ORegAnno 3.0: a community-driven resource for curated regulatory annotation

Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy

(2015) Dénes Türei et al.   Autophagy

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

Genome Modeling System: A Knowledge Management Platform for Genomics

(2015) Malachi Griffith et al.   PLoS Computational Biology

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser

(2014) C. Lee et al.   BIOINFORMATICS

RANK- and c-Met-mediated signal network promotes prostate cancer metastatic colonization

(2014) Gina Chia-Yi Chu et al.   ENDOCRINE-RELATED CANCER

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes

(2014) John D. Eicher et al.   NUCLEIC ACIDS RESEARCH

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

(2013) Dávid Fazekas et al.   BMC Systems Biology

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

The ENCODE project: Missteps overshadowing a success

(2013) Sean R. Eddy   CURRENT BIOLOGY

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

(2013) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications

(2013) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal

(2013) P. J. Killela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Frequency of TERT promoter mutations in human cancers

(2013) João Vinagre et al.   Nature Communications

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A genome-wide association study identifies susceptibility loci for Wilms tumor

(2012) Clare Turnbull et al.   NATURE GENETICS

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

An Integrative Approach to Inferring Gene Regulatory Module Networks

(2012) Michael Baitaluk et al.   PLoS One

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

(2011) N. Stransky et al.   SCIENCE

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities

(2011) Matthew N Bainbridge et al.   GENOME BIOLOGY

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data

(2010) Kakajan Komurov et al.   PLoS Computational Biology

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

(2009) A. L. Hufton et al.   GENOME RESEARCH

Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements

(2009) Monica C. Sleumer et al.   NUCLEIC ACIDS RESEARCH

ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species

(2008) Bart Hooghe et al.   NUCLEIC ACIDS RESEARCH

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

(2008) Elizabeth D. Wederell et al.   NUCLEIC ACIDS RESEARCH

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

(2008) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Identification of Estrogen Receptor α-Binding Sites in Mouse Liver

(2007) Hui Gao et al.   MOLECULAR ENDOCRINOLOGY