The BioGRID interaction database: 2015 update

The binary protein-protein interaction landscape of Escherichia coli

(2014) Seesandra V Rajagopala et al.   NATURE BIOTECHNOLOGY

Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

(2014) Alicia Lundby et al.   NATURE METHODS

Activities at the Universal Protein Resource (UniProt)

(2014)   NUCLEIC ACIDS RESEARCH

A comprehensive survey of non-canonical splice sites in the human transcriptome

(2014) Guillermo E. Parada et al.   NUCLEIC ACIDS RESEARCH

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

(2014) Roser Corominas et al.   Nature Communications

Assisting manual literature curation for protein-protein interactions using BioQRator

(2014) D. Kwon et al.   Database-The Journal of Biological Databases and Curation

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information

(2014) M. Torii et al.   Database-The Journal of Biological Databases and Curation

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

Genetic Interaction Networks: Toward an Understanding of Heritability

(2013) Anastasia Baryshnikova et al.   Annual Review of Genomics and Human Genetics

A Comparative Genomic Approach for Identifying Synthetic Lethal Interactions in Human Cancer

(2013) R. Deshpande et al.   CANCER RESEARCH

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization

(2013) Shireen A. Sarraf et al.   NATURE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

WormBase 2014: new views of curated biology

(2013) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse

(2013) Judith A. Blake et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2013)   NUCLEIC ACIDS RESEARCH

GeneMANIA Prediction Server 2013 Update

(2013) Khalid Zuberi et al.   NUCLEIC ACIDS RESEARCH

FlyBase 102—advanced approaches to interrogating FlyBase

(2013) Susan E. St. Pierre et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update

(2013) I. Sadowski et al.   Database-The Journal of Biological Databases and Curation

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

Methods for Quantification ofin vivoChanges in Protein Ubiquitination following Proteasome and Deubiquitinase Inhibition

(2012) Namrata D. Udeshi et al.   MOLECULAR & CELLULAR PROTEOMICS

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

(2012) Mohan Babu et al.   NATURE

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

(2012) Orit Rozenblatt-Rosen et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

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

(2012) Sandra Orchard et al.   NATURE METHODS

Gene Ontology Annotations and Resources

(2012)   NUCLEIC ACIDS RESEARCH

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

Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development

(2012) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Text mining for the biocuration workflow

(2012) L. Hirschman et al.   Database-The Journal of Biological Databases and Curation

Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes

(2012) Yuanfang Guan et al.   PLoS Computational Biology

Viral Perturbations of Host Networks Reflect Disease Etiology

(2012) Natali Gulbahce et al.   PLoS Computational Biology

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

Prostaglandins and Inflammation

(2011) Emanuela Ricciotti et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID

(2011) Andrew G. Winter et al.   BIOINFORMATICS

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

(2011) Andrew Chatr-aryamontri et al.   BMC BIOINFORMATICS

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

(2011) Martin Krallinger et al.   BMC BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Proteome-wide Identification of Ubiquitylation Sites by Conjugation of Engineered Lysine-less Ubiquitin

(2011) Kiyotaka Oshikawa et al.   JOURNAL OF PROTEOME RESEARCH

Global gene disruption in human cells to assign genes to phenotypes by deep sequencing

(2011) Jan E Carette et al.   NATURE BIOTECHNOLOGY

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda et al.   NATURE METHODS

InterPro in 2011: new developments in the family and domain prediction database

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

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

(2011) D. O. Inglis et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

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

Disease Ontology: a backbone for disease semantic integration

(2011) L. M. Schriml et al.   NUCLEIC ACIDS RESEARCH

PomBase: a comprehensive online resource for fission yeast

(2011) V. Wood et al.   NUCLEIC ACIDS RESEARCH

System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

(2011) K. T. G. Rigbolt et al.   Science Signaling

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

(2011) Mohan Babu et al.   PLoS Genetics

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

A Data Set of Human Endogenous Protein Ubiquitination Sites

(2010) Yi Shi et al.   MOLECULAR & CELLULAR PROTEOMICS

Dissecting spatio-temporal protein networks driving human heart development and related disorders

(2010) Kasper Lage et al.   Molecular Systems Biology

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

ProHits: integrated software for mass spectrometry–based interaction proteomics

(2010) Guomin Liu et al.   NATURE BIOTECHNOLOGY

DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila

(2010) Thilakam Murali et al.   NUCLEIC ACIDS RESEARCH

ZFIN: enhancements and updates to the zebrafish model organism database

(2010) Y. Bradford et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami 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

Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82

(2010) Sylvie Miquel et al.   PLoS One

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

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle

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

Annotating the human genome with Disease Ontology

(2009) John D Osborne et al.   BMC GENOMICS

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

(2009) C. Choudhary et al.   SCIENCE

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Defining genetic interaction

(2008) R. Mani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA