2015-2011 2010-2006 2005-2001 OTHERS

$ corresponding author; * co-first author

2015-2011

    [68] E2F4 regulatory program predicts patient survival prognosis in breast cancer. Khaleel S*, Andrews E*, Ung M, Direnzo J, Cheng C$. Breast Cancer Research. 2014 [Accept].

    [67] OrthoClust: An orthology-based network framework for clustering data across multiple species. Yan K, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M. Genome Biology. 2014 August 28;15:R100. [Pubmed]

    [66] Comparative analysis of regulatory information and circuits across diverse species. Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Nature. 2014 August 28; 512: 453–456. [Pubmed]

    [65] Relating gene expression evolution with CpG content changes. Yang H, Li D, Cheng C$. BMC Genomics. 2014 Aug 20;15(1):693. [Pubmed]

    [64] Comparative analysis of the transcriptome across distant species. Gerstein MB*, Rozowsky J*, Yan KK*, Wang D*, Cheng C*, Brown B*, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Nature. 2014 August 28;512:445-448. [Pubmed]

    [63] Big data bioinformatics. Greene C, Tan J, Ung M, Moore J$, Cheng C$. J. Cell. Physiol. 2014 May 6. doi: 10.1002/jcp.24662. [Pubmed]

    [62] The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis. Mishra B, Zaffuto K, Artinger E, Org T, Mikkola H, Cheng C, Djabali M, Ernst P. Cell Rep. 2014 May 22;7(4):1239-47. [Pubmed]

    [61] Interpretable Sparse High-Order Boltzmann Machines. Min R, Ning X, Cheng C, Gerstein M. Journal of Machine Learning Research. JMLR W&CP 33:614-622, 2014. [Link]

    [60] Effect of estrogen receptor alpha binding on functional DNA methylation in breast cancer. Ung M, Ma X, Johnson K, Christensen B, Cheng C$. Epigenetics. 2014 Jan 16;9(4). [Pubmed]

    [59] DPRP: A database of phenotype-specific regulatory programs derived from transcription factor binding data. David TW*, Tseng Y*, Ung M, Liao I, Liu C, Cheng C$. Nucleic Acids Res. 2014 Jan;42(Database issue):D178-83. [Pubmed]

    [58] Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation. Johnson KC, Koestler DC, Cheng C, Christensen BC. Epigenetics. 2013 Nov 6;9(2). [Pubmed]

    [57] Association of Gamma-Aminobutyric Acid A Receptor α 2 Gene (GABRA2) with Alcohol Use Disorder. Li D, Sulovari A, Cheng C, Zhao H, Kranzler HR, Gelernter J. Neuropsychopharmacology. 2013 Oct 18. [Pubmed]

    [56] Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Grant GD, Brooks L 3rd, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML. Mol Biol Cell. 2013 Oct 9. [Pubmed]

    [55] Identification of yeast cell cycle regulated genes based on genomic features. Cheng C$, Fu Y*, Shen L, Gerstein M. BMC Syst Biol. 2013 Jul 29;7(1):70. [Pubmed]

    [54] REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. Zhu M, Liu CC, Cheng C$. BMC Genomics. 2013 Jul 26;14(1):504. [Pubmed]

    [53] Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. Cheng C$, Ung M, Grant G, Whitfield M. PLoS Computational Biology. 2013. [Pubmed]

    [52] MLL1 coordinates proliferation with self-renewal in hematopoietic stem cells. Artinger E, Mishra B, Artinger K, Li B, Chung E, Moore A, Chen Y, Cheng C, Ernst P. Proc Natl Acad Sci U S A. 2013. [Pubmed]

    [51] Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. Yang C, Buck J.M, Chen M, Chen Y, Lan H, Cheng C, Chen J, Liu C. BMC Genomics. 2013 May 8;14:310. [Pubmed]

    [50] Paeonol induces apoptosis in human ovarian cancer cells. Yin J, Wu N, Zeng F, Cheng C, Kang K, Yang H. Acta Histochemica. 2013 Jun 12. doi:pii: S0065-1281(13)00076-7. [Pubmed]

    [49] Machine learning and genome annotation: A match meant to be? Kevin Y, Cheng C, Gerstein, M. Genome Biology. 2013 May 29;14(5):205. [Pubmed]

    [48] A Comprehensive Nuclear Receptor Network for Breast Cancer Cells. Kittler R, Zhou J, Hua S, Ma L, Liu Y, Pendleton E, Cheng C, Gerstein M, White KP. Cell Rep. 2013 Jan 30. [Pubmed]

    [47] Modeling gene expression using chromatin features in various cellular contexts. Dong X, Greven M, Kundaje A, Djebali S, Brown BJ, Cheng C, Gerstein M, Guigó Serra R, Birney E, Weng Z. Genome Biology. 2012 Sep 5;13(9):R53. [Pubmed]

    [46] The Anti-Apoptotic Effect of Galectin-3 in Human Endometrial Cells under the Regulation of Estrogen and Progesterone. Yang H, Lei C, Cheng C, Feng Y, Zhang W, Petracco RG, Sak S. Biol Reprod. 2012 Jun 6. [Pubmed]

    [45] Analysis of the human regulatory network using ENCODE Data. Gerstein MB*, Kundaje A*, Hariharan M*, Landt SG*, Yan KK*, Cheng C*, Mu XJ*, Khurana E*, Rozowsky J*, Alexander R*, et al. Nature. 2012 Sep 6;489(7414):91-100. [Pubmed]

    [44] An integrated encyclopedia of DNA elements in the human genome. The ENCODE Project Consortium. Nature. 2012 Sep 6;489(7414):57-74. [Pubmed]

    [43] Genome-wide analysis of the binding sites of more than 100 transcription factors defines different types of genomic regions with distinct biological properties. Yip YK, Cheng C, Bhardwaj N, Brown BJ, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel JP, Snyder M and Gerstein M. Genome Biology. 2012 Sep 5;13(9):R48. [Pubmed]

    [42] Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, et al. Genome Res. 2012 Sep;22(9):1658-67. [Pubmed]

    [41] Average rank-based score to measure deregulation of molecular pathway gene sets. Yang H*, Cheng C*$, Zhang W. PLoS One. 2011;6(11):e27579. [Pubmed]

    [40] 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]

    [39] 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. [Pubmed]

    [38] 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]

    [37] 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]

    [36] A User's Guide to the Encyclopedia of DNA Elements (ENCODE). The ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. [Pubmed]

    [35] 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]

    [34] 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]

    [33] 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]

    [32] 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]

    [31] 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]

    [Go back]

2010-2006

    [30] 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]

    [29] 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]

    [28] 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]

    [27] 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]

    [26] 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]

    [25] 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]

    [24] 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]

    [23] 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]

    [22] 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]

    [21] Inferring microRNA activities by combining gene expression with microRNA target prediction. Cheng C, Li LM. PLoS One. 2008 Apr 23;3(4):e1989. [Pubmed]

    [20] 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]

    [19] 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]

    [18] 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]

    [17] Inferring activity changes of transcription factors by binding association with sorted expression profiles. Cheng C, Yan X, Sun F, Li LM. BMC Bioinformatics. 2007 Nov 16;8:452. [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]

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2005-2001

    [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]

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others

Conference publications

[2] Applications of bioinformatics to non-coding rnas in the era of next-generation sequencing. Cheng C, Moore J, Greene C. The Pacific Symposium on Biocomputing (PSB) 2014. [Link]

[1] Interpretable sparse high-order boltzmann machines for transcription factor interaction identification. Min R, Ning X, Cheng C, Gerstein M. Machine Learning in Computational Biology (MLCB), Annual Conference on Neural Information Processing Systems (NIPS) 2013. [Link]

Book Chapters

[1] 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

      Lei M. Li, Chao Cheng, Huanying Ge, SYSTEMS AND METHODS FOR ANALYZING MICROARRAYS. [Link]

Ph.D Thesis

      Chao Cheng, Detecting and Understanding Differentiation of Microarray Expression Data. Computational and Molecular Biology, University of Southern California, 2006. [Link]

Master Thesis

      Chao Cheng, Symmetric and Trimmed Solutions of Simple Linear Regression. Department of Mathematics, University of Southern California, 2006. [Link]

      Chao Cheng, Study of Human Dual Specific Phosphatases. Institute of Genetics, Life Science, Fudan University, 2002.

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Last updated: Sep 1, 2014