Publication

1. Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach

Leyuan Li, Xu Zhang, Zhibin Ning, Janice Mayne, Jasmine I. Moore, James Butcher, Cheng-Kang Chiang, David Mack, Alain Stintzi, Daniel Figeys

Journal of Proteome Research 
2. MetaLab: an automated pipeline for metaproteomic data analysis

Kai Cheng, Zhibin Ning, Xu Zhang, Leyuan Li, Bo Liao, Janice Mayne, Alain Stintzi, Daniel Figeys

Microbiome

3. Proteomic and Metaproteomic Approaches to Understand Host-Microbe Interactions

Amanda E. Starr, Shelley A. Deeke, Leyuan Li, Xu Zhang, Rachid Daoud, James Ryan, Zhibin Ning, Kai Cheng, Linh V.H. Nguyen, Elias Abou Samra, Mathieu Lavallée-Adam, Daniel Figeys

Analytical Chemistry

4. Investigation of copper inhibition of nitrifying moving bed biofilm (MBBR) reactors during long term operations

Alexander Schopf, Delatolla, R., Mathew, R., Alexandra Tsitouras, Kirkwood, KM.

Bioprocess and Biosystems Engineering

5. A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy

Maneka Chitiprolu, Chantal Jagow, Veronique Tremblay, Emma Bondy-Chorney, Geneviève Paris, Alexandre Savard, Gareth Palidwor, Francesca A Barry, Lorne Zinman, Julia Keith, Ekaterina Rogaeva, Janice Robertson, Mathieu Lavallée-Adam, John Woulfe, Jean-François Couture, Jocelyn Côté, Derrick Gibbings

Nature Communications

6. Assessing the impact of protein extraction methods for human gut metaproteomics

Xu Zhang, Leyuan Li, Janice Mayne, Zhibin Ning, Alain Stintzi, Daniel Figeys

Journal of Proteomics

7. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease

Xu Zhang, Shelley A. Deeke, Zhibin Ning, Amanda E. Starr, James Butcher, Jennifer Li, Janice Mayne, Kai Cheng, Bo Liao, Leyuan Li, Ruth Singleton, David Mack, Alain Stintzi, Daniel Figeys

Nature Communications

8. iMetaLab 1.0: A web platform for metaproteomics data analysis

Bo Liao, Zhibin Ning, Kai Cheng, Xu Zhang, Leyuan Li, Janice Mayne, Daniel Figeys

Bioinformatics

9. Enterobacteria and host resistance to infection

Eugene Kang, Alanna Crouse, Lucie Chevallier, Stéphanie M. Pontier, Ashwag Alzahrani, Navoun Silué, François-Xavier Campbell-Valois, Xavier Montagutelli, Samantha Gruenheid, Danielle Malo

Mammalian Genome

10. Partial Nitritation at Elevated Loading Rates: Design Curves and Biofilm Characteristics

Alexander Schopf, Delatolla R., Kirkwood KM.

Bioprocess and Biosystems Engineering

11. Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome

Danielle L. Peters, Wenju Wang, Xu Zhang, Zhibin Ning, Janice Mayne, Daniel Figeys

Proteomics

12. Meso and micro-scale effects of loading and air scouring on nitrifying bio-cord biofilm

Xin Tian, Robert Delatolla

Environmental Science: Water Research & Technology

13. Nitrifying moving bed biofilm reactor: Performance at low temperatures and response to cold-shock

Warsama Ahmed, Xin Tian, Robert Delatolla

Chemosphere

14. RNA-Seq Analysis of the T3SA regulon in Shigella flexneri reveals two new chromosomal genes upregulated in the On-state

Navoun Silué, Endrei Marcantonio, François-Xavier Campbell-Valois

Methods

15. An in vitro model maintaining taxon-specific functional activities of the gut microbiome

Leyuan Li, Elias Abou-Samra, Zhibin Ning, Xu Zhang, Janice Mayne, Janet Wang, Kai Cheng, Krystal Walker, Alain Stintzi, Daniel Figeys

Nature Communications

Conference poster 

1. Expression, purification and characterization of a potential L-cysteine desulfurase in Atopobium parvulum

Amine Belaouad, Jean-François Couture, Alain Stintzi

Department of Biochemistry, Microbiology and Immunology scientific symposium, May 2018

2. Identifying rheumatoid arthritis patients unresponsive to methotrexate using metabolomics

Francis Brière, Nancy Boucher, Pier-Luc Plante, Paul R. Fortin, Nathalie Carrier, Gilles Boire, Jacques Corbeil

American Society for mass spectrometry annual conference, Jun 2018

3. RNA-Seq analysis of Shigella flexneri transcriptional program reveals two putative T3SS substrates

Navoun Silué, François-Xavier Campbell-Valois

68th Annual Confernece of of the Canadian Society of Microbiologists, Jun 2018

4. Characterization of ApCsdA and ApSufS: two potential drug targets associated with iron-sulfur cluster formation and hydrogen sulfide production in Atopobium parvulum

Amine Belaouad, Jean-François Couture, Alain Stintzi

BioMetals 2018 International Conference, July 2018

5. Functional Screening Reveals Individual Gut Microbiome Responses to Xenobiotics

Leyuan Li, Elias Abou-Samra, Zhibin Ning, Xu Zhang, Janice Mayne, Janet Wang, Kai Cheng, Krystal Walker, Alain Stintzi, Daniel Figeys

Keystone Symposia: Microbiome: Chemical Mechanisms and Biological Consequences, Mar 2019

6. MS-PROTINI: A protein-protein interaction-assisted algorithm for the confidence assessment of peptide and protein identifications in mass spectrometry-based proteomics

Francesca A. Barry, Zhibin Ning, Daniel Figeys, Mathieu Lavallée-Adam

Canadian National Proteomics Network Annual Meeting, May 2019

7. Identifying genes required for Saccharomyces cerevisiae growth in mucin

Kevin Mercurio, Dylan Singh, Kristin Baetz

Ottawa Institute of Systems Biology Conference, Cornwall, Canada, May 2019

8. MS-PROTINI: A protein-protein interaction-assisted algorithm for the confidence assessment of peptide and protein identifications in mass spectrometry-based proteomics
Francesca A. Barry, Zhibin Ning, Daniel Figeys, Mathieu Lavallée-Adam American Society of Mass Spectrometry Annual Meeting, Jun 2019
9. Effect of a Mediterranean diet on plasma metabolites

Francis Brière, Nancy Boucher, Pier-Luc Plante, Didier Brassard, Simone Lemieux, Benoit Lamarche and Jacques Corbeil

American Society of Mass Spectrometry Annual Meeting, Jun 2019

10. Identification of 2 novel T3SA substrates in Shigella flexneri

Navoun Silué, François-Xavier Campbell-Valois

69th Annual Confernece of the Canadian Society of Microbiologists, Jun 2019

11. Lighting-up P. aeruginosa for anaerobic tracking

Caetanie Tchagang, François-Xavier Campbell-Valois, Thien Fah Mah

69th Annual Confernece of the Canadian Society of Microbiologists, Jun 2019

Conference presentation

1. Using modern -omics and classical yeast techniques to identify genes required for Saccharomyces cerevisiae growth in mucin

Kevin Mercurio, Dylan Singh, Kristin Baetz

International Conference on Yeast Genetics and Molecular Biology, Aug 2019