Research
Interests
Education
Experiences
Work Experiences
Publications Softwares
Links
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Research
Interests
Education
Experiences
Work Experiences
Publications Softwares
Links
Genomics (Encode project)
Next generation sequencing
Genome Wide Association Study (GWAS)
Microarray Normalization and Data Analysis
Gene Regulatory Network and System Biology
Human Disease and Cancer
microRNA and Cancer
Aging in model organisms
Ph.D. in Computational Biology and Bioinformatics,
University of Southern California, Los Angeles, July 2002 - December 2006 (thesis)
M. Sc. in Statistics, University of Southern California, Los Angeles, September 2004 - July 2006 (thesis)
M. Sc. in Molecular Genetics, Fudan University, Shanghai China, September 1999 - July 2002
B. Sc. in Biochemistry (major), Applied
Mathematics and Software (Second major)
East China University of Science and Technology, Shanghai China, September 1995 - July 1999
Post-doc Research Associate (03/2008 -...), Molecular Biophysics and Biochemistry
Member, the Gerstein Lab, Yale University
Post-doc Research Associate (01/2007 -03/2008), Computational
Biology Department
Member, Yeast Ageing Group, University of
Southern California
Teacher
Assistant (08/2002 -
01/2004), Molecular
and Computational Biology Department
Class, Biochemistry, University of
Southern California
Part-time Teaching
Assistant (09/2001 - 5/2002), Institute
of Genetics
Member, Institute
of Genetics, Fudan
University
Journals/Conferences
[40] Average rank-based score to measure deregulation of molecular pathway gene sets. Yang H*, Cheng C*, Zhang W. PLoS One. 2011;6(11):e27579. (* co-first author) [Pubmed]
[39] Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Cheng C, Gerstein M. Nucleic Acids Research. 2011 Sep 16. [Pubmed]
[38] Genome-wide analysis of chromatin features identifies histone modification-sensitive and insensitive classes of yeast transcription factors. Cheng C*, Shou C*, Yip Y, Gerstein M. Genome Biology. 2011 Nov 7;12(11):R111. (* co-first author) [Pubmed]
[37] A Probabilistic Method for identifying Transcription Factor Target Genes from ChIP-Seq Binding Profiles. Cheng C, Min R, Gerstein M. Bioinformatics. 2011 Dec 1;27(23):3221-7. [Pubmed]
[36] Construction and Analysis of an Integrated Regulatory Network Derived from High-throughput Sequencing Data. Cheng C, Yan, K, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu Z, Niu W, Alves P, Kato M, Snyder M, Gerstein M. PLoS Computational Biology. 2011 Nov;7(11):e1002190. [Pubmed]
[35] A User's Guide to the Encyclopedia of DNA Elements (ENCODE). The ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. [Pubmed]
[34] Hormonal Regulation of Galectin 3 in Trophoblasts and Its Effects on Endometrium. Yang H, Taylor HS, Lei C, Cheng C, Zhang W. Reprod Sci. 2011 May 9. [Pubmed]
[33] A cis-regulatory map of the Drosophila genome. Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP. Nature. 2011 Mar 24;471(7339):527-31. [Pubmed]
[32] A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M. Genome Biol. 2011 Feb 16;12(2):R15. [Pubmed]
[31] Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Genome Res. 2011 Feb;21(2):276-85. [Pubmed]
[30] Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Cheng C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. Genome Res. 2011 Feb;21(2):245-54. [Pubmed]
[29] Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Gerstein MB*, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, Liu T*, Yip KY*, Robilotto R*, Rechtsteiner A*, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Science. 2010 Dec 24;330(6012):1775-87. (* co-first author) [Pubmed]
[28] Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. Pang K, Cheng C, Xuan Z, Sheng H, Ma X. BMC Syst Biol. 2010 Dec 30;4:179. [Pubmed]
[27] Segmental duplications in the human genome reveal details of pseudogene formation. Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB. Nucleic Acids Res. 2010 Jul 8. [Pubmed]
[26] Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW, Gerstein MB, Weichselbaum RR, Xing HR, Lussier YA. PLoS Comput Biol. 2010 Apr 1;6(4):e1000730. [Pubmed]
[25] Comparative analyses of time-course gene expression profiles of the long-lived sch9{Delta} mutant. Ge H, Wei M, Fabrizio P, Hu J, Cheng C, Longo VD, Li LM. Nucleic Acids Res. 2009 Oct 30. [Pubmed]
[24] The relationship between the evolution of microRNA targets and the length of their UTRs. Cheng C, Bhardwaj N, Gerstein M. BMC Genomics. 2009 Sep 14;10(1):431. [Pubmed]
[23] mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer. Cheng C, Fu X, Alves P, Gerstein M. Genome Biol. 2009 Sep 1;10(9):R90. [Pubmed]
[22] Systematic identification of transcription factors associated with patient survival in cancers. Cheng C, Li LM, Alves P, Gerstein M. BMC Genomics. 2009 May 15;10:225. [Pubmed]
[21] Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Genes Dev. 2009 Mar 1;23(5):619-32. [Pubmed]
[20] Inferring microRNA activities by combining gene expression with microRNA target prediction. Cheng C, Li LM. PLoS One. 2008 Apr 23;3(4):e1989. [Pubmed]
[19] A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. Ge H, Cheng C, Li LM. BMC Bioinformatics. 2008 Apr 14;9:194. [Pubmed]
[18] Systematic identification of cell cycle regulated transcription factors from microarray time series data. Cheng C, Li LM. BMC Genomics. 2008 Mar 3;9:116. [Pubmed]
[17] Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9. Wei M, Fabrizio P, Hu J, Ge H, Cheng C, Li L, Longo VD. PLoS Genet. 2008 Jan;4(1):e13. [Pubmed]
[16] Significant and systematic expression differentiation in long-lived yeast strains. Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, Li LM. PLoS One. 2007 Oct 31;2(10):e1095. [Pubmed]
[15] Inference of transcription modification in long-live yeast strains from their expression profiles. Cheng C, Fabrizio P, Ge H, Longo VD, Li LM. BMC Genomics. 2007 Jul 6;8:219. [Pubmed]
[14] MARD: a new method to detect differential gene expression in treatment-control time courses. Cheng C, Ma X, Yan X, Sun F, Li LM. Bioinformatics. 2006, 22(21):2650-7. [Pubmed]
[13] Sub-array normalization subject to differentiation. Cheng C, Li LM. Nucleic Acids Res. 2005, 33(17):5565-73. [Pubmed]
[12] Sir2 blocks extreme life-span extension. Fabrizio P, Gattazzo C, Battistella L, Wei M, Cheng C, McGrew K, Longo VD. Cell. 2005, 123(4):548-50. [Pubmed]
[11] Isolation and characterization of a novel human putative anemia-related gene homologous to mouse sideroflexin. Ye X, Xu J, Cheng C, Yin G, Zeng L, et al. Biochem Genet. 2003, 41(3-4):119-25. [Pubmed]
[10] Isolation and characterization of a human putative receptor protein kinase cDNA STYK1. Ye X, Ji C, Huang Q, Cheng C, Tang R, et al. Mol Biol Rep. 2003, 30(2):91-6. [Pubmed]
[9] Cloning, expression and characterization of a novel human VMP gene. Cheng C, Xu J, Ye X, Dai J, Wu Q, Mao Y, et al. Mol Biol Rep. 2002, 29(3):281-6. [Pubmed]
[8] Cloning and characterization of a novel human transcription factor AP-2 beta like gene (TFAP2BL1). Cheng C, Ying K, Xu M, Zhao W, Zhou Z, et al. Int J Biochem Cell Biol. 2002, 34(1):78-86. [Pubmed]
[7] Identification and characterization of AGTRAP, a human homolog of murine Angiotensin II Receptor-Associated Protein (Agtrap). Wang W, Huang Y, Zhou Z, Tang R, Zhao W, Zeng L, Xu M, Cheng C, Gu S, Ying K, Xie Y, Mao Y. Int J Biochem Cell Biol. 2002 Jan;34(1):93-102. [Pubmed]
[6] Tumor Relevance Analysis of A Highly Conserved Gene by Using Gene Microarray Hybridization. Cheng C, Zhou Z, Xu M, Zhao W, Xu J, et al. Hereditas (BeiJing). 2002, 24(3): 227-231. [Pubmed]
[5] Cloning and characterization of a novel human TEKTIN1 gene. Xu M, Zhou Z, Cheng C, Zhao W, Tang R, et al. Int J Biochem Cell Biol. 2001, 33(12):1172-82. [Pubmed]
[4] Cloning, expression and characterization of a novel human REPS1 gene. Xu J, Zhou Z, Zeng L, Huang Y, Zhao W, Cheng C, Xu M, Xie Y, Mao Y. Biochim Biophys Acta. 2001 Dec 3;1522(2):118-21. [Pubmed]
[3] Molecular cloning and characterization of a novel Dehydrogenase/reductase (SDR family) member 1 genea from human fetal brain. Wu Q, Xu M, Cheng C, Zhou Z, Huang Y, et al. Mol Biol Rep. 2001, 28(4):193-8. [Pubmed]
[2] Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain. Zeng L, Zhou Z, Xu J, Zhao W, Wang W, Huang Y, Cheng C, Xu M, Xie Y, Mao Y. Cytogenet Cell Genet. 2001;95(1-2):43-7. [Pubmed]
[1] A novel human hydroxysteroid dehydrogenase like 1 gene (HSDL1) is highly expressed in reproductive tissues. Huang Y, Tang R, Dai J, Gu S, Zhao W, Cheng C, Xu M, Zhou Z, Ying K, Xi Y, Mao Y. Mol Biol Rep. 2001;28(4):185-91. [Pubmed]
Book Chapters
- Li, L. and Cheng, C., 2007. Differentiation detection in microarray normalization. Book chapter, Methods in Microarray Normalization (Drug Discovery Series), Edited by Phillip Stafford. [Link]
Patents
Ph.D Thesis
Master Thesis