Improving the quality of genome, protein sequence, and taxonomy databases: A prerequisite for microbiome meta-omics 2.0

The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation

(2015) Thilo Muth et al.   JOURNAL OF PROTEOME RESEARCH

Multi-omic data analysis using Galaxy

(2015) Jorrit Boekel et al.   NATURE BIOTECHNOLOGY

Navigating through metaproteomics data: A logbook of database searching

(2015) Thilo Muth et al.   PROTEOMICS

An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

(2015) Adam R Rivers et al.   Standards in Genomic Sciences

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

A Proteome Quality Index

(2014) Jan Zaucha et al.   ENVIRONMENTAL MICROBIOLOGY

RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti

(2014) Arjan de Groot et al.   Genome Biology and Evolution

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

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

N-Terminal-oriented Proteogenomics of the Marine BacteriumRoseobacter DenitrificansOch114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) Labeling and Diagonal Chromatography

(2014) Céline Bland et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomics ofGammarus fossarumto Document the Reproductive System of Amphipods

(2014) Judith Trapp et al.   MOLECULAR & CELLULAR PROTEOMICS

N-terminomics and proteogenomics, getting off to a good start

(2014) Erica M. Hartmann et al.   PROTEOMICS

Magnetic Immunoaffinity Enrichment for Selective Capture and MS/MS Analysis of N-Terminal-TMPP-Labeled Peptides

(2013) Céline Bland et al.   JOURNAL OF PROTEOME RESEARCH

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

(2013) Pratik Jagtap et al.   PROTEOMICS

When Is a Microbial Culture "Pure"? Persistent Cryptic Contaminant Escapes Detection Even with Deep Genome Sequencing

(2013) P. M. Shrestha et al.   mBio

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

(2012) Joseph A Christie-Oleza et al.   BMC GENOMICS

De novo derivation of proteomes from transcriptomes for transcript and protein identification

(2012) Vanessa C Evans et al.   NATURE METHODS

Human Microbiome in Health and Disease

(2011) Kathryn J. Pflughoeft et al.   Annual Review of Pathology-Mechanisms of Disease

Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil

(2011) Maiysha D. Jones et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses

(2010) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

PLAST: parallel local alignment search tool for database comparison

(2009) Van Hoa Nguyen et al.   BMC BIOINFORMATICS

Proteomics-based Refinement ofDeinococcus desertiGenome Annotation Reveals an Unwonted Use of Non-canonical Translation Initiation Codons

(2009) Mathieu Baudet et al.   MOLECULAR & CELLULAR PROTEOMICS

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS