Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Intruders below the Radar: Molecular Pathogenesis of Bartonella spp.

(2012) A. Harms et al.   CLINICAL MICROBIOLOGY REVIEWS

Hemin Binding Protein C Is Found in Outer Membrane Vesicles and Protects Bartonella henselae against Toxic Concentrations of Hemin

(2012) Julie A. Roden et al.   INFECTION AND IMMUNITY

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis

(2012) Denisse L. Leyton et al.   NATURE REVIEWS MICROBIOLOGY

Proteomic and bioinformatic analysis of outer membrane proteins of the protobacterium Bartonella henselae (Bartonellaceae)

(2011) D.M. Li et al.   GENETICS AND MOLECULAR RESEARCH

Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT

(2011) Bryan R. Fonslow et al.   JOURNAL OF PROTEOME RESEARCH

Quantification of mRNA and protein and integration with protein turnover in a bacterium

(2011) T. Maier et al.   Molecular Systems Biology

Absolute quantification of microbial proteomes at different states by directed mass spectrometry

(2011) A. Schmidt et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Adhesion and host cell modulation: critical pathogenicity determinants of Bartonella henselae

(2011) Bettina Franz et al.   Parasites & Vectors

Proteomic Characterization of Cellular and Molecular Processes that Enable the Nanoarchaeum equitans-Ignicoccus hospitalis Relationship

(2011) Richard J. Giannone et al.   PLoS One

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

(2011) Eli Venter et al.   PLoS One

Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella

(2011) Philipp Engel et al.   PLoS Genetics

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Comprehensive proteomics

(2010) Martin Beck et al.   CURRENT OPINION IN BIOTECHNOLOGY

The BatR/BatS Two-Component Regulatory System Controls the Adaptive Response of Bartonella henselae during Human Endothelial Cell Infection

(2010) M. Quebatte et al.   JOURNAL OF BACTERIOLOGY

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Exploring the membrane proteome—Challenges and analytical strategies

(2010) Andreas O. Helbig et al.   Journal of Proteomics

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

PeptideClassifier for protein inference and targeted quantitative proteomics

(2010) Ermir Qeli et al.   NATURE BIOTECHNOLOGY

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes

(2010) Muriel Vayssier-Taussat et al.   PLoS Pathogens

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

(2009) M. A. Grobei et al.   GENOME RESEARCH

Accurate and Sensitive Peptide Identification with Mascot Percolator

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

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

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

Global signatures of protein and mRNA expression levels

(2009) Raquel de Sousa Abreu et al.   Molecular BioSystems

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

(2009) Johan Malmström et al.   NATURE

A Proteomic View of an Important Human Pathogen – Towards the Quantification of the Entire Staphylococcus aureus Proteome

(2009) Dörte Becher et al.   PLoS One

Proteomic analysis of the bacterial pathogen Bartonella henselae and identification of immunogenic proteins for serodiagnosis

(2009) Christian Eberhardt et al.   PROTEOMICS

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Reduction of dynamic protein concentration range of biological extracts for the discovery of low-abundance proteins by means of hexapeptide ligand library

(2008) Luc Guerrier et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Bacterial membrane proteomics

(2008) Ansgar Poetsch et al.   PROTEOMICS

Membrane proteins and membrane proteomics

(2008) Sandra Tan et al.   PROTEOMICS