Studies of transcription factor binding sites and histone modifications using ChIP-chip and Chip-seq assays.

A) Methodology Papers:

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, 
Nussbaum C, Myers RM, Brown M, Li W#, Liu XS#: Model-based Analysis of 
ChIP-Seq (MACS).Genome Biol. 9 (2008) R137

Johnson D*, Li W*, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, 
Brizuela L, Carroll JS, Brown M, Flicek P et al.: Systematic 
evaluation of variability in ChIP-chip experiments using predefined 
DNA targets. Genome Res. 18 (2008) 393-403

Johnson WE*, Li W*, Meyer CA*, Gottardo R, Carroll JS, Brown M and Liu 
XS: Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. 
Acad. Sci. U S A 103 (2006) 12457-12462

B) Biology Papers:

Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, 
Liu XS and Brown M: FoxA1 translates epigenetic signatures into 
lineage-specific transcription.Cell 132 (2008) 958-970

Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, 
Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, 
Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS and Brown M: 
Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 
38 (2006) 1289-1297.

Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, 
Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA and Brown M: 
Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-
Range Regulation Requiring the Forkhead Protein FoxA1. Cell 122 (2005) 
33-43.