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Research Associate

Zhibin Ning obtained his B.S. degree in Life Science at Shandong Normal University, China, in 2003. He received his Ph.D. degree in Biotechnology and Biochemistry from Shanghai Institutes for Biological Sciences in 2008 for the development and applications of liquid-based separation strategies for proteomics. After his postdoctoral training in the OISB, University of Ottawa, under the guidance of Professor Daniel Figeys, he continued his career as a research associate in the same lab. Presently he is focusing on technology development and applications in proteomics and bioinformatics, especially data visualization.


Karunakaran G, Yang Y, Tremblay V, Ning Z, Martin J, Belaouad A, Figeys D, Brunzelle JS, Giguere PM, Stintzi A and Couture JF. Structural analysis of Atopobium parvulum SufS cysteine desulfurase linked to Crohn's disease. (2022) FEBS Lett. Pubmed FEBS Lett
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
Starr AE, Deeke SA, Ning Z, de Nanassy J, Singleton R, Benchimol EI, Mack DR, Stintzi A and Figeys D. Associations between Cellular Energy and Pediatric Inflammatory Bowel Disease Patient Response to Treatment. (2021) J Proteome Res. 20, 4393-4404 Pubmed J Proteome Res
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
Zhang X, Cheng K, Ning Z, Mayne J, Walker K, Chi H, Farnsworth CL, Lee K and Figeys D. Exploring the Microbiome-Wide Lysine Acetylation, Succinylation, and Propionylation in Human Gut Microbiota. (2021) Anal Chem. 93, 6594-6598 Pubmed Anal Chem
Smyth P, Zhang X, Ning Z, Mayne J, Moore JI, Walker K, Lavallée-Adam M and Figeys D. Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics. (2020) Anal Chem. 92, 15711-15718 Pubmed Anal Chem
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
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
Pelletier AR, Chung YE, Ning Z, Wong N, Figeys D and Lavallée-Adam M. MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion. (2020) J Am Soc Mass Spectrom. 31, 1459-1472 Pubmed J Am Soc Mass Spectrom
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
Wang J, Zhang X, Li L, Ning Z, Mayne J, Schmitt-Ulms C, Walker K, Cheng K and Figeys D. Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics. (2020) Anal Chem. 92, 5379-5386 Pubmed Anal Chem
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
Yang Y, Joshi M, Takahashi YH, Ning Z, Qu Q, Brunzelle JS, Skiniotis G, Figeys D, Shilatifard A and Couture JF. A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS. (2020) Nucleic Acids Res. 48, 421-431 Pubmed Nucleic Acids Res PMC Article
Li H, Li L, Cheng K, Ning Z, Mayne J, Zhang X, Walker K, Chen R, Twine S, Li J and Figeys D. Chemoenzymatic Method for Glycoproteomic N-Glycan Type Quantitation. (2020) Anal Chem. 92, 1618-1627 Pubmed Anal Chem
Adler P, Mayne J, Walker K, Ning Z and Figeys D. Therapeutic Targeting of Casein Kinase 1δ/ε in an Alzheimer's Disease Mouse Model. (2019) J Proteome Res. 18, 3383-3393 Pubmed J Proteome Res
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
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
Mayne J, Ooi TC, Tepliakova L, Seebun D, Walker K, Mohottalage D, Ning Z, Abujrad H, Mbikay M, Wassef H, Chrétien M and Figeys D. Associations Between Soluble LDLR and Lipoproteins in a White Cohort and the Effect of PCSK9 Loss-of-Function. (2018) J Clin Endocrinol Metab. 103, 3486-3495 Pubmed J Clin Endocrinol Metab
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
Catelas I, Lehoux EA, Ning Z, Figeys D, Baskey SJ and Beaulé PE. Differential proteomic analysis of synovial fluid from hip arthroplasty patients with a pseudotumor vs. Periprosthetic osteolysis . (2018) J Orthop Res. 36, 1849-1859 Pubmed J Orthop Res
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
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
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
Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M and Figeys D. Proteomic and Metaproteomic Approaches to Understand Host-Microbe Interactions. (2018) Anal Chem. 90, 86-109 Pubmed Anal Chem
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
Chiang CK, Tworak A, Kevany BM, Xu B, Mayne J, Ning Z, Figeys D and Palczewski K. Quantitative phosphoproteomics reveals involvement of multiple signaling pathways in early phagocytosis by the retinal pigmented epithelium. (2017) J Biol Chem. 292, 19826-19839 Pubmed J Biol Chem 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, Chen W, Ning Z, Mayne J, Mack D, Stintzi A, Tian R and Figeys D. Deep Metaproteomics Approach for the Study of Human Microbiomes. (2017) Anal Chem. 89, 9407-9415 Pubmed Anal Chem
Birjandi AP, Bojko B, Ning Z, Figeys D and Pawliszyn J. High throughput solid phase microextraction: A new alternative for analysis of cellular lipidome?. (2017) J Chromatogr B Analyt Technol Biomed Life Sci. 1043, 12-19 Pubmed J Chromatogr B Analyt Technol Biomed Life Sci
Chen R, Cheng K, Ning Z and Figeys D. N-Glycopeptide Reduction with Exoglycosidases Enables Accurate Characterization of Site-Specific N-Glycosylation. (2016) Anal Chem. 88, 11837-11843 Pubmed Anal Chem
Zhang X, Ning Z, Mayne J, Deeke SA, Li J, Starr AE, Chen R, Singleton R, Butcher J, Mack DR, Stintzi A and Figeys D. In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics. (2016) Anal Chem. 88, 6120-5 Pubmed Anal Chem
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
Ning Z, Star AT, Mierzwa A, Lanouette S, Mayne J, Couture JF and Figeys D. A charge-suppressing strategy for probing protein methylation. (2016) Chem Commun (Camb). 52, 5474-7 Pubmed Chem Commun (Camb)
Shao Y, Yamamoto M, Figeys D, Ning Z and Chan HM. Proteome profiling reveals regional protein alteration in cerebrum of common marmoset (Callithrix jacchus) exposed to methylmercury. (2016) Toxicology. 347-349, 29-39 Pubmed Toxicology
Ning Z, Zhang X, Mayne J and Figeys D. Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data. (2016) Anal Chem. 88, 1973-8 Pubmed Anal Chem
Ge Y, Ning Z, Wang Y, Zheng Y, Zhang C and Figeys D. Quantitative proteomic analysis of Dunaliella salina upon acute arsenate exposure. (2016) Chemosphere. 145, 112-8 Pubmed Chemosphere
Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI and Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. (2016) Anal Chem. 88, 95-121 Pubmed Anal Chem
Shao Y, Figeys D, Ning Z, Mailloux R and Chan HM. Methylmercury can induce Parkinson's-like neurotoxicity similar to 1-methyl-4- phenylpyridinium: a genomic and proteomic analysis on MN9D dopaminergic neuron cells. (2015) J Toxicol Sci. 40, 817-28 Pubmed J Toxicol Sci
Nasheri N, Ning Z, Figeys D, Yao S, Goto NK and Pezacki JP. Activity-based profiling of the proteasome pathway during hepatitis C virus infection. (2015) Proteomics. 15, 3815-25 Pubmed Proteomics
Desrochers GF, Sherratt AR, Blais DR, Nasheri N, Ning Z, Figeys D, Goto NK and Pezacki JP. Profiling Kinase Activity during Hepatitis C Virus Replication Using a Wortmannin Probe. (2015) ACS Infect Dis. 1, 443-52 Pubmed ACS Infect Dis
Shao Y, Yamamoto M, Figeys D, Ning Z and Chan HM. Proteomic Analysis of Cerebellum in Common Marmoset Exposed to Methylmercury. (2015) Toxicol Sci. 146, 43-51 Pubmed Toxicol Sci
Gagné JP, Ethier C, Defoy D, Bourassa S, Langelier MF, Riccio AA, Pascal JM, Moon KM, Foster LJ, Ning Z, Figeys D, Droit A and Poirier GG. Quantitative site-specific ADP-ribosylation profiling of DNA-dependent PARPs. (2015) DNA Repair (Amst). 30, 68-79 Pubmed DNA Repair (Amst)
Lanouette S, Davey JA, Elisma F, Ning Z, Figeys D, Chica RA and Couture JF. Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design. (2015) Structure. 23, 206-215 Pubmed Structure
Ning Z, Hawley B, Seebun D and Figeys D. APols-aided protein precipitation: a rapid method for concentrating proteins for proteomic analysis. (2014) J Membr Biol. 247, 941-7 Pubmed J Membr Biol PMC Article
Chiang CK, Mehta N, Patel A, Zhang P, Ning Z, Mayne J, Sun WY, Cheng HY and Figeys D. The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes. (2014) PLoS Genet. 10, e1004695 Pubmed PLoS Genet PMC Article
Sherratt AR, Nasheri N, McKay CS, O'Hara S, Hunt A, Ning Z, Figeys D, Goto NK and Pezacki JP. A new chemical probe for phosphatidylinositol kinase activity. (2014) Chembiochem. 15, 1253-6 Pubmed Chembiochem
Mayne J, Starr AE, Ning Z, Chen R, Chiang CK and Figeys D. Fine tuning of proteomic technologies to improve biological findings: advancements in 2011-2013. (2014) Anal Chem. 86, 176-95 Pubmed Anal Chem
Mitchell L, Huard S, Cotrut M, Pourhanifeh-Lemeri R, Steunou AL, Hamza A, Lambert JP, Zhou H, Ning Z, Basu A, Côté J, Figeys DA and Baetz K. mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases. (2013) Proc Natl Acad Sci U S A. 110, E1641-50 Pubmed Proc Natl Acad Sci U S A PMC Article
Ning Z, Seebun D, Hawley B, Chiang CK and Figeys D. From cells to peptides: "one-stop" integrated proteomic processing using amphipols. (2013) J Proteome Res. 12, 1512-9 Pubmed J Proteome Res
Zhou H, Wang F, Wang Y, Ning Z, Hou W, Wright TG, Sundaram M, Zhong S, Yao Z and Figeys D. Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor. (2011) Mol Cell Proteomics. 10, O111.008425 Pubmed Mol Cell Proteomics PMC Article
Zhou H, Ning Z, Wang F, Seebun D and Figeys D. Proteomic reactors and their applications in biology. (2011) FEBS J. 278, 3796-806 Pubmed FEBS J
Ning Z, Zhou H, Wang F, Abu-Farha M and Figeys D. Analytical aspects of proteomics: 2009-2010. (2011) Anal Chem. 83, 4407-26 Pubmed Anal Chem
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
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
Chiang CK, Xu B, Mehta N, Mayne J, Sun WY, Cheng K, Ning Z, Dong J, Zou H, Cheng HM and Figeys D. Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus. (2017) Front Neurol. 8, 110 Pubmed Front Neurol 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
Ning Z, Hawley B, Chiang CK, Seebun D and Figeys D. Detecting protein-protein interactions/complex components using mass spectrometry coupled techniques. (2014) Methods Mol Biol. 1164, 1-13 Pubmed Methods Mol Biol

Previous Publications:

Wei YN, Hu HY, Xie GC, Fu N, Ning ZB, Zeng R and Khaitovich P. Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. (2015) Genome Biol. 16, 41 Pubmed Genome Biol PMC Article
Yang XL, Li QR, Ning ZB, Zhang Y, Zeng R and Wu JR. Identification of complex relationship between protein kinases and substrates during the cell cycle of HeLa cells by phosphoproteomic analysis. (2013) Proteomics. 13, 1233-46 Pubmed Proteomics
Li QR, Ning ZB, Yang XL, Wu JR and Zeng R. Complementary workflow for global phosphoproteome analysis. (2012) Electrophoresis. 33, 3291-8 Pubmed Electrophoresis
Fu X, Giavalisco P, Liu X, Catchpole G, Fu N, Ning ZB, Guo S, Yan Z, Somel M, Pääbo S, Zeng R, Willmitzer L and Khaitovich P. Rapid metabolic evolution in human prefrontal cortex. (2011) Proc Natl Acad Sci U S A. 108, 6181-6 Pubmed Proc Natl Acad Sci U S A PMC Article
Somel M, Guo S, Fu N, Yan Z, Hu HY, Xu Y, Yuan Y, Ning Z, Hu Y, Menzel C, Hu H, Lachmann M, Zeng R, Chen W and Khaitovich P. MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. (2010) Genome Res. 20, 1207-18 Pubmed Genome Res PMC Article
Nie S, Dai J, Ning ZB, Cao XJ, Sheng QH and Zeng R. Comprehensive profiling of phosphopeptides based on anion exchange followed by flow-through enrichment with titanium dioxide (AFET). (2010) J Proteome Res. 9, 4585-94 Pubmed J Proteome Res
Cao XJ, Dai J, Xu H, Nie S, Chang X, Hu BY, Sheng QH, Wang LS, Ning ZB, Li YX, Guo XK, Zhao GP and Zeng R. High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans. (2010) Cell Res. 20, 197-210 Pubmed Cell Res
Wang Q, Zhang Y, Yang C, Xiong H, Lin Y, Yao J, Li H, Xie L, Zhao W, Yao Y, Ning ZB, Zeng R, Xiong Y, Guan KL, Zhao S and Zhao GP. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. (2010) Science. 327, 1004-7 Pubmed Science PMC Article
Li QR, Ning ZB, Tang JS, Nie S and Zeng R. Effect of peptide-to-TiO2 beads ratio on phosphopeptide enrichment selectivity. (2009) J Proteome Res. 8, 5375-81 Pubmed J Proteome Res
Ning ZB, Li QR, Dai J, Li RX, Shieh CH and Zeng R. Fractionation of complex protein mixture by virtual three-dimensional liquid chromatography based on combined pH and salt steps. (2008) J Proteome Res. 7, 4525-37 Pubmed J Proteome Res
Mazin P, Xiong J, Liu X, Yan Z, Zhang X, Li M, He L, Somel M, Yuan Y, Phoebe Chen YP, Li N, Hu Y, Fu N, Ning Z, Zeng R, Yang H, Chen W, Gelfand M and Khaitovich P. Widespread splicing changes in human brain development and aging. (2013) Mol Syst Biol. 9, 633 Pubmed Mol Syst Biol PMC Article