Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors

(2013) Qian Xiong et al.   BMC GENOMICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Personal and population genomics of human regulatory variation

(2012) B. Vernot et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

ETS-dependent regulation of a distal Gata4 cardiac enhancer

(2011) William Schachterle et al.   DEVELOPMENTAL BIOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH