Popular Computational Methods to Assess Multiprotein Complexes Derived From Label-Free Affinity Purification and Mass Spectrometry (AP-MS) Experiments

Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions

(2012) Chang Ho Sohn et al.   ANALYTICAL CHEMISTRY

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Identification of Core Components and Transient Interactors of the Peroxisomal Importomer by Dual-Track Stable Isotope Labeling with Amino Acids in Cell Culture Analysis

(2012) Silke Oeljeklaus et al.   JOURNAL OF PROTEOME RESEARCH

SAINT-MS1: Protein–Protein Interaction Scoring Using Label-free Intensity Data in Affinity Purification-Mass Spectrometry Experiments

(2012) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry

(2012) Laura Trinkle-Mulcahy   PROTEOMICS

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

(2012) Alexey I. Nesvizhskii   PROTEOMICS

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Joining Forces: Integrating Proteomics and Cross-linking with the Mass Spectrometry of Intact Complexes

(2011) Florian Stengel et al.   MOLECULAR & CELLULAR PROTEOMICS

In VivoAnalysis of Proteomes and Interactomes Using Parallel Affinity Capture (iPAC) Coupled to Mass Spectrometry

(2011) Johanna S. Rees et al.   MOLECULAR & CELLULAR PROTEOMICS

Structural and functional protein network analyses predict novel signaling functions for rhodopsin

(2011) C. Kiel et al.   Molecular Systems Biology

Global landscape of HIV–human protein complexes

(2011) Stefanie Jäger et al.   NATURE

Defining human ERAD networks through an integrative mapping strategy

(2011) John C. Christianson et al.   NATURE CELL BIOLOGY

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda et al.   NATURE METHODS

Comparative interactomics with Funcoup 2.0

(2011) A. Alexeyenko et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

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

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

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

In silico discovery and experimental validation of new protein-protein interactions

(2011) Herman H. H. B. M. van Haagen et al.   PROTEOMICS

Sensitive single-molecule protein quantification and protein complex detection in a microarray format

(2011) Lee A. Tessler et al.   PROTEOMICS

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

The Reactome BioMart

(2011) R. A. Haw et al.   Database-The Journal of Biological Databases and Curation

Protein interaction sentence detection using multiple semantic kernels

(2011) Tamara Polajnar et al.   Journal of Biomedical Semantics

Recent advances in charting protein–protein interaction: mass spectrometry-based approaches

(2010) Anne-Claude Gavin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Modeling Contaminants in AP-MS/MS Experiments

(2010) Mathieu Lavallée-Adam et al.   JOURNAL OF PROTEOME RESEARCH

Extracting gene function from protein–protein interactions using Quantitative BAC InteraCtomics (QUBIC)

(2010) Nina C. Hubner et al.   METHODS

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Exhaustive benchmarking of the yeast two-hybrid system

(2010) Yu-Chi Chen et al.   NATURE METHODS

MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data

(2010) Ravi Gupta et al.   NUCLEIC ACIDS RESEARCH

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

(2010) Sailu Yellaboina et al.   NUCLEIC ACIDS RESEARCH

MIPS: curated databases and comprehensive secondary data resources in 2010

(2010) H. Werner Mewes et al.   NUCLEIC ACIDS RESEARCH

COXPRESdb: a database to compare gene coexpression in seven model animals

(2010) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Wen Yu et al.   PROTEOMICS

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Literature curation of protein interactions: measuring agreement across major public databases

(2010) A. L. Turinsky et al.   Database-The Journal of Biological Databases and Curation

Comparative analysis and unification of domain–domain interaction networks

(2009) Patrik Björkholm et al.   BIOINFORMATICS

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes

(2009) Philippe Cloutier et al.   METHODS

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

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

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

(2009) Timo Glatter et al.   Molecular Systems Biology

Recurated protein interaction datasets

(2009) Lukasz Salwinski et al.   NATURE METHODS

Erratum: Addendum: Literature-curated protein interaction datasets

(2009) Michael E Cusick et al.   NATURE METHODS

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

The Negatome database: a reference set of non-interacting protein pairs

(2009) Pawel Smialowski et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2009 update

(2009) Arnaud Ceol et al.   NUCLEIC ACIDS RESEARCH

Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins

(2009) Seesandra Venkatappa Rajagopala et al.   PROTEOMICS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

TiGER: a database for tissue-specific gene expression and regulation

(2008) Xiong Liu et al.   BMC BIOINFORMATICS

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Mapping multiprotein complexes by affinity purification and mass spectrometry

(2008) Mark O Collins et al.   CURRENT OPINION IN BIOTECHNOLOGY

Evolution of genome architecture

(2008) Eugene V. Koonin   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors

(2008) Sheila J. Barton et al.   MASS SPECTROMETRY REVIEWS

Challenges and Rewards of Interaction Proteomics

(2008) Shoshana J. Wodak et al.   MOLECULAR & CELLULAR PROTEOMICS

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

(2008) David J Lynn et al.   Molecular Systems Biology

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Next-generation high-density self-assembling functional protein arrays

(2008) Niroshan Ramachandran et al.   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

Up-to-date catalogues of yeast protein complexes

(2008) Shuye Pu et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

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

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

(2007) Pawel Michalak   GENOMICS

Literature-based concept profiles for gene annotation: The issue of weighting

(2007) R JELIER et al.   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS