PPIXpress: construction of condition-specific protein interaction networks based on transcript expression

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

(2015) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

Identification of recurrent regulated alternative splicing events across human solid tumors

(2015) Miri Danan-Gotthold et al.   NUCLEIC ACIDS RESEARCH

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

A STIM2 splice variant negatively regulates store-operated calcium entry

(2015) Anna-Maria Miederer et al.   Nature Communications

Identifying transcription factor complexes and their roles

(2014) Thorsten Will et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines

(2014) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Coverage of protein domain families with structural protein–protein interactions: Current progress and future trends

(2014) Alexander Goncearenco et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants

(2014) Anupam Sinha et al.   PROTEOMICS

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

(2014) Ruth Barshir et al.   PLoS Computational Biology

Edgotype: a fundamental link between genotype and phenotype

(2013) Nidhi Sahni et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Alternative splicing and protein interaction data sets

(2013) David Talavera et al.   NATURE BIOTECHNOLOGY

A unique Oct4 interface is crucial for reprogramming to pluripotency

(2013) Daniel Esch et al.   NATURE CELL BIOLOGY

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

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

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

(2013) Diego Diez et al.   NUCLEIC ACIDS RESEARCH

3did: a catalog of domain-based interactions of known three-dimensional structure

(2013) Roberto Mosca 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 challenge of increasing Pfam coverage of the human proteome

(2013) Jaina Mistry et al.   Database-The Journal of Biological Databases and Curation

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

Protein complex prediction based on maximum matching with domain–domain interaction

(2012) Wenji Ma et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

(2012) I. Ezkurdia et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

IDDI: integrated domain-domain interaction and protein interaction analysis system

(2012) Yul Kim et al.   Proteome Science

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

(2012) Oded Magger et al.   PLoS Computational Biology

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases

(2011) Tiago J. S. Lopes et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions

(2010) Yosuke Ozawa et al.   BMC BIOINFORMATICS

Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged

(2010) C. J. David et al.   GENES & DEVELOPMENT

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2010) Sailu Yellaboina et al.   NUCLEIC ACIDS RESEARCH

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

(2010) Dorothea Emig et al.   NUCLEIC ACIDS RESEARCH

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

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

(2009) Da Wei Huang et al.   Nature Protocols

Cancer-associated regulation of alternative splicing

(2009) Julian P Venables et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS