With the genetic portraits of all major human malignancies now available, we next face the
challenge of characterizing the function of mutated genes, their downstream targets …

A vast number of small-molecule ligands, including therapeutic drugs under development
and in clinical use, elicit their effects by binding specific proteins associated with the …

No existing method to characterize transcription factor (TF) binding to DNA allows genome-
wide measurement of all TF-binding activity in cells. Here we present a massively parallel …

It is currently not possible to resolve the genome-wide relationship of transcription factors
(TFs) and nucleosomes at the level of individual chromatin templates despite rapidly …

Technologies that profile chromatin modifications at single-cell resolution offer enormous
promise for functional genomic characterization, but the sparsity of the measurements and …

Transcription factors are managers of the cellular factory, and key components to many
diseases. Many non-coding single nucleotide polymorphisms affect transcription factors …

In vivo protein-DNA interactions connect each transcription factor with its direct targets to
form a gene network scaffold. To map these protein-DNA interactions comprehensively …

Chromatin immunoprecipitation experiments followed by sequencing (ChIP–seq) detect
protein–DNA binding events and chemical modifications of histone proteins. Challenges in …

We describe protein interaction quantitation (PIQ), a computational method for modeling the
magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify …

Sequencing of exomes and genomes has revealed abundant genetic variation affecting the
coding sequences of human transcription factors (TFs), but the consequences of such …