EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

Presenting ENCODE

(2012) Magdalena Skipper et al.   NATURE

Studying the epigenome using next generation sequencing

(2011) C. S. Ku et al.   JOURNAL OF MEDICAL GENETICS

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

(2011) R. Yamashita et al.   NUCLEIC ACIDS RESEARCH

RSAT 2011: regulatory sequence analysis tools

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

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

(2011) Elizabeth A. Rach et al.   PLoS Genetics

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

(2010) Christoph D. Schmid et al.   PLoS One

Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis

(2010) Qiang Gan et al.   GENOME BIOLOGY

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

MEME SUITE: tools for motif discovery and searching

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

MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database

(2008) B. Ahsan et al.   NUCLEIC ACIDS RESEARCH