Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes

(2017) Kevin Drew et al.   Molecular Systems Biology

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles

(2017) Michiel van de Waterbeemd et al.   NATURE METHODS

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

An informatic framework for decoding protein complexes by top-down mass spectrometry

(2016) Owen S Skinner et al.   NATURE METHODS

The BioGRID interaction database: 2017 update

(2016) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification

(2015) Matthew M. Makowski et al.   MOLECULAR & CELLULAR PROTEOMICS

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells

(2015) Mathieu Dalvai et al.   Cell Reports

Human protein interaction networks across tissues and diseases

(2015) Esti Yeger-Lotem et al.   Frontiers in Genetics

Empowering biologists with multi-omics data: colorectal cancer as a paradigm

(2014) Jing Zhu et al.   BIOINFORMATICS

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer

(2014) Richard Alexander Scheltema et al.   MOLECULAR & CELLULAR PROTEOMICS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

A mass spectrometry–based hybrid method for structural modeling of protein complexes

(2014) Argyris Politis et al.   NATURE METHODS

MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities

(2014) G. Launay et al.   NUCLEIC ACIDS RESEARCH

Human-Chromatin-Related Protein Interactions Identify a Demethylase Complex Required for Chromosome Segregation

(2014) Edyta Marcon et al.   Cell Reports

Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization

(2013) Hua Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics

(2013) Kathryn J. Kirkwood et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

GeneMANIA Prediction Server 2013 Update

(2013) Khalid Zuberi et al.   NUCLEIC ACIDS RESEARCH

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

ComplexQuant: High-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS

(2012) Cuihong Wan et al.   Journal of Proteomics

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

(2012) Mohan Babu et al.   NATURE

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

(2012) Anders R Kristensen et al.   NATURE METHODS

High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies

(2012) Rebecca J Rose et al.   NATURE METHODS

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

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

(2012) Sandra Orchard et al.   NATURE METHODS

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

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The tandem affinity purification technology: an overview

(2011) Yifeng Li   BIOTECHNOLOGY LETTERS

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

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

Predicting protein functions by relaxation labelling protein interaction network

(2010) Pingzhao Hu et al.   BMC BIOINFORMATICS

Computational approaches for detecting protein complexes from protein interaction networks: a survey

(2010) Xiaoli Li et al.   BMC GENOMICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

ConsensusPathDB: toward a more complete picture of cell biology

(2010) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

The tandem affinity purification method: An efficient system for protein complex purification and protein interaction identification

(2010) Xiaoli Xu et al.   PROTEIN EXPRESSION AND PURIFICATION

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Affinity Purification Combined with Mass Spectrometry-Based Proteomic Strategy to Study Mammalian Protein Complex and Protein-Protein Interactions

(2009) Shufang Liang et al.   Current Proteomics

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2009 update

(2009) Arnaud Ceol et al.   NUCLEIC ACIDS RESEARCH

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

MPIDB: the microbial protein interaction database

(2008) Johannes Goll et al.   BIOINFORMATICS

Gene function prediction using labeled and unlabeled data

(2008) Xing-Ming Zhao et al.   BMC BIOINFORMATICS

Arena3D: visualization of biological networks in 3D

(2008) Georgios A Pavlopoulos et al.   BMC Systems Biology

Native mass spectrometry: a bridge between interactomics and structural biology

(2008) Albert J R Heck   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE