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

NERC Independent Research Fellow & Lord Kelvin Adam Smith Leadership Fellow (Equivalent: UK Upper-level lecturer/US Assistant Professor)
Director, Environmental 'Omics Lab
Sysadmin and owner, Orion Cluster
PI, Water and Environment Group, School of Engineering, University of Glasgow
PI, Bacteria Immunology Nutrition Gastroenterology Omics (BINGO) Group, School of Medicine, University of Glasgow
PI, Diversity Group,The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow
PI, Clostridium difficile ~ patients pathways pathogenesis (C3P) Group, University of Dundee

Contact

School of Engineering
Oakfield Avenue
University of Glasgow
Glasgow
G12 8LT
Email: Umer.Ijaz  @  glasgow.ac.uk

Profile

Summary statistics
18 years of work experience (since 1999)
Contribution to 25+ research grants (6 RCUK) since 2004 (played a signficant role in generated ~£7.5M as a PI/Co-I)
79 peer-reviewed publications (47 in journals of international repute)
Completed research supervision to date (since 2012): 2 PostDoc, 2 PhD, 2 MSc


Content

Orion Cluster
Research Grants
Supervisions
Teaching
Bioinformatics
Selected Publications

Introduction

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. 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. 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.

Recent Invites and Organizations

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 Lead 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 research lab is a newly-launched bioinformatics cluster called Orion [I own a total of 9 servers (4 more ordered) 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.

Acknowledgements

Funded projects and inkind support have contributed ~£114K to the development of Orion:

Research Grants

Supervision

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

Teaching

Bioinformatics

Selected Publications

[P60] M Castelino, M Tutino, J Moat, UZ Ijaz, R Parslew, A Al-Sharqi, RB Warren, C Quince, P Ho, M Upton, S Eyre, and A Barton
Comparison of the bacterial stool microbiota in established psoriatic arthritis (PSA) and psoriasis (PSC) - exploratory analysis of pilot data [Abstract]
Annals of the Rheumatic Diseases, 76:1087, 2017. DOI:10.1136/annrheumdis-2017-eular.3404
[P59] V Svolos, R Hansen, UZ Ijaz, C Quince, D Watson, A Alghamdi, A Brejnrod, C Ansalone, R Klopfleisch, S Milling, DR Gaya, RK Russell, and K Gerasimidis
Dietary manipulation of the healthy human and colitic rat gut microbiome by cd-treat diet and exclusive enteral nutrition [Abstract]
Gut, 66:A202, 2017. DOI:10.1136/gutjnl-2017-314472.394
[P58] BN Parsons*, UZ Ijaz*, R D'Amore, M Burkitt, R Eccles, L Lenzi, CA Duckworth, AR Moore, L Tiszlavicz, A Varro, N Hall, and DM Pritchard
Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use
bioRxiv 144907. DOI:10.1101/144907
*Joint first authors
[P57] A Ho*, UZ Ijaz*, TKS Janssens, R Ruijs, SY Kim, W de Boer, A Temorshuizen, WH van der Putten, and PLE Bodelier
Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition
Global Change Biology Bioenergy, 2017. DOI:10.1111/gcbb.12457
*Joint first authors
[P56] S Connelley, SG Shin, RJ Dillon, UZ Ijaz, C Quince, WT Sloan, and G Collins
Bioreactor scalability: laboratory-scale idealisation influences performance, ecology and community physiology in expanded granular sludge bioreactors
Frontiers in Microbiology, 8:664, 2017. DOI:10.3389/fmicb.2017.00664
[P55] V Svolos, R Hansen, UZ Ijaz, C Quince, D Watson, A Alghamdi, A Brejnrod, C Ansalone, S Milling, D Gaya, R Russell, and K Gerasimidis
Dietary manipulation of the healthy human and colitic murine gut microbiome by CD-TREAT diet and exclusive enteral nutrition; a proof of concept study [Abstract]
Journal of Crohn's and Colitis, 11 (suppl 1): S29-S30, 2017. DOI: 10.1093/ecco-jcc/jjx002.045
[P54] UZ Ijaz, C Quince, L Hanske, N Loman, ST Calus, M Bertz, CA Edwards, DR Gaya, R Hansen, P McGrogan, RK Russell, and K Gerasimidis
The microbial 'dysbiosis' of Crohn's disease patients does not occur in their unaffected, genetically linked kindred
PLoS ONE, 12(2): e0172605, 2017. DOI: 10.1371/journal.pone.0172605
[P53] J De Vrieze, ME Christiaens, D Walraedt, A Devooght, UZ Ijaz, and N Boon
Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure
Water Research, 111:109-117, 2017. DOI:10.1016/j.watres.2016.12.042
[P52] C Pedersen, P Hinton, E Gallagher, F Horton, R Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, GR Gibson, T Duparc, PD Cani, J Wright, D Russell-Jones, RL Ragione, and MD Robertson
Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 Diabetes [Abstract]
Proceedings of the Nutrition Society, 75(OCE3), 2016. DOI:10.1017/S0029665116001191
[P51] C Pedersen, E Gallagher, F Horton, RJ Ellis, UZ Ijaz, H Wu, E Jaiyeola, O Diribe, T Duparc, PD Cani, GR Gibson, P Hinton, J Wright, D Russell-Jones, R La Ragione, and MD Robertson
Host-microbiome interactions in human type 2 diabetes following prebiotic dietary fibre (galacto-oligosaccharide) intake
British Journal of Nutrition, 116(11):1869-1877, 2016. DOI:10.1017/S0007114516004086
[P50] JL Ray, J Althammer, KS Skaar, P Simonelli, A Larsen, D Stoecker, A Sazhin, UZ Ijaz, C Quince, JC Nejstgaard, M Frischer, G Pohnert, and C Troedsson
Metabarcoding and metabolome analysis of copepod grazing reveals feeding preference and linkage to metabolite classes in dynamic microbial plankton communities
Molecular Ecology, 2016. DOI:10.1111/mec.13844
[P49] L Sinclair*, UZ Ijaz*, LJ Jensen, M Coolen, C Gubry-Rangin, A Chronakova, A Oulas, C Pavloudi, J Schnetzer, A Weimann, AZ Ijaz, A Eiler, C Quince, and E Pafilis
Seqenv: linking microbes to environments through text mining
PeerJ, 4:e2690, 2016. DOI:10.7717/peerj.2690
Accompanying Software: seqenv
*Joint first authors
[P48] K Gerasimidis, M Bertz, C Quince, K Brunner, A Bruce, E Combet, ST Calus, N Loman, and UZ Ijaz
The effect of DNA extraction methodology on gut microbiota research applications
BMC Research Notes, 9:365, 2016. DOI:10.1186/s13104-016-2171-7
[P47] V Svolos, R Hansen, K Hughes, UZ Ijaz, C Quince, D Gaya, R Russell, and K Gerasimidis
The impact of 'Crohn's Disease-TReatment-with-EATing' diet (CD-TREAT diet) and exclusive enteral nutrition on healthy gut bacteria metabolism [Abstract]
Journal of Crohn's and Colitis, 10(suppl 1):S14-S15, 2016. DOI:10.1093/ecco-jcc/jjw019.017
[P46] C Varsos, T Patkos, A Oulas, C Pavloudi, A Gougousis, UZ Ijaz, I Filiopoulou, N Pattakos, EV Berghe, A Fernandez-Guerra, S Faulwetter, E Chatzinikolaou, E Pafilis, C Beikiari, M Doerr, and C Arvantidis
Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)
Biodiversity Data Journal, 4:e8357, 2016. DOI:10.3897/BDJ.4.e8357
Accompanying Software: RvLab
[P45] N De Souza, G Douce, C Goswami, UZ Ijaz, D 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
Code
[P41] AJ Pinto, DN Marcus, UZ Ijaz, QM Bautista-de los Santos, GJ Dick, and L Raskin
Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in drinking water system
mSphere, 1 (1): e00054-15, 2015. DOI:10.1128/mSphere.00054-15
Data
[P40] M Castelino, S Eyre, M Tutino, J Moat, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, A Barton
Bacterial Skin Microbiome in Psoriatic Arthritis - Pilot Data from Psoriatic Plaques on Dry Skin Sites from Patients with Psoriasis (PsC) and Psoriatic Arthritis (PsA) [abstract]
Arthritis & Rheumatology, 67 (suppl 10), 2015. DOI:10.1002/art.39448
[P39] R D'Amore*, UZ Ijaz*, M Schirmer, J Kenny, R Gregory, AC Darby, M Shakya, M Podar, C Quince, and N Hall
A comprehensive benchmarking study of next-generation sequencing platforms for 16S rRNA community profiling
BMC Genomics, 17:55, 2016. DOI:10.1186/s12864-015-2194-9
Code
*Joint first authors
[P38] B Torondel, JHJ Ensink, O Gundogdu, UZ Ijaz, J Parkhill, F Abdelahi, V-A Nguyen, S Sudgen, W Gibson, AW Walker, and C Quince.
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
Microbial Biotechnology, 9(2):209-223, 2016. DOI:10.1111/1751-7915.12334
Code
[P37] E Pafilis, S Frankfield, L Fanini, S Faulwetter, C Pavloudi, J Schnetzer, A Vasileiadou, UZ Ijaz, C Arvanitidis, R Stevenson, and LJ Jensens
Identification of Environmental Ontology terms in text and the annotation of the Encyclopedia of Life
In TDWG 2014 Annual Conference, Jönköping, Sweden, October 27-31, 2014.
[P36] C Quince*, UZ Ijaz*, N Loman, AM Eren, D Saulnier, J Russell, SJ Haig, ST Calus, J Quick, A Barclay, M Bertz, M Blaut, R Hansen, P McGrogan, RK Russell, C Edwards, and K Gerasimidis
Extensive modulation of the fecal metagenome in children with Crohn's disease during exclusive enteral nutrition
American Journal of Gastroenterology, 110:1718-1729, 2015. DOI:10.1038/ajg.2015.357
*Joint first authors
[P35] C Goswami, UZ Ijaz, DJ 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 [Abstract]
Proceedings of the Nutrition Society, 74(OCE1):E75, 2015.
[P33] M Castelino, S Eyre, J Moat, G Fox, P Martin, UZ Ijaz, C Quince, P Ho, M Upton, and A Barton
The skin microbiome in psoriatic arthritis: methodology development and pilot data [Abstract]
Lancet, 385(Supplement 1):S27, 2015.
[P32] JM Couto, UZ Ijaz, VR Phoenix, M Schirmer, and WT Sloan
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment
Current Microbiology,71(2), 296-302, 2015.
[P31] M Schirmer, UZ Ijaz, R D'Amore, N Hall, WT Sloan, and C Quince
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
Nucleic Acids Research, 2015.
Code
[P30] D Savio, L Sinclair, UZ Ijaz, P Stadler, AP Blaschke, GH Reischer, G Bloeschl, RL Mach, AKT Kirschner, AH Farnleitner, and A Eiler
Bacterial diversity along a 2 600 km river continuum
Environmental Microbiology. doi: 10.1111/1462-2920.12886, 2015.
[P29] K Harris, TL Parsons, UZ Ijaz, L Lahti, I Holmes, and C Quince
Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process
Proceedings of the IEEE, 105(3):516-529, 2017.
Accompanying Software: NMGS
[P28] J Alneberg, BS Bjarnason, I de Bruijn, M Schirmer, J Quick, UZ Ijaz, L Lahti, NJ Loman, AF Andersson, and C Quince
Binning metagenomic contigs by coverage and composition.
Nature Methods, 2014.
Accompanying Software: CONCOCT, TAXAassign
[P27] K Gerasimidis, N Loman, J Quick, ST Calus, UZ Ijaz, P McGrogan, CA Edwards, C Quince, and R. K. Russell
Metagenomic analysis of the gut microbiome during a course of Exclusive Enteral Nutrition (EEN) provides novel insights on mechanism of EEN action [Abstract]
Journal of Crohn's and Colitis, 8(Supplement 2):S393-S394, 2014.
[P26] UZ Ijaz, RJ Housden, GM Treece, RW Prager, and AH Gee.
Multi-directional scattering models for 3-dimensional ultrasound imaging

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

Last Updated by Dr Umer Zeeshan Ijaz on May, 2017.