An atlas of protein-protein interactions across mouse tissues

PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data

(2021) Michael A Skinnider et al.   BIOINFORMATICS

Differential network analysis of multiple human tissue interactomes highlights tissue-selective processes and genetic disorder genes

(2020) Omer Basha et al.   BIOINFORMATICS

Mechanisms of tissue and cell-type specificity in heritable traits and diseases

(2020) Idan Hekselman et al.   NATURE REVIEWS GENETICS

A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS

(2020) Moritz Heusel et al.   Cell Systems

A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies

(2020) Claire D. McWhite et al.   CELL

A reference map of the human binary protein interactome

(2020) Katja Luck et al.   NATURE

Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes

(2020) Isabell Bludau et al.   Nature Protocols

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

(2020) Frederic B Bastian et al.   NUCLEIC ACIDS RESEARCH

A large accessory protein interactome is rewired across environments

(2020) Zhimin Liu et al.   eLife

SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles

(2020) George Rosenberger et al.   Cell Systems

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

(2019) Lukas Minus Orre et al.   MOLECULAR CELL

Complex‐centric proteome profiling by SEC‐SWATH‐MS

(2019) Moritz Heusel et al.   Molecular Systems Biology

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

(2019) Aikaterini Geladaki et al.   Nature Communications

An integrative systems genetic analysis of mammalian lipid metabolism

(2019) Benjamin L. Parker et al.   NATURE

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

(2019) Natalie Romanov et al.   CELL

Evaluating measures of association for single-cell transcriptomics

(2019) Michael A. Skinnider et al.   NATURE METHODS

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Co-regulation map of the human proteome enables identification of protein functions

(2019) Georg Kustatscher et al.   NATURE BIOTECHNOLOGY

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

GeneGini: Assessment via the Gini Coefficient of Reference “Housekeeping” Genes and Diverse Human Transporter Expression Profiles

(2018) Steve O'Hagan et al.   Cell Systems

Context-specific interactions in literature-curated protein interaction databases

(2018) R. Greg Stacey et al.   BMC GENOMICS

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Genomic data integration systematically biases interactome mapping

(2018) Michael A. Skinnider et al.   PLoS Computational Biology

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

(2017) Ashis Saha et al.   GENOME RESEARCH

Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein–Protein Interactions

(2017) Nikolaus Fortelny et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative analysis of protein interaction network dynamics in yeast

(2017) Albi Celaj et al.   Molecular Systems Biology

Interactome disassembly during apoptosis occurs independent of caspase cleavage

(2017) Nichollas E Scott et al.   Molecular Systems Biology

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities

(2017) John D Lapek et al.   NATURE BIOTECHNOLOGY

A multiregional proteomic survey of the postnatal human brain

(2017) Becky C. Carlyle et al.   NATURE NEUROSCIENCE

The BioStudies database—one stop shop for all data supporting a life sciences study

(2017) Ugis Sarkans et al.   NUCLEIC ACIDS RESEARCH

Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle

(2017) Leoš Shivaya Valášek et al.   NUCLEIC ACIDS RESEARCH

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

(2017) Cynthia L Smith et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation of αB-crystallin supports reactive astrogliosis in demyelination

(2017) Hedwich F. Kuipers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A mouse tissue transcription factor atlas

(2017) Quan Zhou et al.   Nature Communications

Emergence and evolution of an interaction between intrinsically disordered proteins

(2017) Greta Hultqvist et al.   eLife

Expression of Muscle-Specific Ribosomal Protein L3-Like Impairs Myotube Growth

(2016) Thomas Chaillou et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function

(2016) Brendan J. Floyd et al.   MOLECULAR CELL

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

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

(2016) Taibo Li et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system

(2016) Alexis Vandenbon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring genetic suppression interactions on a global scale

(2016) J. van Leeuwen et al.   SCIENCE

Cross-Disciplinary Network Comparison: Matchmaking between Hairballs

(2016) Koon-Kiu Yan et al.   Cell Systems

Tissue Specificity of Human Disease Module

(2016) Maksim Kitsak et al.   Scientific Reports

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

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

Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments

(2015) Nichollas E. Scott et al.   Journal of Proteomics

Fundamentals of protein interaction network mapping

(2015) J. Snider et al.   Molecular Systems Biology

∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis

(2015) Sandra Pankow et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

(2015) Tiannan Guo et al.   NATURE MEDICINE

Integrated interactions database: tissue-specific view of the human and model organism interactomes

(2015) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

(2015) Emma Pierson et al.   PLoS Computational Biology

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

In silico prediction of physical protein interactions and characterization of interactome orphans

(2014) Max Kotlyar et al.   NATURE METHODS

Capping protein regulators fine-tune actin assembly dynamics

(2014) Marc Edwards et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The GOA database: Gene Ontology annotation updates for 2015

(2014) Rachael P. Huntley et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases

(2014) Ruth Barshir et al.   PLoS Computational Biology

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing

(2013) Sereina Riniker et al.   Journal of Chemical Information and Modeling

Initial Quantitative Proteomic Map of 28 Mouse Tissues Using the SILAC Mouse

(2013) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

mentha: a resource for browsing integrated protein-interaction networks

(2013) Alberto Calderone 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

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Probing Dynamic Conformations of the High-Molecular-Weight αB-Crystallin Heat Shock Protein Ensemble by NMR Spectroscopy

(2012) Andrew J. Baldwin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

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

(2012) Anders R Kristensen et al.   NATURE METHODS

Network Organization of the Huntingtin Proteomic Interactome in Mammalian Brain

(2012) Dyna I. Shirasaki et al.   NEURON

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

(2012) John A. Capra et al.   PLoS Computational Biology

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks

(2012) Oded Magger et al.   PLoS Computational Biology

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

Attributes of short linear motifs

(2011) Norman E. Davey et al.   Molecular BioSystems

Global landscape of HIV–human protein complexes

(2011) Stefanie Jäger et al.   NATURE

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

An integrated global strategy for cell lysis, fractionation, enrichment and mass spectrometric analysis of phosphorylated peptides

(2010) Lindsay D. Rogers et al.   Molecular BioSystems

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Prediction of Protein Binding Regions in Disordered Proteins

(2009) Bálint Mészáros et al.   PLoS Computational Biology

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function

(2008) Marcus Krüger et al.   CELL

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

(2008) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation

(2008) J. Gsponer et al.   SCIENCE