Proteogenomic Analysis ofBradyrhizobium japonicumUSDA110 Using Genosuite, an Automated Multi-algorithmic Pipeline

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

Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs

(2012) Takashi Okubo et al.   MICROBES AND ENVIRONMENTS

Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

(2012) Amit Kumar Yadav et al.   PLoS One

Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601

(2011) Yi Zhong et al.   CELL RESEARCH

A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

(2011) R. Chaerkady et al.   GENOME RESEARCH

MassWiz: A Novel Scoring Algorithm with Target-Decoy Based Analysis Pipeline for Tandem Mass Spectrometry

(2011) Amit Kumar Yadav et al.   JOURNAL OF PROTEOME RESEARCH

FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines

(2011) David C. Wedge et al.   JOURNAL OF PROTEOME RESEARCH

Extracellular Matrix Composition and Remodeling in Human Abdominal Aortic Aneurysms: A Proteomics Approach

(2011) Athanasios Didangelos et al.   MOLECULAR & CELLULAR PROTEOMICS

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery

(2011) Amit Kumar Yadav et al.   PLoS One

Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study

(2011) Eli Venter et al.   PLoS One

Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

(2011) Takakazu Kaneko et al.   Genes

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome

(2010) Julie Lamontagne et al.   BMC GENOMICS

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

Bacterial protein acetylation: the dawning of a new age

(2010) Linda I. Hu et al.   MOLECULAR MICROBIOLOGY

Rhizobial Adaptation to Hosts, a New Facet in the Legume Root-Nodule Symbiosis

(2010) Marion Koch et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines

(2010) Wen Yu et al.   PROTEOMICS

An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules

(2010) Nathanaël Delmotte et al.   PROTEOMICS

A Novel Pathway for the Biosynthesis of Heme inArchaea: Genome-Based Bioinformatic Predictions and Experimental Evidence

(2010) Sonja Storbeck et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Accurate and Sensitive Peptide Identification with Mascot Percolator

(2009) Markus Brosch et al.   JOURNAL OF PROTEOME RESEARCH

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 Proteomics Identifications database: 2010 update

(2009) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol

(2008) S. Gallien et al.   GENOME RESEARCH

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

(2008) N. Gupta et al.   GENOME RESEARCH

PepLine: A Software Pipeline for High-Throughput Direct Mapping of Tandem Mass Spectrometry Data on Genomic Sequences

(2008) Myriam Ferro et al.   JOURNAL OF PROTEOME RESEARCH

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH