Michael Q. Zhang

TL;DR: High-throughput DNase hypersensitivity analysis is employed to find regions of altered chromatin structure surrounding key adipocyte genes that suggest an important role for IRF proteins in adipocyte biology and demonstrates the utility of this approach in identifying cis- and trans-acting factors not previously suspected to participate in adipogenesis.

TL;DR: OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads, achieves high sensitivity of junction detection by strategic searches with small seeds and identified hundreds of novel micro-exons in the mouse transcriptome.

TL;DR: A PFM similarity quantification method based on product multinomial distributions is described, shown to have a better false positive to false negative ratio compared to existing methods and known frequency matrices and matrix families that were strongly similar to the matrices given by Wasserman and Fickett.

TL;DR: Promoters with enriched activity in mouse embryonic stem cells as well as adult brain, heart, kidney, and liver are characterized, showing that promoters with CpG islands are typically non-tissue specific and that a subset appear to be persistently marked by active chromatin modifications in the absence of detectable Polr2a binding.

TL;DR: The identification in proximal promoters of cis-regulatory modules with tissue-specific activity lays the groundwork for complete characterization and deciphering of cis -regulatory DNA code in mammalian genomes.