, and C Quince
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
Nucleic Acids Research, 2015.
[P30] D Savio, L Sinclair, UZ Ijaz, P Stadler, AP Blaschke, GH Reischer, G Bloeschl, RL Mach, AKT Kirschner, AH Farnleitner, and A Eiler
Bacterial diversity along a 2 600 km river continuum
Environmental Microbiology. doi: 10.1111/1462-2920.12886, 2015.
[P29] K Harris, TL Parsons, UZ Ijaz, L Lahti, I Holmes, and C Quince
Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process
Proceedings of the IEEE, pp. 1-14 (Early Online Publication)
Accompanying Software: NMGS
[P28] J Alneberg, BS Bjarnason, I de Bruijn, M Schirmer, J Quick, UZ Ijaz, L Lahti, NJ Loman, AF Andersson, and C Quince
Binning metagenomic contigs by coverage and composition.
Nature Methods, 2014.
Accompanying Software: CONCOCT, TAXAassign
[P27] K Gerasimidis, N Loman, J Quick, ST Calus, UZ Ijaz, P McGrogan, CA Edwards, C Quince, and R. K. Russell
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(Supplement 2):S393-S394, 2014.
[P26] UZ Ijaz, RJ Housden, GM Treece, RW Prager, and AH Gee.
Multi-directional scattering models for 3-dimensional ultrasound imaging

Journal of Ultrasound in Medicine, 32(4):699-714, April 2013.
[P25] E Dyer, UZ Ijaz, RJ Housden, RW Prager, AH Gee, and GM Treece.
A clinical system for three-dimensional extended field of view ultrasound
British Journal of Radiology, 85: e919-e924, October 2012.
Relevant Software: Stradwin
[P24] UZ Ijaz, RW Prager, AH Gee, and GM Treece
A study of similarity measures for in vivo 3D ultrasound volume registration
Acoustical Imaging, 30:315-323, 2011.
[P23] UZ Ijaz, RW Prager, AH Gee, and GM Treece
Particle swarm optimization for in vivo 3D ultrasound volume registration
Acoustical Imaging, 30:345-354, 2011.
[P22] UZ Ijaz, RW Prager, AH Gee, and GM Treece
Optimisation strategies for ultrasound volume registration
Measurement Science and Technology, 21(8): 085803 (17pp), July 2010.
[P21] RW Prager, UZ Ijaz , AH Gee, and GM Treece
Three-dimensional ultrasound imaging
Proceedings of the Institution of Mechanical Engineers Part H-Journal of Engineering in Medicine, 224(2):193-223, 2010.
[P20] AK Khambampati, UZ Ijaz, JS Lee, S Kim, and KY Kim
Phase boundary estimation in electrical impedance tomography using Hooke and Jeeves pattern search method
Measurement Science and Technology, 21(3):035501 (13pp), March 2010.
[P19] UZ Ijaz, AK Khambampati, JS Lee, S Kim, and KY Kim
Nonstationary phase boundary estimation in electrical impedance tomography using unscented Kalman filter
Journal of Computational Physics , 227(15):7089.7112, July 2008.
[P18] UZ Ijaz, AK Khambampati, MC Kim, S Kim, JS Lee, and KY Kim
Particle swarm optimization technique for elliptic region boundary estimation in electrical impedance tomography
AIP Conference Proceedings, 914:896-901, 2007.
[P17] UZ Ijaz, AK Khambampati, JS Lee, KY Kim, MC Kim, and S Kim
Electrical resistance imaging of two-phase flow through rod bundles
AIP Conference Proceedings, 914:844-849, 2007.
[P16] BS Kim, UZ Ijaz, JH Kim, MC Kim, S Kim, and KY Kim
Nonstationary phase boundary estimation in electrical impedance tomography based on the interacting multiple model scheme
Measurement Science and Technology, 18(1):62-70, January 2007.
[P15] UZ Ijaz
Dynamic phase boundary estimation in electrical impedance tomography
PhD thesis, Cheju National University, Korea, December 2007.
slides [PPT]
[P14] AK Khambampati, A Rashid, UZ Ijaz, S Kim, M Soleimani, and KY Kim
Unscented Kalman filter approach to tracking a moving interfacial boundary in sedimentation process using three-dimensional electrical impedance tomography
Philosophical Transactions of The Royal Society A - Mathematical Physical and Engineering Sciences, 367:3095-3120, August 2009.
[P13] UZ Ijaz, SI Chung, AK Khambampati, KY Kim, and S Kim
Electrical resistance imaging of time-varying interface in stratified flows using unscented Kalman filter
Measurement Science and Technology, 19(6) 065501 (11pp), June 2008.
[P12] S Kim, UZ Ijaz, AK Khambampati, KY Kim, MC Kim, and SI Chung
Moving interfacial boundary estimation in stratified flows of two immiscible liquids using electrical resistance tomography
Measurement Science and Technology, 18(5):1257-1269, May 2007.
[P11] JH Kim, BC Kang, SH Lee, BY Choi, MC Kim, BS Kim, UZ Ijaz, KY Kim, and S Kim
Phase boundary estimation in electrical resistance tomography with weighted multi-layered neural networks and front point approach
Measurement Science and Technology, 17(10):2731-2739, October 2006.
[P10] UZ Ijaz, BS Kim, TJ Kao, AK Khambampati, S Kim, MC Kim, JC Newell, D Isaacson, and KY Kim
Mammography phantom studies using 3D electrical impedance tomography with numerical forward solver
In FBIT 2007:379-383.
[P9] UZ Ijaz, JH Kim, AK Khambampati, MC Kim, S Kim, and KY Kim
Concentration distribution estimation of fluid through electrical impedance tomography based on interacting multiple model scheme
Flow Measurement and Instrumentation, 18(1):47-56, March 2007.
[P8] JH Kim, BY Choi, UZ Ijaz, BS Kim, S Kim, and KY Kim
Directional algebraic reconstruction technique for electrical impedance tomography
Journal of The Korean Physical Society, 54(4):1439-1447, April 2009.
[P7] YS Kim, SH Lee, UZ Ijaz, KY Kim, and BY Choi
Sensitivity map generation in electrical capacitance tomography using mixed normalization models
Measurement Science and Technology, 18(7):2092-2102, July 2007.
[P6] FA Khan, UZ Ijaz, KY Kim, MJ Kang, and WC Song
Policy-based management in ad hoc network using geographic routing
Lecture Notes in Computer Science, 3961:237-246, 2006.
[P5] S Kim, UZ Ijaz, AK Khambampati, KY Kim, and MC Kim
Effect of Current Injection Patterns on Dynamic Electrical Resistance Imaging for Fast Transient Processes
In 5th IEEE Conference on Sensors, 2006.
[P4] UZ Ijaz, JH Kim, MC Kim, S Kim, JW Park, and KY Kim
Nondestructive dynamic process monitoring using electrical capacitance tomography
Key Engineering Materials, 321-323(2):1671-1674, 2006.
[P3] UZ Ijaz, AK Khambampati, MC Kim, S Kim, and KY Kim
Estimation of time-dependent heat flux and measurement bias in two-dimensional heat conduction problems
International Journal of Heat and Mass Transfer, 50(21-22):4117-4130, October 2007.
[P2] UZ Ijaz, SU Chaudhary, SM Ahn, BH Lee, and KY Kim
Computational strategies for protein quantitation in 2D electrophoresis gel image processor for Matlab
In FBIT 2007: 129-134.
[P1] UZ Ijaz, SU Chaudhary, SM Ahn, BH Lee, and KY Kim
2D electrophoresis gel image processor for Matlab
In ICHIT 2006, Jeju, Korea, November 9-11, 2006.

Key Collaborators

Professor William Sloan
Dr Caroline Gauchotte-Lindsay
Dr Jillian Couto
Dr Cindy Smith
Infrastructure & Environment
Professor Barbara Mable
Professor Neil Metcalfe
Dr Jan Lindstrom
Institute of Biodiversity, Animal Health and Comparative Medicine
Dr Christina Cobbold School of Mathematics and Statistics
Dr Huabing Yin Biomedical Engineering
Dr Martin Llewellyn School of Life Sciences
Dr Gillian Douce
Dr Simon Milling
Dr Andrew Roe
Institute of Infection, Immunity and Inflammation
Professor Christine Edwards
Dr Konstantinos Gerasimidis
School of Medicine (Human Nutrition)
Dr Jaime Toney
Professor Maggie Cusack
School of Geographical and Earth Sciences
Dr Ameet Pinto
Dr Richard Russell
Dr Richard Hansen
Dr Daniel Gaya
Dr Seung Gu Shin
Dr Juhee Shin
Dr Douglas Morrison

Scottish Salmonella, Shigella and
Clostridium difficile Reference Laboratory (SSSCdRL)
Professor John E Coia
Dr Derek Brown
Dr Charis Marwick
Professor Peter T Donnan
Dr Phillip McGinnity
Dr Thomas Reed
Dr Christopher Quince
Dr Leo Lahti
Dr Gavin Collin
Dr Florence Abram
Professor Anne Barton
Dr Madhura Castelino
Dr Belen Torondel
Dr Ozan Gundogdu
Dr Alan Walker
Professor Mark Pritchard
Professor Neil Hall
Dr Jessica Louise Ray
Professor Lars Juhl Jensen
Dr Evangelos Pafilis
Dr. R.J.J.H. (Rob) van Son

Last Updated by Dr Umer Zeeshan Ijaz on September, 2016.