• Publications
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Model-based Analysis of ChIP-Seq (MACS)
  • Yong Zhang, T. Liu, +8 authors X. Liu
  • Medicine, Biology
  • Genome Biology
  • 17 September 2008
This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. Expand
Genome-wide analysis of estrogen receptor binding sites
All estrogen receptor and RNA polymerase II binding sites are mapped on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells, and distinct temporal mechanisms of estrogen-mediated gene regulation are demonstrated. Expand
Cofactor Dynamics and Sufficiency in Estrogen Receptor–Regulated Transcription
It is shown that recruitment of the p160 class of coactivators is sufficient for gene activation and for the growth stimulatory actions of estrogen in breast cancer supporting a model in which ER cofactors play unique roles in estrogen signaling. Expand
Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1
The unbiased sequence interrogation of the genuine chromatin binding sites suggests that direct ER binding requires the presence of Forkhead factor binding in close proximity, demonstrating the necessity of FoxA1 in mediating an estrogen response in breast cancer cells. Expand
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) demonstrates better performance compared with existing methods, identifies both positively and negatively selected genes simultaneously, and reports robust results across different experimental conditions. Expand
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.
The majority of AR binding regions contain noncanonical AR-responsive elements (AREs) and are identified as a cis-regulatory target of AR action in TMPRSS2, a gene fused to ETS transcription factors in the majority of prostate cancers. Expand
FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription
It is demonstrated that genome-wide positional analyses suggest that methylation of histone H3 lysine 4 is part of the epigenetic signature that defines lineage-specific FoxA1 recruitment sites in chromatin. Expand
Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer
The role of AR in androgen-independent cancer cells is not to direct the androgen -dependent gene expression program without androgen, but rather to execute a distinct program resulting in androgens-independent growth. Expand
Model-based analysis of tiling-arrays for ChIP-chip
  • W. Johnson, Wei Li, +4 authors X. Liu
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences
  • 15 August 2006
A fast and powerful analysis algorithm to reliably detect regions enriched by transcription factor chromatin immunoprecipitation on Affymetrix tiling arrays (ChIP-chip), developed in open-source Python and available at http://chip.dfci.harvard.edu/∼wli/MAT. Expand
EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent
It is found that the oncogenic function of EZH2 in cells of castration-resistant prostate cancer is independent of its role as a transcriptional repressor, and involves the ability of EzH2 to act as a coactivator for critical transcription factors including the androgen receptor. Expand