ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

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

(2008) Xi Chen et al.   CELL

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells

(2008) Jiancong Liang et al.   NATURE CELL BIOLOGY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Extracting sequence features to predict protein–DNA interactions: a comparative study

(2008) Qing Zhou et al.   NUCLEIC ACIDS RESEARCH

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY