Although it was originally believed that enhancers activate only the nearest promoter, recent
global analyses enabled by high-throughput technology suggest that the network of …

… Tomas Rube and other members of the Bussemaker and Mann labs for valuable discussions.
This work was supported by an HHMI International Student Research Fellowship (to JFK) …

… Bussemaker, Remo Rohs, Evolving insights on how cytosine methylation affects protein–DNA
binding, Briefings in Functional Genomics, Volume 14, Issue 1, January 2015, Pages 61–…

Chromatin is important for the regulation of transcription and other functions, yet the
diversity of chromatin composition and the distribution along chromosomes are still poorly …

We present here a new computational method for discovering cis-regulatory elements that
circumvents the need to cluster genes based on their expression profiles. Based on a model …

Members of transcription factor families typically have similar DNA binding specificities yet
execute unique functions in vivo. Transcription factors often bind DNA as multiprotein …

We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura,
and compared this to the genome sequence of Drosophila melanogaster, a primary …

The Myc/Max/Mad transcription factor network is critically involved in cell behavior; however,
there is relatively little information on its genomic binding sites. We have employed the …

The chromosomal gene expression profiles established by the Human Transcriptome Map (HTM)
revealed a clustering of highly expressed genes in about 30 domains, called ridges. …

Genomic analyses often involve scanning for potential transcription factor (TF) binding sites
using models of the sequence specificity of DNA binding proteins. Many approaches have …