Publications – NorthOmics

Publications Up-to-date

Creskey M, Li L, Ning Z, Fekete EE, Mayne J, Walker K, Ampaw A, Ben R, Zhang X and Figeys D. An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis. (2023) Proteomics. 23, e2200116 Pubmed Proteomics

Almasi S, SarmastiEmami S, Baird S, Ning Z, Figeys D, Côté J, Cowan KN and Jasmin BJ. Staufen1 controls mitochondrial metabolism via HIF2α in embryonal rhabdomyosarcoma and promotes tumorigenesis. (2023) Cell Mol Life Sci. 80, 328 Pubmed Cell Mol Life Sci

Morales SV, Mahmood A, Pollard J, Mayne J, Figeys D and Wiseman PW. The LDL receptor is regulated by membrane cholesterol as revealed by fluorescence fluctuation analysis. (2023) Biophys J. 122, 3783-3797 Pubmed Biophys J PMC Article

Comerlato CB, Zhang X, Walker K, Mayne J, Figeys D and Brandelli A. The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome. (2023) Probiotics Antimicrob Proteins. Pubmed Probiotics Antimicrob Proteins

Li L, Wang T, Ning Z, Zhang X, Butcher J, Serrana JM, Simopoulos CMA, Mayne J, Stintzi A, Mack DR, Liu YY and Figeys D. Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics. (2023) Nat Commun. 14, 3428 Pubmed Nat Commun PMC Article

Hao Z, Meng C, Li L, Feng S, Zhu Y, Yang J, Han L, Sun L, Lv W, Figeys D and Liu H. Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the "Lunar Palace 365" experiment. (2023) Microbiome. 11, 88 Pubmed Microbiome PMC Article

Duan H, Zhang X and Figeys D. An emerging field: Post-translational modification in microbiome. (2023) Proteomics. 23, e2100389 Pubmed Proteomics

Hodgkinson K, El Abbar F, Dobranowski P, Manoogian J, Butcher J, Figeys D, Mack D and Stintzi A. Butyrate's role in human health and the current progress towards its clinical application to treat gastrointestinal disease. (2023) Clin Nutr. 42, 61-75 Pubmed Clin Nutr

Cheng K, Ning Z, Li L, Zhang X, Serrana JM, Mayne J and Figeys D. MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database. (2023) J Proteome Res. 22, 387-398 Pubmed J Proteome Res PMC Article

Liu Y, Bilen M, McNicoll MM, Harris RA, Fong BC, Iqbal MA, Paul S, Mayne J, Walker K, Wang J, Figeys D and Slack RS. Early postnatal defects in neurogenesis in the 3xTg mouse model of Alzheimer's disease. (2023) Cell Death Dis. 14, 138 Pubmed Cell Death Dis PMC Article

Duan H, Cheng K, Ning Z, Li L, Mayne J, Sun Z and Figeys D. Assessing the Dark Field of Metaproteome. (2022) Anal Chem. 94, 15648-15654 Pubmed Anal Chem PMC Article

Tilocca B, Soggiu A, Iavarone F, Greco V, Putignani L, Ristori MV, Macari G, Spina AA, Morittu VM, Ceniti C, Piras C, Bonizzi L, Britti D, Urbani A, Figeys D and Roncada P. The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective. (2022) Int J Mol Sci. 23, Pubmed Int J Mol Sci PMC Article

Sun Z, Wang W, Li L, Zhang X, Ning Z, Mayne J, Walker K, Stintzi A and Figeys D. Comprehensive Assessment of Functional Effects of Commonly Used Sugar Substitute Sweeteners on Human Gut Microbiome. (2022) Microbiol Spectr. 10, e0041222 Pubmed Microbiol Spectr PMC Article

Simopoulos CMA, Ning Z, Li L, Khamis MM, Zhang X, Lavallée-Adam M and Figeys D. MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening. (2022) mSystems. 7, e0038122 Pubmed mSystems PMC Article

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. 596, 898-909 Pubmed FEBS Lett

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

Chang L, Lin F, Cheng K, Li J, Sun X, Figeys D, Jiang J, Ye Y and Liu J. A simultaneous identification and quantification strategy for determination of sulfhydryl-containing metabolites in normal- and high-fat diet hamsters using stable isotope labeling combined with LC-MS. (2021) Anal Chim Acta. 1184, 339016 Pubmed Anal Chim Acta

Robichaud S, Fairman G, Vijithakumar V, Mak E, Cook DP, Pelletier AR, Huard S, Vanderhyden BC, Figeys D, Lavallée-Adam M, Baetz K and Ouimet M. Identification of novel lipid droplet factors that regulate lipophagy and cholesterol efflux in macrophage foam cells. (2021) Autophagy. 17, 3671-3689 Pubmed Autophagy PMC Article

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

Wislet-Gendebien S, Visanji NP, Whitehead SN, Marsilio D, Hou W, Figeys D, Fraser PE, Bennett SAL and Tandon A. Retraction Note to: Differential regulation of wild-type and mutant alpha-synuclein binding to synaptic membranes by cytosolic factors. (2021) BMC Neurosci. 22, 40 Pubmed BMC Neurosci 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

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

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

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 and Figeys D. Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface. (2020) Mol Cell Proteomics. 19, 1409-1417 Pubmed Mol Cell Proteomics 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

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

Duval S, Abu-Thuraia A, Elkholi IE, Chen R, Seebun D, Mayne J, Côté JF, Figeys D and Seidah NG. Shedding of cancer susceptibility candidate 4 by the convertases PC7/furin unravels a novel secretory protein implicated in cancer progression. (2020) Cell Death Dis. 11, 665 Pubmed Cell Death Dis 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

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

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

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

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

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

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

Sulaiman A, McGarry S, El-Sahli S, Li L, Chambers J, Phan A, Côté M, Cron GO, Alain T, Le Y, Lee SH, Liu S, Figeys D, Gadde S and Wang L. Co-targeting Bulk Tumor and CSCs in Clinically Translatable TNBC Patient-Derived Xenografts via Combination Nanotherapy. (2019) Mol Cancer Ther. 18, 1755-1764 Pubmed Mol Cancer Ther

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

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

Boonying W, Joselin A, Huang E, Qu D, Safarpour F, Iyirhiaro GO, Gonzalez YR, Callaghan SM, Slack RS, Figeys D, Chung YH and Park DS. Pink1 regulates FKBP5 interaction with AKT/PHLPP and protects neurons from neurotoxin stress induced by MPP. (2019) J Neurochem. 150, 312-329 Pubmed J Neurochem

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

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

Huang E, Qu D, Huang T, Rizzi N, Boonying W, Krolak D, Ciana P, Woulfe J, Klein C, Slack RS, Figeys D and Park DS. PINK1-mediated phosphorylation of LETM1 regulates mitochondrial calcium transport and protects neurons against mitochondrial stress. (2017) Nat Commun. 8, 1399 Pubmed Nat Commun 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

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

Jia D, Li L, Andrew S, Allan D, Li X, Lee J, Ji G, Yao Z, Gadde S, Figeys D and Wang L. An autocrine inflammatory forward-feedback loop after chemotherapy withdrawal facilitates the repopulation of drug-resistant breast cancer cells. (2017) Cell Death Dis. 8, e2932 Pubmed Cell Death Dis PMC Article

Mendoza-Viveros L, Chiang CK, Ong JLK, Hegazi S, Cheng AH, Bouchard-Cannon P, Fana M, Lowden C, Zhang P, Bothorel B, Michniewicz MG, Magill ST, Holmes MM, Goodman RH, Simonneaux V, Figeys D and Cheng HM. miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock. (2017) Cell Rep. 19, 505-520 Pubmed Cell Rep PMC Article

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

Mottawea W, Chiang CK, Mühlbauer M, Starr AE, Butcher J, Abujamel T, Deeke SA, Brandel A, Zhou H, Shokralla S, Hajibabaei M, Singleton R, Benchimol EI, Jobin C, Mack DR, Figeys D and Stintzi A. Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn's disease. (2016) Nat Commun. 7, 13419 Pubmed Nat Commun PMC Article

Liu X, Xu Y, Meng Q, Zheng Q, Wu J, Wang C, Jia W, Figeys D, Chang Y and Zhou H. Proteomic analysis of minute amount of colonic biopsies by enteroscopy sampling. (2016) Biochem Biophys Res Commun. 476, 286-292 Pubmed Biochem Biophys Res Commun

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

Chen R, Zou H and Figeys D. Detergent-Assisted Glycoprotein Capture: A Versatile Tool for In-Depth N-Glycoproteome Analysis. (2016) J Proteome Res. 15, 2080-6 Pubmed J Proteome Res

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)

Ryczko MC, Pawling J, Chen R, Abdel Rahman AM, Yau K, Copeland JK, Zhang C, Surendra A, Guttman DS, Figeys D and Dennis JW. Metabolic Reprogramming by Hexosamine Biosynthetic and Golgi N-Glycan Branching Pathways. (2016) Sci Rep. 6, 23043 Pubmed Sci Rep PMC Article

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

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

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

Xu J, Gao J, Yu C, He H, Yang Y, Figeys D and Zhou H. Development of Online pH Gradient-Eluted Strong Cation Exchange Nanoelectrospray-Tandem Mass Spectrometry for Proteomic Analysis Facilitating Basic and Histidine-Containing Peptides Identification. (2016) Anal Chem. 88, 583-91 Pubmed Anal Chem

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

Qu D, Hage A, Don-Carolis K, Huang E, Joselin A, Safarpour F, Marcogliese PC, Rousseaux MW, Hewitt SJ, Huang T, Im DS, Callaghan S, Dewar-Darch D, Figeys D, Slack RS and Park DS. BAG2 Gene-mediated Regulation of PINK1 Protein Is Critical for Mitochondrial Translocation of PARKIN and Neuronal Survival. (2015) J Biol Chem. 290, 30441-52 Pubmed J Biol Chem PMC Article

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

Tan Y, AlKhamees B, Jia D, Li L, Couture JF, Figeys D, Jinushi M and Wang L. MFG-E8 Is Critical for Embryonic Stem Cell-Mediated T Cell Immunomodulation. (2015) Stem Cell Reports. 5, 741-752 Pubmed Stem Cell Reports PMC Article

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

Mehta N, Cheng AH, Chiang CK, Mendoza-Viveros L, Ling HH, Patel A, Xu B, Figeys D and Cheng HY. GRK2 Fine-Tunes Circadian Clock Speed and Entrainment via Transcriptional and Post-translational Control of PERIOD Proteins. (2015) Cell Rep. 12, 1272-88 Pubmed Cell Rep

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

Starr AE, Lemieux V, Noad J, Moore JI, Dewpura T, Raymond A, Chrétien M, Figeys D and Mayne J. β-Estradiol results in a proprotein convertase subtilisin/kexin type 9-dependent increase in low-density lipoprotein receptor levels in human hepatic HuH7 cells. (2015) FEBS J. 282, 2682-96 Pubmed FEBS J PMC Article

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)

Huang TS, Li L, Moalim-Nour L, Jia D, Bai J, Yao Z, Bennett SA, Figeys D and Wang L. A Regulatory Network Involving β-Catenin, e-Cadherin, PI3k/Akt, and Slug Balances Self-Renewal and Differentiation of Human Pluripotent Stem Cells In Response to Wnt Signaling. (2015) Stem Cells. 33, 1419-33 Pubmed Stem Cells PMC Article

Jia D, Yang W, Li L, Liu H, Tan Y, Ooi S, Chi L, Filion LG, Figeys D and Wang L. β-Catenin and NF-κB co-activation triggered by TLR3 stimulation facilitates stem cell-like phenotypes in breast cancer. (2015) Cell Death Differ. 22, 298-310 Pubmed Cell Death Differ PMC Article

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

Wang PW, Abedini MR, Yang LX, Ding AA, Figeys D, Chang JY, Tsang BK and Shieh DB. Gelsolin regulates cisplatin sensitivity in human head-and-neck cancer. (2014) Int J Cancer. 135, 2760-9 Pubmed Int J Cancer

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

Cheng K, Chen R, Seebun D, Ye M, Figeys D and Zou H. Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method. (2014) J Proteomics. 110, 145-54 Pubmed J Proteomics

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

Mazereeuw G, Herrmann N, Xu H, Figeys D, Oh PI, Bennett SA and Lanctôt KL. Platelet-activating factors are associated with cognitive deficits in depressed coronary artery disease patients: a hypothesis-generating study. (2014) J Neuroinflammation. 11, 119 Pubmed J Neuroinflammation PMC Article

Parsanejad M, Zhang Y, Qu D, Irrcher I, Rousseaux MW, Aleyasin H, Kamkar F, Callaghan S, Slack RS, Mak TW, Lee S, Figeys D and Park DS. Regulation of the VHL/HIF-1 pathway by DJ-1. (2014) J Neurosci. 34, 8043-50 Pubmed J Neurosci 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

Chen R, Seebun D, Ye M, Zou H and Figeys D. Site-specific characterization of cell membrane N-glycosylation with integrated hydrophilic interaction chromatography solid phase extraction and LC-MS/MS. (2014) J Proteomics. 103, 194-203 Pubmed J Proteomics

Lanouette S, Mongeon V, Figeys D and Couture JF. The functional diversity of protein lysine methylation. (2014) Mol Syst Biol. 10, 724 Pubmed Mol Syst Biol PMC Article

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

Miller Jenkins LM and Figeys D. Dynamic proteins: changes in structures, activities and networks. (2013) FEBS J. 280, 5569 Pubmed FEBS J

Xu H, Valenzuela N, Fai S, Figeys D and Bennett SA. Targeted lipidomics - advances in profiling lysophosphocholine and platelet-activating factor second messengers. (2013) FEBS J. 280, 5652-67 Pubmed FEBS J

Fowler SL, Akins M, Zhou H, Figeys D and Bennett SA. The liver connexin32 interactome is a novel plasma membrane-mitochondrial signaling nexus. (2013) J Proteome Res. 12, 2597-610 Pubmed J Proteome Res PMC Article

Wang F, Blanchard AP, Elisma F, Granger M, Xu H, Bennett SA, Figeys D and Zou H. Phosphoproteome analysis of an early onset mouse model (TgCRND8) of Alzheimer's disease reveals temporal changes in neuronal and glia signaling pathways. (2013) Proteomics. 13, 1292-305 Pubmed Proteomics

Yao Z, Zhou H, Figeys D, Wang Y and Sundaram M. Microsome-associated lumenal lipid droplets in the regulation of lipoprotein secretion. (2013) Curr Opin Lipidol. 24, 160-70 Pubmed Curr Opin Lipidol

Figeys D. Integrative proteomics. (2013) Proteomics. 13, 1231-2 Pubmed Proteomics

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

Blanchard AP, McDowell GS, Valenzuela N, Xu H, Gelbard S, Bertrand M, Slater GW, Figeys D, Fai S and Bennett SA. Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass. (2013) Bioinformatics. 29, 284-5 Pubmed Bioinformatics PMC Article

Zhu J, Wang F, Cheng K, Song C, Qin H, Hu L, Figeys D, Ye M and Zou H. Analysis of human serum phosphopeptidome by a focused database searching strategy. (2013) J Proteomics. 78, 389-97 Pubmed J Proteomics

Ryan T, Shelton M, Lambert JP, Malecova B, Boisvenue S, Ruel M, Figeys D, Puri PL and Skerjanc IS. Myosin phosphatase modulates the cardiac cell fate by regulating the subcellular localization of Nkx2.5 in a Wnt/Rho-associated protein kinase-dependent pathway. (2013) Circ Res. 112, 257-66 Pubmed Circ Res PMC Article

Wang F, Wei X, Zhou H, Liu J, Figeys D and Zou H. Combination of online enzyme digestion with stable isotope labeling for high-throughput quantitative proteome analysis. (2012) Proteomics. 12, 3129-37 Pubmed Proteomics

Kaluarachchi Duffy S, Friesen H, Baryshnikova A, Lambert JP, Chong YT, Figeys D and Andrews B. Exploring the yeast acetylome using functional genomics. (2012) Cell. 149, 936-48 Pubmed Cell PMC Article

Knight JD, Tian R, Lee RE, Wang F, Beauvais A, Zou H, Megeney LA, Gingras AC, Pawson T, Figeys D and Kothary R. A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts. (2012) Skelet Muscle. 2, 5 Pubmed Skelet Muscle PMC Article

Zhou H, Ning Z, Starr AE, Abu-Farha M and Figeys D. Advancements in top-down proteomics. (2012) Anal Chem. 84, 720-34 Pubmed Anal Chem

Kurat CF, Lambert JP, van Dyk D, Tsui K, van Bakel H, Kaluarachchi S, Friesen H, Kainth P, Nislow C, Figeys D, Fillingham J and Andrews BJ. Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein. (2011) Genes Dev. 25, 2489-501 Pubmed Genes Dev PMC Article

Tian R, Alvarez-Saavedra M, Cheng HY and Figeys D. Uncovering the proteome response of the master circadian clock to light using an AutoProteome system. (2011) Mol Cell Proteomics. 10, M110.007252 Pubmed Mol Cell Proteomics PMC Article

Song C, Wang F, Ye M, Cheng K, Chen R, Zhu J, Tan Y, Wang H, Figeys D and Zou H. Improvement of the quantification accuracy and throughput for phosphoproteome analysis by a pseudo triplex stable isotope dimethyl labeling approach. (2011) Anal Chem. 83, 7755-62 Pubmed Anal Chem

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

Wang S, Tian R, Li L, Figeys D and Wang L. An enhanced chemically defined SILAC culture system for quantitative proteomics study of human embryonic stem cells. (2011) Proteomics. 11, 4040-6 Pubmed Proteomics

Abu-Farha M, Lanouette S, Elisma F, Tremblay V, Butson J, Figeys D and Couture JF. Proteomic analyses of the SMYD family interactomes identify HSP90 as a novel target for SMYD2. (2011) J Mol Cell Biol. 3, 301-8 Pubmed J Mol Cell Biol

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

Wang S, Circu ML, Zhou H, Figeys D, Aw TY and Feng J. Highly sensitive detection of S-nitrosylated proteins by capillary gel electrophoresis with laser induced fluorescence. (2011) J Chromatogr A. 1218, 6756-62 Pubmed J Chromatogr A PMC Article

Qin W, Sundaram M, Wang Y, Zhou H, Zhong S, Chang CC, Manhas S, Yao EF, Parks RJ, McFie PJ, Stone SJ, Jiang ZG, Wang C, Figeys D, Jia W and Yao Z. Missense mutation in APOC3 within the C-terminal lipid binding domain of human ApoC-III results in impaired assembly and secretion of triacylglycerol-rich very low density lipoproteins: evidence that ApoC-III plays a major role in the formation of lipid precursors within the microsomal lumen. (2011) J Biol Chem. 286, 27769-80 Pubmed J Biol Chem PMC Article

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

Tian R, Hoa XD, Lambert JP, Pezacki JP, Veres T and Figeys D. Development of a multiplexed microfluidic proteomic reactor and its application for studying protein-protein interactions. (2011) Anal Chem. 83, 4095-102 Pubmed Anal Chem

Al Madhoun AS, Mehta V, Li G, Figeys D, Wiper-Bergeron N and Skerjanc IS. Skeletal myosin light chain kinase regulates skeletal myogenesis by phosphorylation of MEF2C. (2011) EMBO J. 30, 2477-89 Pubmed EMBO J PMC Article

Denis N, Palmer-Smith H, Elisma F, Busuttil A, Wright TG, Bou Khalil M, Prat A, Seidah NG, Chrétien M, Mayne J and Figeys D. Quantitative proteomic analysis of PCSK9 gain of function in human hepatic HuH7 cells. (2011) J Proteome Res. 10, 2011-26 Pubmed J Proteome Res

Tian R, Wang S, Elisma F, Li L, Zhou H, Wang L and Figeys D. Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation. (2011) Mol Cell Proteomics. 10, M110.000679 Pubmed Mol Cell Proteomics PMC Article

Gyamera-Acheampong C, Sirois F, Denis NJ, Mishra P, Figeys D, Basak A and Mbikay M. The precursor to the germ cell-specific PCSK4 proteinase is inefficiently activated in transfected somatic cells: evidence of interaction with the BiP chaperone. (2011) Mol Cell Biochem. 348, 43-52 Pubmed Mol Cell Biochem

Kennedy MA, Kabbani N, Lambert JP, Swayne LA, Ahmed F, Figeys D, Bennett SA, Bryan J and Baetz K. Srf1 is a novel regulator of phospholipase D activity and is essential to buffer the toxic effects of C16:0 platelet activating factor. (2011) PLoS Genet. 7, e1001299 Pubmed PLoS Genet PMC Article

Hou W, Zhou H, Bou Khalil M, Seebun D, Bennett SA and Figeys D. Lyso-form fragment ions facilitate the determination of stereospecificity of diacyl glycerophospholipids. (2011) Rapid Commun Mass Spectrom. 25, 205-17 Pubmed Rapid Commun Mass Spectrom

Bou Khalil M, Blais A, Figeys D and Yao Z. Lipin - The bridge between hepatic glycerolipid biosynthesis and lipoprotein metabolism. (2010) Biochim Biophys Acta. 1801, 1249-59 Pubmed Biochim Biophys Acta

Lambert JP, Fillingham J, Siahbazi M, Greenblatt J, Baetz K and Figeys D. Defining the budding yeast chromatin-associated interactome. (2010) Mol Syst Biol. 6, 448 Pubmed Mol Syst Biol PMC Article

Wall ML, Wheeler HL, Smith J, Figeys D and Altosaar I. Mass spectrometric analysis reveals remnants of host-pathogen molecular interactions at the starch granule surface in wheat endosperm. (2010) Phytopathology. 100, 848-54 Pubmed Phytopathology

Zhou H, Hou W, Lambert JP and Figeys D. New ammunition for the proteomic reactor: strong anion exchange beads and multiple enzymes enhance protein identification and sequence coverage. (2010) Anal Bioanal Chem. 397, 3421-30 Pubmed Anal Bioanal Chem

Sundaram M, Zhong S, Bou Khalil M, Zhou H, Jiang ZG, Zhao Y, Iqbal J, Hussain MM, Figeys D, Wang Y and Yao Z. Functional analysis of the missense APOC3 mutation Ala23Thr associated with human hypotriglyceridemia. (2010) J Lipid Res. 51, 1524-34 Pubmed J Lipid Res PMC Article

Labriola JM, daCosta CJ, Wang S, Figeys D, Smith JC, Sturgeon RM and Baenziger JE. Phospholipase C activity affinity purifies with the Torpedo nicotinic acetylcholine receptor. (2010) J Biol Chem. 285, 10337-43 Pubmed J Biol Chem PMC Article

Gyamera-Acheampong C, Vasilescu J, Figeys D and Mbikay M. PCSK4-null sperm display enhanced protein tyrosine phosphorylation and ADAM2 proteolytic processing during in vitro capacitation. (2010) Fertil Steril. 93, 1112-23 Pubmed Fertil Steril

Zhou H, Elisma F, Denis NJ, Wright TG, Tian R, Zhou H, Hou W, Zou H and Figeys D. Analysis of the subcellular phosphoproteome using a novel phosphoproteomic reactor. (2010) J Proteome Res. 9, 1279-88 Pubmed J Proteome Res

Zhou H, Hou W, Lambert JP, Tian R and Figeys D. Analysis of low-abundance proteins using the proteomic reactor with pH fractionation. (2010) Talanta. 80, 1526-31 Pubmed Talanta

Zhong S, Magnolo AL, Sundaram M, Zhou H, Yao EF, Di Leo E, Loria P, Wang S, Bamji-Mirza M, Wang L, McKnight CJ, Figeys D, Wang Y, Tarugi P and Yao Z. Nonsynonymous mutations within APOB in human familial hypobetalipoproteinemia: evidence for feedback inhibition of lipogenesis and postendoplasmic reticulum degradation of apolipoprotein B. (2010) J Biol Chem. 285, 6453-64 Pubmed J Biol Chem PMC Article

Lambert JP, Baetz K and Figeys D. Of proteins and DNA--proteomic role in the field of chromatin research. (2010) Mol Biosyst. 6, 30-7 Pubmed Mol Biosyst

Ryan SD, Whitehead SN, Swayne LA, Moffat TC, Hou W, Ethier M, Bourgeois AJ, Rashidian J, Blanchard AP, Fraser PE, Park DS, Figeys D and Bennett SA. Amyloid-beta42 signals tau hyperphosphorylation and compromises neuronal viability by disrupting alkylacylglycerophosphocholine metabolism. (2009) Proc Natl Acad Sci U S A. 106, 20936-41 Pubmed Proc Natl Acad Sci U S A PMC Article

Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J and Andrews BJ. Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. (2009) Mol Cell. 35, 340-51 Pubmed Mol Cell

Abu-Farha M, Elisma F, Zhou H, Tian R, Zhou H, Asmer MS and Figeys D. Proteomics: from technology developments to biological applications. (2009) Anal Chem. 81, 4585-99 Pubmed Anal Chem

Lambert JP, Mitchell L, Rudner A, Baetz K and Figeys D. A novel proteomics approach for the discovery of chromatin-associated protein networks. (2009) Mol Cell Proteomics. 8, 870-82 Pubmed Mol Cell Proteomics PMC Article

Zhou H, Hou W, Denis NJ, Zhou H, Vasilescu J, Zou H and Figeys D. Glycoproteomic reactor for human plasma. (2009) J Proteome Res. 8, 556-66 Pubmed J Proteome Res

Bhattacharya S, Shcherbik N, Vasilescu J, Smith JC, Figeys D and Haines DS. Identification of lysines within membrane-anchored Mga2p120 that are targets of Rsp5p ubiquitination and mediate mobilization of tethered Mga2p90. (2009) J Mol Biol. 385, 718-25 Pubmed J Mol Biol PMC Article

Bazile F, Gagné JP, Mercier G, Lo KS, Pascal A, Vasilescu J, Figeys D, Poirier GG, Kubiak JZ and Chesnel F. Differential proteomic screen to evidence proteins ubiquitinated upon mitotic exit in cell-free extract of Xenopus laevis embryos. (2008) J Proteome Res. 7, 4701-14 Pubmed J Proteome Res

Smith JC, Hou W, Whitehead SN, Ethier M, Bennett SA and Figeys D. Identification of lysophosphatidylcholine (LPC) and platelet activating factor (PAF) from PC12 cells and mouse cortex using liquid chromatography/multi-stage mass spectrometry (LC/MS3). (2008) Rapid Commun Mass Spectrom. 22, 3579-87 Pubmed Rapid Commun Mass Spectrom

Hou W, Zhou H, Elisma F, Bennett SA and Figeys D. Technological developments in lipidomics. (2008) Brief Funct Genomic Proteomic. 7, 395-409 Pubmed Brief Funct Genomic Proteomic

Wislet-Gendebien S, Visanji NP, Whitehead SN, Marsilio D, Hou W, Figeys D, Fraser PE, Bennett SA and Tandon A. Differential regulation of wild-type and mutant alpha-synuclein binding to synaptic membranes by cytosolic factors. (2008) BMC Neurosci. 9, 92 Pubmed BMC Neurosci PMC Article

Figeys D. Mapping the human protein interactome. (2008) Cell Res. 18, 716-24 Pubmed Cell Res

Mitchell L, Lambert JP, Gerdes M, Al-Madhoun AS, Skerjanc IS, Figeys D and Baetz K. Functional dissection of the NuA4 histone acetyltransferase reveals its role as a genetic hub and that Eaf1 is essential for complex integrity. (2008) Mol Cell Biol. 28, 2244-56 Pubmed Mol Cell Biol PMC Article

Smith JC and Figeys D. Recent developments in mass spectrometry-based quantitative phosphoproteomics. (2008) Biochem Cell Biol. 86, 137-48 Pubmed Biochem Cell Biol

Vasilescu J, Smith JC, Zweitzig DR, Denis NJ, Haines DS and Figeys D. Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometry. (2008) J Mass Spectrom. 43, 296-304 Pubmed J Mass Spectrom

Abu-Farha M, Lambert JP, Al-Madhoun AS, Elisma F, Skerjanc IS and Figeys D. The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase. (2008) Mol Cell Proteomics. 7, 560-72 Pubmed Mol Cell Proteomics

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P and Pandey A. Human Proteinpedia enables sharing of human protein data. (2008) Nat Biotechnol. 26, 164-7 Pubmed Nat Biotechnol

Whitehead SN, Hou W, Ethier M, Smith JC, Bourgeois A, Denis R, Bennett SA and Figeys D. Identification and quantitation of changes in the platelet activating factor family of glycerophospholipids over the course of neuronal differentiation by high-performance liquid chromatography electrospray ionization tandem mass spectrometry. (2007) Anal Chem. 79, 8539-48 Pubmed Anal Chem

Sopko R, Huang D, Smith JC, Figeys D and Andrews BJ. Activation of the Cdc42p GTPase by cyclin-dependent protein kinases in budding yeast. (2007) EMBO J. 26, 4487-500 Pubmed EMBO J PMC Article

Smith JC, Duchesne MA, Tozzi P, Ethier M and Figeys D. A differential phosphoproteomic analysis of retinoic acid-treated P19 cells. (2007) J Proteome Res. 6, 3174-86 Pubmed J Proteome Res

Smith JC, Lambert JP, Elisma F and Figeys D. Proteomics in 2005/2006: developments, applications and challenges. (2007) Anal Chem. 79, 4325-43 Pubmed Anal Chem

Denis NJ, Vasilescu J, Lambert JP, Smith JC and Figeys D. Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. (2007) Proteomics. 7, 868-74 Pubmed Proteomics

Hou W, Ethier M, Smith JC, Sheng Y and Figeys D. Multiplexed proteomic reactor for the processing of proteomic samples. (2007) Anal Chem. 79, 39-44 Pubmed Anal Chem

Vasilescu J, Zweitzig DR, Denis NJ, Smith JC, Ethier M, Haines DS and Figeys D. The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells. (2007) J Proteome Res. 6, 298-305 Pubmed J Proteome Res

Ethier M, Hou W, Duewel HS and Figeys D. The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis. (2006) J Proteome Res. 5, 2754-9 Pubmed J Proteome Res

Smith JC and Figeys D. Proteomics technology in systems biology. (2006) Mol Biosyst. 2, 364-70 Pubmed Mol Biosyst

Vasilescu J and Figeys D. Mapping protein-protein interactions by mass spectrometry. (2006) Curr Opin Biotechnol. 17, 394-9 Pubmed Curr Opin Biotechnol

Ethier M, Lambert JP, Vasilescu J and Figeys D. Analysis of protein interaction networks using mass spectrometry compatible techniques. (2006) Anal Chim Acta. 564, 10-8 Pubmed Anal Chim Acta

Lambert JP, Ethier M, Smith JC and Figeys D. Proteomics: from gel based to gel free. (2005) Anal Chem. 77, 3771-87 Pubmed Anal Chem

Figeys D. Combining different 'omics' technologies to map and validate protein-protein interactions in humans. (2004) Brief Funct Genomic Proteomic. 2, 357-65 Pubmed Brief Funct Genomic Proteomic

Olsen JV, Andersen JR, Nielsen PA, Nielsen ML, Figeys D, Mann M and Wisniewski JR. HysTag--a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain. (2004) Mol Cell Proteomics. 3, 82-92 Pubmed Mol Cell Proteomics

Le Bihan T, Duewel HS and Figeys D. On-line strong cation exchange micro-HPLC-ESI-MS/MS for protein identification and process optimization. (2003) J Am Soc Mass Spectrom. 14, 719-27 Pubmed J Am Soc Mass Spectrom

Figeys D. Proteomics in 2002: a year of technical development and wide-ranging applications. (2003) Anal Chem. 75, 2891-905 Pubmed Anal Chem

Figeys D. Novel approaches to map protein interactions. (2003) Curr Opin Biotechnol. 14, 119-25 Pubmed Curr Opin Biotechnol

Lin Y, Khokhlatchev A, Figeys D and Avruch J. Death-associated protein 4 binds MST1 and augments MST1-induced apoptosis. (2002) J Biol Chem. 277, 47991-8001 Pubmed J Biol Chem

Vasilescu J, Smith JC, Ethier M and Figeys D. Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry. (2005) J Proteome Res. 4, 2192-200 Pubmed J Proteome Res

Sun Z, Ning Z, Cheng K, Duan H, Wu Q, Mayne J and Figeys D. MetaPep: A core peptide database for faster human gut metaproteomics database searches. (2023) Comput Struct Biotechnol J. 21, 4228-4237 Pubmed Comput Struct Biotechnol J 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

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

Ling HH, Beaulé C, Chiang CK, Tian R, Figeys D and Cheng HY. Time-of-day- and light-dependent expression of ubiquitin protein ligase E3 component N-recognin 4 (UBR4) in the suprachiasmatic nucleus circadian clock. (2014) PLoS One. 9, e103103 Pubmed PLoS One PMC Article

Parsanejad M, Bourquard N, Qu D, Zhang Y, Huang E, Rousseaux MW, Aleyasin H, Irrcher I, Callaghan S, Vaillant DC, Kim RH, Slack RS, Mak TW, Reddy ST, Figeys D and Park DS. DJ-1 interacts with and regulates paraoxonase-2, an enzyme critical for neuronal survival in response to oxidative stress. (2014) PLoS One. 9, e106601 Pubmed PLoS One PMC Article

Lee JW, Figeys D and Vasilescu J. Biomarker assay translation from discovery to clinical studies in cancer drug development: quantification of emerging protein biomarkers. (2007) Adv Cancer Res. 96, 269-98 Pubmed Adv Cancer Res

Le Bihan T, Robinson MD, Stewart II and Figeys D. Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures. (2004) J Proteome Res. 3, 1138-48 Pubmed J Proteome Res

Bennett SA, Valenzuela N, Xu H, Franko B, Fai S and Figeys D. Using neurolipidomics to identify phospholipid mediators of synaptic (dys)function in Alzheimer's Disease. (2013) Front Physiol. 4, 168 Pubmed Front Physiol PMC Article

McDowell GS, Blanchard AP, Taylor GP, Figeys D, Fai S and Bennett SA. Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification)--an online bioinformatic search engine. (2014) Biomed Res Int. 2014, 818670 Pubmed Biomed Res Int PMC Article

Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T and Figeys D. Large-scale mapping of human protein-protein interactions by mass spectrometry. (2007) Mol Syst Biol. 3, 89 Pubmed Mol Syst Biol PMC Article

Mitchell L, Lau A, Lambert JP, Zhou H, Fong Y, Couture JF, Figeys D and Baetz K. Regulation of septin dynamics by the Saccharomyces cerevisiae lysine acetyltransferase NuA4. (2011) PLoS One. 6, e25336 Pubmed PLoS One PMC Article

Bou Khalil M, Hou W, Zhou H, Elisma F, Swayne LA, Blanchard AP, Yao Z, Bennett SA and Figeys D. Lipidomics era: accomplishments and challenges. (2010) Mass Spectrom Rev. 29, 877-929 Pubmed Mass Spectrom Rev

Figeys D. Mapping protein-protein interactions. (2005) Methods Biochem Anal. 45, 63-84 Pubmed Methods Biochem Anal

Fekete EE, Figeys D and Zhang X. Microbiota-directed biotherapeutics: considerations for quality and functional assessment. (2023) Gut Microbes. 15, 2186671 Pubmed Gut Microbes PMC Article

Figeys D. Proteomics: the basic overview. (2005) Methods Biochem Anal. 45, 1-62 Pubmed Methods Biochem Anal

Simopoulos CMA, Figeys D and Lavallée-Adam M. Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies. (2022) Methods Mol Biol. 2456, 319-338 Pubmed Methods Mol Biol

Stewart II, Zhao L, Le Bihan T, Larsen B, Scozzaro S, Figeys D, Mao GD, Ornatsky O, Dharsee M, Orsi C, Ewing R and Goh T. The reproducible acquisition of comparative liquid chromatography/tandem mass spectrometry data from complex biological samples. (2004) Rapid Commun Mass Spectrom. 18, 1697-710 Pubmed Rapid Commun Mass Spectrom

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

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. (2022) Gut Microbes. 14, 2035658 Pubmed Gut Microbes PMC Article

Ethier M, Figeys D and Perreault H. N-glycosylation analysis using the StrOligo algorithm. (2006) Methods Mol Biol. 328, 187-97 Pubmed Methods Mol Biol

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

Ethier M and Figeys D. Strategy to design improved proteomic experiments based on statistical analyses of the chemical properties of identified peptides. (2005) J Proteome Res. 4, 2201-6 Pubmed J Proteome Res

Mazereeuw G, Herrmann N, Xu H, Blanchard AP, Figeys D, Oh PI, Bennett SA and Lanctôt KL. Platelet activating factors are associated with depressive symptoms in coronary artery disease patients: a hypothesis-generating study. (2015) Neuropsychiatr Dis Treat. 11, 2309-14 Pubmed Neuropsychiatr Dis Treat PMC Article

Abu-Farha M, Elisma F and Figeys D. Identification of protein-protein interactions by mass spectrometry coupled techniques. (2008) Adv Biochem Eng Biotechnol. 110, 67-80 Pubmed Adv Biochem Eng Biotechnol