Tag Archive: Publications

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

Li L, Ning Z, Zhang X, Mayne J, Cheng K, Stintzi A, Figeys D Microbiome 2020 Mar;8(1):33 PMID: 32160905 Abstract BACKGROUND: Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of…
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Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics

Wang J, Zhang X, Li L, Ning Z, Mayne J, Schmitt-Ulms C, Walker K, Cheng K, Figeys D Anal. Chem. 2020 Mar; PMID: 32096399 Abstract Changes in microbiome composition and function have been linked to human health and diseases. Metaproteomics…
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An in vitro model maintaining taxon-specific functional activities of the gut microbiome

Li L, Abou-Samra E, Ning Z, Zhang X, Mayne J, Wang J, Cheng K, Walker K, Stintzi A, Figeys D Nat Commun 2019 09;10(1):4146 PMID: 31515476 Abstract In vitro gut microbiome models could provide timely and cost-efficient solutions to study…
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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

Wang Y, Niu Q, Zhang X, Liu L, Wang Y, Chen Y, Negi M, Figeys D, Li YY, Zhang T Microbiome 2019 08;7(1):122 PMID: 31462278 Abstract BACKGROUND: The metabolic capacities of anammox bacteria and associated microbial community interactions in partial-nitritation…
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Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease

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, Figeys D Nat Commun 2018 07;9(1):2873 PMID: 30030445 Abstract Alterations in gut microbiota have…
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MetaLab: an automated pipeline for metaproteomic data analysis

Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J, Stintzi A, Figeys D Microbiome 2017 Dec;5(1):157 PMID: 29197424 Abstract BACKGROUND: Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions…
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Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach

Li L, Zhang X, Ning Z, Mayne J, Moore JI, Butcher J, Chiang CK, Mack D, Stintzi A, Figeys D J. Proteome Res. 2018 01;17(1):154-163 PMID: 29130306 Abstract In vitro culture based approaches are time- and cost-effective solutions for rapidly…
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