MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

Bottom-Up Proteomics (2013–2015): Keeping up in the Era of Systems Biology

(2015) Janice Mayne et al.   ANALYTICAL CHEMISTRY

Monitoring host responses to the gut microbiota

(2015) Joshua S Lichtman et al.   ISME Journal

Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics

(2015) Bobbie-Jo M. Webb-Robertson et al.   JOURNAL OF PROTEOME RESEARCH

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Navigating through metaproteomics data: A logbook of database searching

(2015) Thilo Muth et al.   PROTEOMICS

The Unipept metaproteomics analysis pipeline

(2015) Bart Mesuere et al.   PROTEOMICS

Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota

(2015) Weili Xiong et al.   PROTEOMICS

Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats

(2015) Xu Zhang et al.   Scientific Reports

Site-specific characterization of cell membrane N-glycosylation with integrated hydrophilic interaction chromatography solid phase extraction and LC–MS/MS

(2014) Rui Chen et al.   Journal of Proteomics

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

Mitochondrial dysfunction and tissue injury by alcohol, high fat, nonalcoholic substances and pathological conditions through post-translational protein modifications

(2014) Byoung-Joon Song et al.   Redox Biology

High-fat diet alters gut microbiota physiology in mice

(2013) Hannelore Daniel et al.   ISME Journal

Increased Proportions of Bifidobacterium and the Lactobacillus Group and Loss of Butyrate-Producing Bacteria in Inflammatory Bowel Disease

(2013) W. Wang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

(2012) Bart Mesuere et al.   JOURNAL OF PROTEOME RESEARCH

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

(2012) Thilo Muth et al.   Molecular BioSystems

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Techniques used to characterize the gut microbiota: a guide for the clinician

(2012) Marianne H. Fraher et al.   Nature Reviews Gastroenterology & Hepatology

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

(2012) Carolin A. Kolmeder et al.   PLoS One

Structural Changes of Gut Microbiota during Berberine-Mediated Prevention of Obesity and Insulin Resistance in High-Fat Diet-Fed Rats

(2012) Xu Zhang et al.   PLoS One

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Comparison of Two Common Outpatient Preparations for Colonoscopy in Children and Youth

(2009) Carolina Jimenez-Rivera et al.   Gastroenterology Research and Practice

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

(2008) Peter J. Turnbaugh et al.   Cell Host & Microbe

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiotic gut microbes modulate human metabolic phenotypes

(2008) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA