Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions

NOA: a cytoscape plugin for network ontology analysis

(2013) Chao Zhang et al.   BIOINFORMATICS

Genome editing of human pluripotent stem cells to generate human cellular disease models

(2013) K. Musunuru   Disease Models & Mechanisms

Identification of Protein Interactions Involved in Cellular Signaling

(2013) Jukka Westermarck et al.   MOLECULAR & CELLULAR PROTEOMICS

The functional interactome landscape of the human histone deacetylase family

(2013) P. Joshi et al.   Molecular Systems Biology

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Protein Interaction Network of the Mammalian Hippo Pathway Reveals Mechanisms of Kinase-Phosphatase Interactions

(2013) A. L. Couzens et al.   Science Signaling

ACBD3 Interaction with TBC1 Domain 22 Protein Is Differentially Affected by Enteroviral and Kobuviral 3A Protein Binding

(2013) A. L. Greninger et al.   mBio

Structure, Function and Regulation of the Hsp90 Machinery

(2013) Johannes Buchner et al.   Biomedical Journal

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

(2012) John H Morris et al.   BMC BIOINFORMATICS

Estimating relative abundances of proteins from shotgun proteomics data

(2012) Sean McIlwain et al.   BMC BIOINFORMATICS

A Ribosome-Bound Quality Control Complex Triggers Degradation of Nascent Peptides and Signals Translation Stress

(2012) Onn Brandman et al.   CELL

Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions

(2012) Anne-Claude Gingras et al.   FEBS LETTERS

The 3A Protein from Multiple Picornaviruses Utilizes the Golgi Adaptor Protein ACBD3 To Recruit PI4KIII 

(2012) A. L. Greninger et al.   JOURNAL OF VIROLOGY

Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins

(2012) Michelle J. Kean et al.   METHODS

Interaction Proteomics Identify NEURL4 and the HECT E3 Ligase HERC2 as Novel Modulators of Centrosome Architecture

(2012) Abdallah K. Al-Hakim et al.   MOLECULAR & CELLULAR PROTEOMICS

Topological analysis and interactive visualization of biological networks and protein structures

(2012) Nadezhda T Doncheva et al.   Nature Protocols

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Affinity-purification coupled to mass spectrometry: Basic principles and strategies

(2012) Wade H. Dunham et al.   PROTEOMICS

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

ACBD3-mediated recruitment of PI4KB to picornavirus RNA replication sites

(2011) Jun Sasaki et al.   EMBO JOURNAL

Global landscape of HIV–human protein complexes

(2011) Stefanie Jäger et al.   NATURE

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda et al.   NATURE METHODS

A proteomic view of the host-pathogen interaction: The host perspective

(2011) Anetta Hartlova et al.   PROTEOMICS

Protein Complexes are Central in the Yeast Genetic Landscape

(2011) Magali Michaut et al.   PLoS Computational Biology

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

(2010) J. Montojo et al.   BIOINFORMATICS

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

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

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

Purification and characterization of HIV–human protein complexes

(2010) Stefanie Jäger et al.   METHODS

Profiling of Protein Interaction Networks of Protein Complexes Using Affinity Purification and Quantitative Mass Spectrometry

(2010) Robyn M. Kaake et al.   MOLECULAR & CELLULAR PROTEOMICS

Orm family proteins mediate sphingolipid homeostasis

(2010) David K. Breslow et al.   NATURE

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

Global Self-Regulation of the Cellular Metabolic Structure

(2010) Ildefonso M. De la Fuente et al.   PLoS One

The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

(2010) Matthew D. Dyer et al.   PLoS One

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Analyzing biological network parameters with CentiScaPe

(2009) Giovanni Scardoni et al.   BIOINFORMATICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Evaluation of Clustering Algorithms for Protein Complex and Protein Interaction Network Assembly

(2009) Mihaela E. Sardiu et al.   JOURNAL OF PROTEOME RESEARCH

A Targeted Spatial-Temporal Proteomics Approach Implicates Multiple Cellular Trafficking Pathways in Human Cytomegalovirus Virion Maturation

(2009) Nathaniel J. Moorman et al.   MOLECULAR & CELLULAR PROTEOMICS

Differential 14-3-3 Affinity Capture Reveals New Downstream Targets of Phosphatidylinositol 3-Kinase Signaling

(2009) Fanny Dubois et al.   MOLECULAR & CELLULAR PROTEOMICS

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

(2009) Noelle M Griffin et al.   NATURE BIOTECHNOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

A Rab GAP cascade defines the boundary between two Rab GTPases on the secretory pathway

(2009) F. E. Rivera-Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Characterization of Genes Required for Protein Folding in the Endoplasmic Reticulum

(2009) M. C. Jonikas et al.   SCIENCE

A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity

(2009) Xueping Yu et al.   PLoS Computational Biology

Topological properties of protein interaction networks from a structural perspective

(2008) Attila Gursoy et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A PP2A Phosphatase High Density Interaction Network Identifies a Novel Striatin-interacting Phosphatase and Kinase Complex Linked to the Cerebral Cavernous Malformation 3 (CCM3) Protein

(2008) Marilyn Goudreault et al.   MOLECULAR & CELLULAR PROTEOMICS

In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types

(2008) Robert J. Chalkley et al.   MOLECULAR & CELLULAR PROTEOMICS

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

(2008) Hyungwon Choi et al.   MOLECULAR & CELLULAR PROTEOMICS

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

An in vitro microfluidic approach to generating protein-interaction networks

(2008) Doron Gerber et al.   NATURE METHODS

Structure/function relationships underlying regulation of FOXO transcription factors

(2008) T Obsil et al.   ONCOGENE

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

(2008) Matthew D. Dyer et al.   PLoS Pathogens

Application of proteomics technology for analyzing the interactions between host cells and intracellular infectious agents

(2008) Mayte Coiras et al.   PROTEOMICS