Postdoctoral, 2003, Harvard University, Cambridge, MA
PhD, 2000, University of Michigan, Ann Arbor, MI
BS, 1994, Peking University, Beijing, China
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Additional Appointment(s):
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Department of Medical Informatics
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Center for Comprehensive Informatics
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Courses Taught:
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BIOS 760R: Special Topics
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Career Overview:
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My research is in the areas of statistical genetics, genomics and bioinformatics. Motivated by scientific needs in these area and new technologies, I am undertaking both methodological and collaborative research. A major focus of my research is on developing and evaluating model-based methods to analyze genetics and genomics data, in particular, next generation sequencing data, and on developing software so that the methods can be easily adopted by the research community.
For more information, please visit my personal website
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Areas of Interest/Research:
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Bioinformatics
Statistical Modeling
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Selected Research Projects:
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Model based methods to analyze ChIP-Seq, RNA-Seq and resequencing data.
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Selected Publications:
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Hu M, Zhu Y, Taylor JMG, Liu JS, S
Using Poisson mixed-effects model to quantify exon-level gene expression in RNA-seq.
Bioinformatics , 28: 63-68, 2012.
http://www.ncbi.nlm.nih.gov/pubmed/22072384
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Zhao JC, Yu J, Runkle C, Wu L, Hu M, Wu D, Liu JS, Wang Q, S, Yu J.
Cooperation Between Polycomb and Androgen Receptor during Oncogenic Transformation.
Genome Research , 22: 322-331, 2012.
http://genome.cshlp.org/content/22/2/322.long
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Li X, Li L, Byun JS, Pandey R, Gardner K, S, Dou Y.
The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network.
Cell Stem Cell , 11: 163-178, 2012.
http://www.sciencedirect.com/science/article/pii/S1934590912...
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Hou C, Li L, S, Corces, VG
Gene Density, Transcription and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains.
Mol Cell , 48: 471-484, 2012.
http://www.sciencedirect.com/science/article/pii/S1097276512...
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Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Shankar S, Jing X, Iyer M, Hu M, Sam L, Grasso C, Maher CA, Palanisamy N, Mehra R, Huang C, Siddiqui J, Yu Y, S, Chinnaiyan AM.
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.
Genome Research , 21: 1028-1041, 2011.
http://www.ncbi.nlm.nih.gov/pubmed/21724842
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Katoh H, S, Liu R, Wang L, Li W, Li X, Wu L, Du Z, Lyons R, Liu CG, Liu X, Dou Y, Zheng P, Liu Y.
FOXP3 Orchestrates H4K16 Acetylation and H3K4 Trimethylation for Activation of Multiple Genes by Recruiting MOF and Causing Displacement of PLU-1.
Mol Cell , 44: 770-784, 2011.
http://www.ncbi.nlm.nih.gov/pubmed/22152480
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Breitkreutz A, Choi H, Sharom J, Boucher L, Neduva V, Larsen B, Lin Z, Breitkreutz B, Stark C, Liu G, Ahn J, Dewar-Darch D, S, Pawson T, Gingras A, Nesvizhskii AI, Tyers M.
A global protein kinase and phosphatase interaction network in yeast.
Science , 328: 1043-1046, 2010.
http://www.ncbi.nlm.nih.gov/pubmed/20489023
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S, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM
HPeak: An HMM-based Algorithm for Defining Read-enriched Regions in ChIP-Seq Data.
BMC Bioinformatics. , 11: 369, 2010.
http://www.ncbi.nlm.nih.gov/pubmed/20598134
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Yu J, Yu J, Mani R, Cao X, Cao Q, Brenner CJ, Cao X, Wang GX, Wu L, Li J, *Hu M, Gong Y, Cheng H, Laxman B, Vellaichamy A, Shankar S, Li Y, Dhanasekaran SM, Morey R, Barrette T, Lonigro RJ, Tomlins SA, Varambally S, S, Chinnaiyan, AM
Integrated Network of Androgen Receptor, Polycomb and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression.
Cancer Cell , 17: 443, 2010.
http://www.ncbi.nlm.nih.gov/pubmed/20478527
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Hu M, Yu J, Taylor, JM, Chinnaiyan AM, S
On the Detection and Refinement of Transcription Factor Binding Sites Using ChIP-Seq Data.
Nucleic Acids Res. , 38: 2154, 2010.
http://www.ncbi.nlm.nih.gov/pubmed/20056654
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Choi H, Nesvizhskii A, Ghosh D, S
Hierarchical Hidden Markov Model with Application to Joint Analysis of ChIP-chip and ChIP-seq Data.
Bioinformatics , 25: 1715, 2009.
http://www.ncbi.nlm.nih.gov/pubmed/19447789
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Other affiliations and Activities:
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The Center for Comprehensive Informatics (CCI)
Michigan Center for Translational Pathology
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Curriculum Vitae
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Link to this page: http://www.sph.emory.edu/faculty/ZQIN4
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