Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

Understanding the regulatory and transcriptional complexity of the genome through structure

(2013) T. R. Mercer et al.   GENOME RESEARCH

Mapping functional transcription factor networks from gene expression data

(2013) B. C. Haynes et al.   GENOME RESEARCH

Construction of human activity-based phosphorylation networks

(2013) R. H. Newman et al.   Molecular Systems Biology

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

FunCoup 3.0: database of genome-wide functional coupling networks

(2013) Thomas Schmitt et al.   NUCLEIC ACIDS RESEARCH

Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells

(2013) J.-Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

(2013) Christopher Y. Park et al.   PLoS Computational Biology

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

iELM--a web server to explore short linear motif-mediated interactions

(2012) R. J. Weatheritt et al.   NUCLEIC ACIDS RESEARCH

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

(2012) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

(2012) Aaron K. Wong et al.   NUCLEIC ACIDS RESEARCH

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

IKBKE is induced by STAT3 and tobacco carcinogen and determines chemosensitivity in non-small cell lung cancer

(2012) J Guo et al.   ONCOGENE

Development of a High-Throughput Assay for Identifying Inhibitors of TBK1 and IKKε

(2012) Jessica E. Hutti et al.   PLoS One

A chromatin-modifying function of JNK during stem cell differentiation

(2011) Vijay K Tiwari et al.   NATURE GENETICS

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

(2010) Sailu Yellaboina et al.   NUCLEIC ACIDS RESEARCH

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

(2010) M. Gremse et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes

(2010) Daniel S. Lieber et al.   PLoS One

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

The Sleipnir library for computational functional genomics

(2008) C. Huttenhower et al.   BIOINFORMATICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Predicting Co-Complexed Protein Pairs from Heterogeneous Data

(2008) Jian Qiu et al.   PLoS Computational Biology

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY