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

Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case

(2015) Jacque C. Young et al.   PROTEOMICS

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

(2014) Juanjuan Chai et al.   BMC EVOLUTIONARY BIOLOGY

15N- and2H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity

(2014) Nicholas B. Justice et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial protein signals are associated with Crohn’s disease

(2014) Catherine Juste et al.   GUT

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

(2014) Morgan M Steffen et al.   ISME Journal

The African Genome Variation Project shapes medical genetics in Africa

(2014) Deepti Gurdasani et al.   NATURE

Meconium Microbiome Analysis Identifies Bacteria Correlated with Premature Birth

(2014) Alexandria N. Ardissone et al.   PLoS One

Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages

(2014) E. A. Ottesen et al.   SCIENCE

Development of the preterm infant gut microbiome: a research priority

(2014) Maureen W Groer et al.   Microbiome

Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific

(2013) Curt R. Fischer et al.   ACS Chemical Biology

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

Sipros/ProRata: a versatile informatics system for quantitative community proteomics

(2013) Yingfeng Wang et al.   BIOINFORMATICS

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

(2013) Martin von Bergen et al.   ISME Journal

Metaproteomics of our microbiome — Developing insight in function and activity in man and model systems

(2013) Carolin A. Kolmeder et al.   Journal of Proteomics

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative Microbial Analysis of Paired Amniotic Fluid and Cord Blood from Pregnancies Complicated by Preterm Birth and Early-Onset Neonatal Sepsis

(2013) Xiaowei Wang et al.   PLoS One

Quantitative proteomics in the field of microbiology

(2013) Andreas Otto et al.   PROTEOMICS

Development of intestinal microbiota in infants and its impact on health

(2013) Sebastien Matamoros et al.   TRENDS IN MICROBIOLOGY

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

Exhaustive database searching for amino acid mutations in proteomes

(2012) Doug Hyatt et al.   BIOINFORMATICS

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

(2012) Jose C. Clemente et al.   CELL

Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

(2012) Robert L. Hettich et al.   CURRENT OPINION IN MICROBIOLOGY

Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure

(2012) Manuel Ferrer et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring mixed microbial community functioning: recent advances in metaproteomics

(2012) Alma Siggins et al.   FEMS MICROBIOLOGY ECOLOGY

Coupling a Detergent Lysis/Cleanup Methodology with Intact Protein Fractionation for Enhanced Proteome Characterization

(2012) Ritin Sharma et al.   JOURNAL OF PROTEOME RESEARCH

A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data

(2012) Carrie C Buchanan et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Protein-based stable isotope probing (protein-SIP) in functional metaproteomics

(2012) Jana Seifert et al.   MASS SPECTROMETRY REVIEWS

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

(2012) Thilo Muth et al.   Molecular BioSystems

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

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

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

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

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Combining gene prediction methods to improve metagenomic gene annotation

(2011) Non G Yok et al.   BMC BIOINFORMATICS

An iterative workflow for mining the human intestinal metaproteome

(2011) Koos Rooijers et al.   BMC GENOMICS

Host–microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal–luminal interface

(2011) Laura L. Presley et al.   INFLAMMATORY BOWEL DISEASES

Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics

(2011) Paul Abraham et al.   JOURNAL OF PROTEOME RESEARCH

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

(2011) Zhou Li et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

(2011) Chongle Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination

(2011) Kerstin Berer et al.   NATURE

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface

(2011) Xiaoxiao Li et al.   PLoS One

Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments

(2011) Brandi L. Cantarel et al.   PLoS One

Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

(2010) Karuna Chourey et al.   JOURNAL OF PROTEOME RESEARCH

The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models

(2010) Sandra Nell et al.   NATURE REVIEWS MICROBIOLOGY

Adaptation of protein expression byEscherichia coliin the gastrointestinal tract of gnotobiotic mice

(2009) Carl Alpert et al.   ENVIRONMENTAL MICROBIOLOGY

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level

(2009) M. Keller et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multidimensional LC Separations in Shotgun Proteomics

(2008) Akira Motoyama et al.   ANALYTICAL CHEMISTRY

SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function

(2008) Marcus Krüger et al.   CELL

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Proteomic investigation of the adaptation ofLactococcus lactis to the mouse digestive tract

(2008) Karine Roy et al.   PROTEOMICS