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Research Associate
Xu Zhang completed a B.Sc. degree in Biotechnology (2006) and M.Sc. degree in Microbiology (2009) in Lanzhou University, China. He obtained his Ph.D. degree in Microbiology from the Shanghai Jiao Tong University in 2013. He is currently a postdoctoral fellow at the OISB, University of Ottawa, under the supervision of Professors Daniel Figeys and Alain Stintzi. His research focuses on the host–gut microbe interactions with multiomic strategies including proteomics/metaproteomics, metagenomics, and metatranscriptomics, in the context of human disease including metabolic syndrome and inflammatory bowel disease.
Publications in NorthOmics lab:
Dong L, Lu D, Chen R, Lin Y, Zhu H, Zhang Z, Cai S, Cui P, Song G, Rao D, Yi X, Wu Y, Song N, Liu F, Zou Y, Zhang S, Zhang X, Wang X, Qiu S, Zhou J, Wang S, Zhang X, Shi Y, Figeys D, Ding L, Wang P, Zhang B, Rodriguez H, Gao Q, Gao D, Zhou H and Fan J.
Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma.
(2022) Cancer Cell. 40, 70-87.e15
Pubmed
Cancer Cell
Li H, Zhang X, Chen R, Cheng K, Ning Z, Li J, Twine S, Stintzi A, Mack D and Figeys D.
Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis.
(2021) J Proteomics. 249, 104369
Pubmed
J Proteomics
Mayne J, Zhang X, Butcher J, Walker K, Ning Z, Wójcik E, Dastych J, Stintzi A and Figeys D.
Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach.
(2021) Viruses. 13,
Pubmed
Viruses
PMC Article
D'Aoust PM, Graber TE, Mercier E, Montpetit D, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Servos MR, Srikanthan N, MacKenzie M, Figeys D, Manuel D, Jüni P, MacKenzie AE and Delatolla R.
Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 h before COVID-19 clinical tests and 96 h before hospitalizations.
(2021) Sci Total Environ. 770, 145319
Pubmed
Sci Total Environ
PMC Article
D'Aoust PM, Mercier E, Montpetit D, Jia JJ, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Langlois MA, Servos MR, MacKenzie M, Figeys D, MacKenzie AE, Graber TE and Delatolla R.
Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence.
(2021) Water Res. 188, 116560
Pubmed
Water Res
PMC Article
Li L, Chang L, Zhang X, Ning Z, Mayne J, Ye Y, Stintzi A, Liu J and Figeys D.
Berberine and its structural analogs have differing effects on functional profiles of individual gut microbiomes.
(2020) Gut Microbes. 11, 1348-1361
Pubmed
Gut Microbes
PMC Article
Simopoulos CMA, Ning Z, Zhang X, Li L, Walker K, Lavallée-Adam M and Figeys D.
pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies.
(2020) Bioinformatics. 36, 4171-4179
Pubmed
Bioinformatics
Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A and Figeys D.
Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease.
(2020) Nat Commun. 11, 4120
Pubmed
Nat Commun
PMC Article
Hao Z, Li L, Ning Z, Zhang X, Mayne J, Cheng K, Walker K, Liu H and Figeys D.
Metaproteomics Reveals Growth Phase-Dependent Responses of an Gut Microbiota to Metformin.
(2020) J Am Soc Mass Spectrom. 31, 1448-1458
Pubmed
J Am Soc Mass Spectrom
Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J and Figeys D.
MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics.
(2020) J Am Soc Mass Spectrom. 31, 1473-1482
Pubmed
J Am Soc Mass Spectrom
Comerlato CB, Zhang X, Walker K, Brandelli A and Figeys D.
Comparative proteomic analysis reveals metabolic variability of probiotic Enterococcus durans during aerobic and anaerobic cultivation.
(2020) J Proteomics. 220, 103764
Pubmed
J Proteomics
Li L, Ning Z, Zhang X, Mayne J, Cheng K, Stintzi A and Figeys D.
RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs.
(2020) Microbiome. 8, 33
Pubmed
Microbiome
PMC Article
Zhang X, Li L, Butcher J, Stintzi A and Figeys D.
Advancing functional and translational microbiome research using meta-omics approaches.
(2019) Microbiome. 7, 154
Pubmed
Microbiome
PMC Article
Li L, Abou-Samra E, Ning Z, Zhang X, Mayne J, Wang J, Cheng K, Walker K, Stintzi A and Figeys D.
An in vitro model maintaining taxon-specific functional activities of the gut microbiome.
(2019) Nat Commun. 10, 4146
Pubmed
Nat Commun
PMC Article
Peters DL, Wang W, Zhang X, Ning Z, Mayne J and Figeys D.
Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome.
(2019) Proteomics. 19, e1800363
Pubmed
Proteomics
Wang Y, Niu Q, Zhang X, Liu L, Wang Y, Chen Y, Negi M, Figeys D, Li YY and Zhang T.
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics.
(2019) Microbiome. 7, 122
Pubmed
Microbiome
PMC Article
Zhang X and Figeys D.
Perspective and Guidelines for Metaproteomics in Microbiome Studies.
(2019) J Proteome Res. 18, 2370-2380
Pubmed
J Proteome Res
Liao B, Ning Z, Cheng K, Zhang X, Li L, Mayne J and Figeys D.
iMetaLab 1.0: a web platform for metaproteomics data analysis.
(2018) Bioinformatics. 34, 3954-3956
Pubmed
Bioinformatics
Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, Mayne J, Cheng K, Liao B, Li L, Singleton R, Mack D, Stintzi A and Figeys D.
Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease.
(2018) Nat Commun. 9, 2873
Pubmed
Nat Commun
PMC Article
Zhang X, Li L, Mayne J, Ning Z, Stintzi A and Figeys D.
Assessing the impact of protein extraction methods for human gut metaproteomics.
(2018) J Proteomics. 180, 120-127
Pubmed
J Proteomics
Deeke SA, Starr AE, Ning Z, Ahmadi S, Zhang X, Mayne J, Chiang CK, Singleton R, Benchimol EI, Mack DR, Stintzi A and Figeys D.
Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis.
(2018) Am J Gastroenterol. 113, 713-724
Pubmed
Am J Gastroenterol
Li L, Zhang X, Ning Z, Mayne J, Moore JI, Butcher J, Chiang CK, Mack D, Stintzi A and Figeys D.
Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach.
(2018) J Proteome Res. 17, 154-163
Pubmed
J Proteome Res
Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J, Stintzi A and Figeys D.
MetaLab: an automated pipeline for metaproteomic data analysis.
(2017) Microbiome. 5, 157
Pubmed
Microbiome
PMC Article
Starr AE, Deeke SA, Ning Z, Chiang CK, Zhang X, Mottawea W, Singleton R, Benchimol EI, Wen M, Mack DR, Stintzi A and Figeys D.
Proteomic analysis of ascending colon biopsies from a paediatric inflammatory bowel disease inception cohort identifies protein biomarkers that differentiate Crohn's disease from UC.
(2017) Gut. 66, 1573-1583
Pubmed
Gut
PMC Article
Zhang X, Ning Z, Mayne J, Moore JI, Li J, Butcher J, Deeke SA, Chen R, Chiang CK, Wen M, Mack D, Stintzi A and Figeys D.
MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.
(2016) Microbiome. 4, 31
Pubmed
Microbiome
PMC Article
Li L, Ryan J, Ning Z, Zhang X, Mayne J, Lavallée-Adam M, Stintzi A and Figeys D.
A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches.
(2020) Comput Struct Biotechnol J. 18, 3833-3842
Pubmed
Comput Struct Biotechnol J
PMC Article
Zhang X, Walker K, Mayne J, Li L, Ning Z, Stintzi A and Figeys D.
Evaluating live microbiota biobanking using an microbiome assay and metaproteomics.
Gut Microbes. 14, 2035658
Pubmed
Gut Microbes
PMC Article
Adler P, Chiang CK, Mayne J, Ning Z, Zhang X, Xu B, Cheng HM and Figeys D.
Aging Disrupts the Circadian Patterns of Protein Expression in the Murine Hippocampus.
(2019) Front Aging Neurosci. 11, 368
Pubmed
Front Aging Neurosci
PMC Article
Previous Publications:
Zhang X, Zheng J, Zhao L, Zhao Y and Ma S.
[The role and research progress of IL-17 in the pathogenesis of osteoarthritis].
(2021) Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 37, 1138-1142
Pubmed
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi
Zhao L, Zhang X, Wang X, Guan X, Zhang W and Ma J.
Recent advances in selective photothermal therapy of tumor.
(2021) J Nanobiotechnology. 19, 335
Pubmed
J Nanobiotechnology
PMC Article
Wang J, Tang H, Wang X, Zhang X, Zhang C, Zhang M, Zhao Y, Zhao L and Shen J.
The structural alteration of gut microbiota in low-birth-weight mice undergoing accelerated postnatal growth.
(2016) Sci Rep. 6, 27780
Pubmed
Sci Rep
PMC Article
Zhang X, Zhao Y, Xu J, Xue Z, Zhang M, Pang X, Zhang X and Zhao L.
Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats.
(2015) Sci Rep. 5, 14405
Pubmed
Sci Rep
PMC Article
Xu J, Lian F, Zhao L, Zhao Y, Chen X, Zhang X, Guo Y, Zhang C, Zhou Q, Xue Z, Pang X, Zhao L and Tong X.
Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula.
(2015) ISME J. 9, 552-62
Pubmed
ISME J
PMC Article
Yin X, Peng J, Zhao L, Yu Y, Zhang X, Liu P, Feng Q, Hu Y and Pang X.
Structural changes of gut microbiota in a rat non-alcoholic fatty liver disease model treated with a Chinese herbal formula.
(2013) Syst Appl Microbiol. 36, 188-96
Pubmed
Syst Appl Microbiol
Zhao L, Nicholson JK, Lu A, Wang Z, Tang H, Holmes E, Shen J, Zhang X, Li JV and Lindon JC.
Targeting the human genome-microbiome axis for drug discovery: inspirations from global systems biology and traditional Chinese medicine.
(2012) J Proteome Res. 11, 3509-19
Pubmed
J Proteome Res
Zhang X, Zhao Y, Zhang M, Pang X, Xu J, Kang C, Li M, Zhang C, Zhang Z, Zhang Y, Li X, Ning G and Zhao L.
Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats.
(2012) PLoS One. 7, e42529
Pubmed
PLoS One
PMC Article
Wang J, Wang Y, Zhang X, Liu J, Zhang Q, Zhao Y, Peng J, Feng Q, Dai J, Sun S, Zhao Y, Zhao L, Zhang Y, Hu Y and Zhang M.
Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients.
(2017) Front Microbiol. 8, 2222
Pubmed
Front Microbiol
PMC Article