Metaproteomic analysis using the Galaxy framework

Multi-omic data analysis using Galaxy

(2015) Jorrit Boekel et al.   NATURE BIOTECHNOLOGY

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

The Unipept metaproteomics analysis pipeline

(2015) Bart Mesuere et al.   PROTEOMICS

In situexpression of nitrite-dependent anaerobic methane oxidation proteins byCandidatusMethylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer

(2015) Buck T. Hanson et al.   Environmental Microbiology Reports

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

(2014) Zhihua Bao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO2-Fixing Constituent in a Self-Regenerating Biocathode

(2014) Zheng Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics

(2014) Anke Penzlin et al.   BIOINFORMATICS

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study

(2014) David C. Gillan et al.   ENVIRONMENTAL MICROBIOLOGY

Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents

(2014) Hung-Jen Huang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

(2014) Anna A Georges et al.   ISME Journal

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

(2014) Weili Xiong et al.   JOURNAL OF PROTEOME RESEARCH

MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics

(2014) Timo Sachsenberg et al.   JOURNAL OF PROTEOME RESEARCH

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

(2014) Pratik D. Jagtap et al.   JOURNAL OF PROTEOME RESEARCH

Metaproteomics of soils from semiarid environment: Functional and phylogenetic information obtained with different protein extraction methods

(2014) F. Bastida et al.   Journal of Proteomics

Metaproteomic Survey of Six Aquatic Habitats: Discovering the Identities of Microbial Populations Active in Biogeochemical Cycling

(2014) Buck T. Hanson et al.   MICROBIAL ECOLOGY

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

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

Metaproteomics: Evaluation of protein extraction from activated sludge

(2014) Susan Hove Hansen et al.   PROTEOMICS

High-throughput parallel proteogenomics: A bacterial case study

(2014) Brett Chapman et al.   PROTEOMICS

Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria

(2014) Dragana Bozinovski et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants

(2013) F. Kohrs et al.   ANAEROBE

Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

(2013) Yue Tang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial colonization of microbial biofilms in oral squamous cell carcinoma

(2013) J. Bolz et al.   Clinical Oral Investigations

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

(2013) Fan Lü et al.   ISME Journal

Which metaproteome? The impact of protein extraction bias on metaproteomic analyses

(2013) Dagmar Hajkova Leary et al.   MOLECULAR AND CELLULAR PROBES

Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

(2013) Alessandro Tanca et al.   PLoS One

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

(2013) Pratik Jagtap et al.   PROTEOMICS

Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach

(2013) M. Albertsen et al.   WATER SCIENCE AND TECHNOLOGY

Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts

(2013) M. Kleiner et al.   mBio

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

Identification and Distribution of High-Abundance Proteins in the Octopus Spring Microbial Mat Community

(2012) Courtney S. Schaffert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma

(2012) Smruti Pushalkar et al.   BMC MICROBIOLOGY

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley et al.   JOURNAL OF PROTEOME RESEARCH

Metaproteome Analysis and Molecular Genetics of Rat Intestinal Microbiota Reveals Section and Localization Resolved Species Distribution and Enzymatic Functionalities

(2012) Sven-Bastiaan Haange et al.   JOURNAL OF PROTEOME RESEARCH

Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury

(2012) Derrick E Fouts et al.   Journal of Translational Medicine

A framework for human microbiome research

(2012)   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

Deep metaproteomic analysis of human salivary supernatant

(2012) Pratik Jagtap et al.   PROTEOMICS

Soil metaproteomics – Comparative evaluation of protein extraction protocols

(2012) Katharina M. Keiblinger et al.   SOIL BIOLOGY & BIOCHEMISTRY

A metaproteomic approach gives functional insights into anaerobic digestion

(2011) F. Abram et al.   JOURNAL OF APPLIED MICROBIOLOGY

Comparative Metaproteomic Analysis on Consecutively Rehmannia glutinosa-Monocultured Rhizosphere Soil

(2011) Linkun Wu et al.   PLoS One

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

Proteomic Analysis of Ethene-Enriched Groundwater Microcosms from a Vinyl Chloride-Contaminated Site

(2010) Adina S. Chuang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

(2010) Robert M Morris et al.   ISME Journal

A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry

(2010) J.D. Rudney et al.   Molecular Oral Microbiology

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms

(2009) Florence Abram et al.   ELECTROPHORESIS

A Dynamic Range Compression and Three-Dimensional Peptide Fractionation Analysis Platform Expands Proteome Coverage and the Diagnostic Potential of Whole Saliva

(2009) Sricharan Bandhakavi et al.   JOURNAL OF PROTEOME RESEARCH

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

(2008) Paul Wilmes et al.   PLoS One