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

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

(2019) Robert H. Mills et al.   mSystems

Separating host and microbiome contributions to drug pharmacokinetics and toxicity

(2019) Michael Zimmermann et al.   SCIENCE

Perspective and Guidelines for Metaproteomics in Microbiome Studies

(2019) Xu Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

(2019) Manuel Kleiner   mSystems

A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip

(2019) Sasan Jalili-Firoozinezhad et al.   Nature Biomedical Engineering

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

(2019) Leyuan Li et al.   Nature Communications

Berberine treatment increases Akkermansia in the gut and improves high-fat diet-induced atherosclerosis in Apoe −/− mice

(2018) Lin Zhu et al.   ATHEROSCLEROSIS

iMetaLab 1.0: a web platform for metaproteomics data analysis

(2018) Bo Liao et al.   BIOINFORMATICS

Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection

(2018) Maria Guirro et al.   ELECTROPHORESIS

Assessing the impact of protein extraction methods for human gut metaproteomics

(2018) Xu Zhang et al.   Journal of Proteomics

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Xu Zhang et al.   Nature Communications

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Regulatory watch: FDA new drug approvals in Q2 2018

(2018) Lisa Urquhart   NATURE REVIEWS DRUG DISCOVERY

Tablets of multi-unit pellet system for controlled drug delivery

(2017) Tongkai Chen et al.   JOURNAL OF CONTROLLED RELEASE

Pathview Web: user friendly pathway visualization and data integration

(2017) Weijun Luo et al.   NUCLEIC ACIDS RESEARCH

Assessing species biomass contributions in microbial communities via metaproteomics

(2017) Manuel Kleiner et al.   Nature Communications

MetaLab: an automated pipeline for metaproteomic data analysis

(2017) Kai Cheng et al.   Microbiome

A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies

(2017) Gift Nyamundanda et al.   Scientific Reports

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

(2016) Pranjul Shah et al.   Nature Communications

Co-culture of Living Microbiome with Microengineered Human Intestinal Villi in a Gut-on-a-Chip Microfluidic Device

(2016) Hyun Jung Kim et al.   Jove-Journal of Visualized Experiments

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

(2016) Xu Zhang et al.   Microbiome

Antimicrobial activity of ibuprofen: New perspectives on an “Old” non-antibiotic drug

(2015) Jelena Obad et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

The re-emergence of natural products for drug discovery in the genomics era

(2015) Alan L. Harvey et al.   NATURE REVIEWS DRUG DISCOVERY

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)

(2015) Jennifer M. Auchtung et al.   Microbiome

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

(2013) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Inhibition of bacterial thioredoxin reductase: an antibiotic mechanism targeting bacteria lacking glutathione

(2012) Jun Lu et al.   FASEB JOURNAL

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

(2012) Pieter Van den Abbeele et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour

(2012) John F. Cryan et al.   NATURE REVIEWS NEUROSCIENCE

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

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods

(2011) Chao Chen et al.   PLoS One

Gut microbiota: a potential new territory for drug targeting

(2008) Wei Jia et al.   NATURE REVIEWS DRUG DISCOVERY