Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis

(2015) Olga T. Schubert et al.   Cell Host & Microbe

Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves

(2015) Florian Ryffel et al.   ISME Journal

Reproducible and Consistent Quantification of theSaccharomyces cerevisiaeProteome by SWATH-mass spectrometry

(2015) Nathalie Selevsek et al.   MOLECULAR & CELLULAR PROTEOMICS

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

Building high-quality assay libraries for targeted analysis of SWATH MS data

(2015) Olga T Schubert et al.   Nature Protocols

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

Methylobacterium extorquens: methylotrophy and biotechnological applications

(2014) Andrea M. Ochsner et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

(2014) George Rosenberger et al.   BIOINFORMATICS

DIANA—algorithmic improvements for analysis of data-independent acquisition MS data

(2014) Johan Teleman et al.   BIOINFORMATICS

Commensal bacteria mediated defenses against pathogens

(2014) Michael C Abt et al.   CURRENT OPINION IN IMMUNOLOGY

Spatial distribution analyses of natural phyllosphere-colonizing bacteria onArabidopsis thalianarevealed by fluorescencein situhybridization

(2014) Mitja N. P. Remus-Emsermann et al.   ENVIRONMENTAL MICROBIOLOGY

Nature's microbiome: introduction

(2014) Jacob A. Russell et al.   MOLECULAR ECOLOGY

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans

(2014) Thomas Kost et al.   Frontiers in Microbiology

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere

(2013) P. Stiefel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis

(2013) Olga T. Schubert et al.   Cell Host & Microbe

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

(2013) Natacha Bodenhausen et al.   PLoS One

Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites

(2013) X. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant-bacterium interactions analyzed by proteomics

(2013) Amber Afroz et al.   Frontiers in Plant Science

Forward GeneticIn PlantaScreen for Identification of Plant-Protective Traits of Sphingomonas sp. Strain Fr1 against Pseudomonas syringae DC3000

(2012) Christine Vogel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

(2012) Fredrik Bäckhed et al.   Cell Host & Microbe

Oxalyl-Coenzyme A Reduction to Glyoxylate Is the Preferred Route of Oxalate Assimilation in Methylobacterium extorquens AM1

(2012) K. Schneider et al.   JOURNAL OF BACTERIOLOGY

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

Bacterial anoxygenic photosynthesis on plant leaf surfaces

(2012) Nof Atamna-Ismaeel et al.   Environmental Microbiology Reports

Protection of Arabidopsis thaliana against Leaf-Pathogenic Pseudomonas syringae by Sphingomonas Strains in a Controlled Model System

(2011) Gerd Innerebner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mechanism for sulfur acquisition by the alkanesulfonate monooxygenase system

(2011) Holly R. Ellis   BIOORGANIC CHEMISTRY

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

(2011) Claudia Knief et al.   ISME Journal

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry

(2011) Christina Ludwig et al.   MOLECULAR & CELLULAR PROTEOMICS

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Microbiology of the phyllosphere: a playground for testing ecological concepts

(2011) Katrin M. Meyer et al.   OECOLOGIA

Bacterial adaptation to life in association with plants - A proteomic perspective from culture to in situ conditions

(2011) Claudia Knief et al.   PROTEOMICS

Competitiveness of Diverse Methylobacterium Strains in the Phyllosphere of Arabidopsis thaliana and Identification of Representative Models, Including M. extorquens PA1

(2010) Claudia Knief et al.   MICROBIAL ECOLOGY

Functional investigation of methanol dehydrogenase-like protein XoxF in Methylobacterium extorquens AM1

(2010) S. Schmidt et al.   MICROBIOLOGY-SGM

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Plant-Growth-Promoting Rhizobacteria

(2009) Ben Lugtenberg et al.   Annual Review of Microbiology

Characterization of Alanine Catabolism in Pseudomonas aeruginosa and Its Importance for Proliferation In Vivo

(2009) M. L. Boulette et al.   JOURNAL OF BACTERIOLOGY

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

(2009) Lukas Reiter et al.   MOLECULAR & CELLULAR PROTEOMICS

Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics

(2009) R. Peyraud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

(2009) N. Delmotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivation-Independent Characterization of Methylobacterium Populations in the Plant Phyllosphere by Automated Ribosomal Intergenic Spacer Analysis

(2008) C. Knief et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE