kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

(2012) D. U. Gorkin et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

(2012) S. Luehr et al.   NUCLEIC ACIDS RESEARCH

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription

(2011) M. Patel et al.   GENOME RESEARCH

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways

(2009) Deepak Sharma et al.   NUCLEIC ACIDS RESEARCH

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

(2008) C. Linhart et al.   GENOME RESEARCH

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology