张奇伟

 

张奇伟

清华大学 信息学院与医学院双聘教授

生命学院兼职教授

博士生导师

清华信息国家实验室合成与系统生物实验室主任

首批千人计划教授

长江学者讲座教授

主要科研领域与方向  

计算生物学与生物信息学,合成生物与系统生物学,特别是利用高通量组学技术和高性能计算机模拟,研究细胞发育、分化、凋亡的基因调控和代谢网络,以及它们在癌症等疾病、生物能源、和环境中的应用。

研究及工作经历 

1977-1981 中科大近代力学系, 学士

1981-1987 Rutgers U, 统计物理博士

1987-1991 美国NYU Courant Inst.,应用数学博士后

1991-1996 美国冷泉港实验室基因组研究Fellow

1996-1998 美国冷泉港实验室,Assistant Staff

1999-2001 美国冷泉港实验室,Associate Professor

2002-2010 美国冷泉港实验室, Full Professor

2009-至今 清华大学信息学院与医学院双聘教授,生命学院兼职教授, 博导,清华信息国家实验室合成与系统生物实验室主任

2010-至今 美国UT DallasCecil H. and Ida Green Distinguished Chair ProfessorDirector of Center for Systems Biology

发表论文及著作

2015

Djekidel MN, Liang ZY, Wang Q, Hu Z, Li G, Chen Y, Zhang MQ, (2015) 3CPET: Finding Co-factor Complexes from ChIA-PET data by using Hierarchical Dirichlet Process. Genome Biol. In press.

Zhang H*, Zhu C*, Zhao Y*, Li M, Wu L, Yang X, Wan X, Wang A, Zhang MQ+, Sang X+, Zhao H+ (2015) Long non-coding RNA expression profiles of Hepatitis Cvirus-related dysplasia and hepatocellular carcinoma. Oncotarget, DOI: 10.18632/oncotarget.6087.

Zhao, Yi; Li, Hui; Fang, shuangsang; Kang, Yue; Wu, Wei; Hao, Yajing; Li, Ziyang; Bu, Dechao; Sun, Ninghui; Zhang MQ*; Chen, Runsheng* (2015) NONCODE 2016: an informative and valuable data source of long noncoding RNAs. NAR, In press

Wu D, Wang D, Zhang MQ, Jin Gu (2015) Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification. MBC Genomics, In press.

Sathe, A.; Zhang, Yu-An; Ma, X.; Ray, P.; Cadinu, D.; Wang, Yi-Wei; Yao, X.; Liu, Xiao-Yun; Tang, H.; Wang, Y.; Huang, Y.; Liu, C.; Gu, J.; Akerman, M.; Mo, Y.; Cheng, C.; Xuan, Z.; Chen, L.; Xiao, G.; Xie, Y.; Girard, L.; Wang, H.; Lam, S.; Wistuba, I.I.; Zhang, L.; Gazdar, A.F.; Zhang MQ. (2015) "SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers," in Life Sciences Letters, IEEE , vol.PP, no.99, pp.1-1. doi: 10.1109/LLS.2015.2488438

Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park I, Kim TH (2015) Histone deacetylases positively regulate transcription through the elongation machinery. Cell Rep. in press.

Mehta, H. H., Liu, Y., Zhang MQ, & Spiro, S. (2015). Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073. Microbial Genomics, 1(4).

He C, Zhang MQ, Wang X (2015) MICC: an R package for identifying chromatin interactions from ChIA-PET data. Bioinformatics, in press.

Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T, Wu Q (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell 162:900-10. PMID: 26276636.

Ehrhardt K, Guinn MT, Quarton T, Zhang MQ, Bleris L (2015) Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting. Biosens Bioelectron. 74:744-750. PMID: 26210472

Hu L, Di C, Kai M, Yang Y-C, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ (2015) A common set of distinct features that characterize noncoding RNAs across multiple species. NAR. 43:104-14. PMID: 25505163, PMCID: PMC4288202.

Orozco LD, Marco Morselli M, Rubbi L, Guo W, Go J, Shi H, Lopez D, Furlotte NA, Bennett BJ, Charles R. Farber CR, Ghazalpour A, Zhang MQ, Bahous R, Rozen R, Lusis AJ, Pellegrini M (2015) Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice. Cell Metabolism, 21:905-17. PMID: 26039453, PMCID: PMC4454894.

Sun G, Hu Z, Min Z, Yan X, Guan Z, Su H, Fu Y, Ma X, Chen Y-G, Zhang MQ*, Tao Q*, Wu W* (2015) Small C-terminal Domain Phosphatase 3 Dephosphorylates the Linker Sites of Receptor-regulated Smads (R-Smads) to Ensure Transforming Growth Factor β (TGFβ)-mediated Germ Layer Induction in Xenopus Embryos. JBC, 290:17239-49. PMID: 26013826, PMCID: PMC4498063.

Akerman M, Fregoso O, Das S, Ruse C, Jensen MA, Pappin DL, Zhang MQ, Krainer A. (2015) Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biol. 16:119. PMID: 26047612, PMCID: PMC4502471.

Wang T, Xiao G; Chu Y, Zhang MQ, Corey D, Xie Y (2015) Design and bioinformatics analysis of genome-wide CLIP experiments. NAR, PMID:25958398.

Huo W, Adams HM, Zhang MQ, Palmer KL (2015) Genome modification in Enterococcus faecalisOG1RF assessed by bisulfite sequencing and single molecule real time sequencing. J. Bacteriology 1971939-51. PMID25825433.

Yuan Y, Liu B, Xie P, Zhang MQ, Li Y, Zhen X, Wang X (2015) Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit. PNAS, 112:3158-63. PMID:25713348.

Raodmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518:317-30. PMID:25693563

Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B (2015) Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature, 518:350-4. PMID:25693566

Li L, Tang J, Zhang B, Yang W, Liugao M, Wang R, Tan Y, Fan J, Chang Y, Fu J, Jiang F, Chen C, Yang Y, Gu J, Wu D, Guo L, Cao D, Li H, Cao G, Wu M, Zhang MQ, Chen L, Wang H (2015) Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut 64:156-67. PMID: 24572141.

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2014   

Hu L, kai M, Di C, Li Y, Qiu Y, Yu Y, Wang Y, Yang Y-C, Yuan J, Yip KY, Zhang MQ, Lu ZJ (2014) An inter-species feature selection method to characterize non-coding RNAs and their functional domains. Submitted.

Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. (2014) Genome-wide map of regulatory interactions in the human genome. Genome Res. 2014 Dec;24(12):1905-17. doi: 10.1101/gr.176586.114.

Sephton CF, Tang AA, Kulkarni A, West J, Brooks M, Stubblefield JJ, Liu Y, Zhang MQ, Green CB, Huber KM, Huang EJ, Herz J, Yu G. (2014) Activity-dependent FUS dysregulation disrupts synaptic homeostasis. Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4769-78. doi: 10.1073/pnas.1406162111.

Cheng J, Zhou X, Lu Y, Chen J, Han B, Zhu Y, Liu L, Choy K-W, Han D, Sham PC, Zhang MQ, Zhang X, Yuan H (2014) Exome sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nosyndromic hearing loss in a Chinese family. AHG. 78:410-423. PMID:25227905 pdf

Sheng MM, Zhong Y, Chen Y, Du JC, Ju XW, Zhao C, Zhang GG, Zhang LF, Liu KT, Yang N, Xie P, Li DS, Zhang MQ*, Jiang CY*(2014) Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Science China Life Sciences, 57(10), 959-972.

Liao W, Ouyang W, Zhang MQ, Li MO. (2014) Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes. Genom Data. 2014 Dec 1;2:280-281.

Nisha Rajagopal, Jason Ernst, Pradipta Ray, Jie Wu, Zhang MQ, Monolis Kellis, and Bing Ren (2014) Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers and Gene Bodies. G3 g3.114.013565; Early Online.

Huijun Yuan, Yu Lu, Xueya Zhou, Zhanguo Jin, Jing Cheng, Weidong Shen, Fei Ji, Liyang Liu, Xuegong Zhang, Zhang MQ, Ye Cao, Don Yi Han, and Richard Choy (2014) Resolving the Genetic Heterogeneity of Prelingual Hearing Loss within One Family: Performance Comparison and Application of Two Targeted Next Generation Sequencing Approaches. Journal of human genetics, 59(11), 599-607.

Li Y, Ehrhardt K, Zhang MQ, Bleris L (2014) Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries. Sci. Rep. 4:4857. PMID:24798576.

He C, Wang X*, Zhang MQ* (2014) Nucleosome eviction and multiple co-factor binding predict estrogen receoptor alpha associated long-range interactions. Nucl. Acids Res. (2014) doi:10.1093/nar/gku327

Li W, Wu J, Kim S-Y, Zhao M, Zhang MQ, Meistrich ML, Mills AA (2014) Chd5 orchestrates chromatin remodeling during sperm development. Nat. Comm. 5:3812. PMID:24818823.

Xie P, Liu Y, Li Y, Zhang MQ*, Wang X* (2014) MIROR: a method for cell-type specific microRNA occupancy rate prediction. Mol. BioSyst. 2014,10,1377-1384 DOI:10.1039/C3MB70610A

Li GP, Li M, Zhang YW, Wang D, Li R, Guimera R, Gao J*, Zhang MQ* (2014) ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks. PLoS One. 2014;9(5):e94608.

Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X, Zhang S, Yu D, Song L, Zhang H, Zhang C, Huo L, Huo C, Wang Y, Du Y, Zhang H, Zhang P, Na H, Xu S, Zhu Y, Xie Z, He T, Zhang Y, Wang G, Fan Z, Yang F, Liu H, Wang X, Zhang X, Zhang MQ, Li Y, Steinbuchel A, Fujimoto T, Cichello S, Yu J, Liu P. (2014) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Res. 2014 Jan;42(2):1052-64. doi: 10.1093/nar/gkt932.

Chen L, Zhang H, Li L, Yan Z, Wu DM, Liu Y, Liu K, Liu M, Hu L, Tu Q, Chang Y, Tan Y, Yang C, Song D, Fu J, Yang X, Feng Q, Chen H, Wu M, Yang H, Zhang MQ, Zhang Y, Wang J, Wang H (2014) Integrative whole genome analyses revealing clonal HBV integrations and abnormal enrichment of variable number tandem repeats in human hepatocellular carcinoma. J.Clinical Invest. Submitted.

Weyn-Vanhentenryck S, Sun S, Yan Q, Mele A, Farny N, Silver Z, Zhang MQ, Krainer AR, Darnell RB, Zhang C (2014) HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Reports, S2211-1247(14)00084-9. PMID:24613350.

Jin Gu, Yang Chen, Huiya Huang, Lingyun Yin, Zhen Xie, Michael Zhang*. Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular BioSystems 2014, 10(12):3249-3254.

Guo W, Chung, W-Y, Qian, M, Pellegrini, M, Zhang MQ (2014). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. 42:3009-16. PMID:24343027.

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2013  

Steijger T, .., Akerman M,..Wu J. Zhang MQ, Hubbard TJ, Guigo R, Harrow J, Bertone P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat. Meth. 10:1177-84. PMID:24185837.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013 Nov 10;14(1):774. PMID:24206606.

Jiang R, Zhang X, Zhang MQ (2013) Basics of Bioinformatics: Lecture Notes of Graduate Summer School on Bioinformatics of China. Book, ISBN-10:3642389503, ISBN-13: 978-3642389504. Springer 2013 edition.

Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X, Zhang S, Yu D, Song L, Zhang H, Zhang C, Huo L, Huo C, Wang Y, Du Y, Zhang H, Zhang P, Na H, Xu S, Zhu Y, Xie Z, He T, Zhang Y, Wang G, Fan Z, Yang F, Liu H, Wang X, Zhang X, Zhang MQ, Li Y, Steinbüchel A, Fujimoto T, Cichello S, Yu J, Liu P. (2013) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. NAR, [Epub ahead of print], PMID:24150943.

Tam KW, Zhang W, Soh J, Stastny V, Chen M, Sun H, Thu K, Rios JJ, Yang C, Marconett CN, Selamat SA, Laird-Offringa IA, Taguchi A, Hanash S, Shames D, Ma X, Zhang MQ, Lam WL, Gazdar A (2013) CDKN2A/p16 Inactivation Mechanisms and Their Relationship to Smoke Exposure and Molecular Features in Non-Small-Cell Lung Cancer. J Thorac Oncol. 8:1378-88. PMID:24077454.

Wu D, Gu J, Zhang MQ. (2013) FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS One. 2013 Sep 5;8(9):e74275. PMID:24040221.

Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. (2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity. 39:286-97. PMID:23924514.

Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. Mol. Cell. Proteomics, [PubMed – in process] PMID:23924514.

Zhou D, Wu D, Li Z, Qian M, Zhang MQ (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol. 2:2095-4689. DOI: 10.1007/s40484-013-0014-2.

Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tiam S, Hawkins DR, Leung D, Yang H, Wang T, Swanson SA, Zhang J, Zhu Y, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Eckert JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 153:1134-48. PMID:23664764.

Wen-Yu Chung, Robert J. Schmitz, Tanya Biorac, Delia Ye, Miroslav Dudas, Gavin D. Meredith, Christopher C. Adams, Joseph R. Ecker and Michael Q. Zhang (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, 4:335-346.

May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nat. Comm. 4:2145. PMID:23900278.

Ma X, Wang YW, Zhang MQ, Gazdar AF (2013) DNA methylation data analysis and its application to cancer research. Epigenomics. 5:301-16. PMID:23750645.

Wu J, Anczuków O, Krainer AR, Zhang MQ*, Zhang C* (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl. Acid. Res. 41:5149-5163. PMID:23571760.

Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics, Proteomics Bioinformatics, pii:S1672-0229(13)00047-8. PMID:23685394.

Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8:e66264. PMID:23805207.

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2012   

Xing H, Liao W, Mo Y, Zhang MQ. 2012A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types. J Vis Exp, Dec 10;(70). doi:pii: 4273. We H*, Li Y*, Malek SN, Kim YC, Xu J, Chen P, Xiao F, Huang X, Zhou X, Xuan Z, Mankala S, Rowley JD, Zhang MQ, Wang SM (2012) New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS ONE. 7:e51203.

Ouyang W, Will L, Luo CT, Yin N, Huse M, Kim MV, Peng M, Chan P, Ma Q, Mo Y, Meijer D, Zhao K, Rudensky AY, Atwal G, Zhang MQ*, Li MO* (2012) Novel Foxo1-dependent Transcriptional Programs Control Treg Cell Function. Nature, 491(7425), 554-559.

Xing H, Liao W, Mo Y, Zhang MQ (2012) A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types. J Vis Exp, Dec 10;(70). doi:pii: 4273.

Xing H*, Mo Y, Liao W, Zhang MQ* (2012) Genomewide localization of protein-DNA binding and histone modification by BCP with ChIP-seq data. PLoS CB, 8(7): e1002613.

Sleumer MC, Wei G, Wang Y, Chang H, Xu T, Chen R, Zhang MQ (2012) Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BMC Genomics. 13:433. PMID:22401550.

Li R, Guo W, Gu J, Zhang MQ, Wang XW (2012) Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics. [Epub ahead of print] PMID:22824656..

Zhang Z, Ma X, Zhang MQ (2012) Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS ONE, 7:e38112. PMID:22768038.

Chicas A*, Kapoor A*, Wang X*, Evertts AG, Benjam G, Zhang MQ, Bernstein E, Lowe SW, (2012) H3K4 demethylation by Jarid1a and Jarid1b contributes to RB-mediated gene silencing during cellular senescence. PNAS, 109:8971-6. PMID:22615382.

Zhang J, Wu Z, Gao C, Zhang MQ (2012) High-order interactions in Rheumatoid Arthritis detected by Bayesian method using GWAS data. American Medical Journal, 3:56-66.

Zhang C, Zhang MQ (2012) Identification of Splicing Factor Target Genes by High-throughput Sequencing. Chap. 51 in Alternative pre-mRNA Splicing: Theory and Protocols. Eds. Stamm S, Smith C, Luhrmann R. Wiley-Blackwell, Weinheim, Germany.

Zhang MQ (2012), Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data. Chap 12 in Bioinformatics for High Throughput Sequencing, eds. Rodriguez-Ezpeleta N, Hackenberg M, Aransay AM. p209. ISBN978-1-4614-0781-2, Springer.

Zhang J, Zhang Q, Lewis D, Zhang MQ (2012) A Bayesian Method for Disentangling Dependent Structure of Epistatic Interaction. Am. J. Biostat., 2:1-10.

He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ (2012) Cell-type based analysis of microRNA profiles in the mouse brain. Neuron. 73:35-48. PMID:22243745.

Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ (2012) POSMO: A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucl. Acid. Res. PMID:22228832.

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2011  

Rajan P, Dalgliesh C, Carling P, Buist T, Zhang C, Grellscheid SN, Armstrong K, Stockley J, Simillion C, Gaughan L, Kalna G, Zhang MQ, Robson CN, Leung HY, Elliott DJ. (2011) Identification of novel androgen-related pathways and mRNAs isoforms through genome-wide exon-specific profiling of LNCaP transcriptome. Endocrine-Related Cancer, PLoS ONE, 6(12):e29088. PMID:22194994.

Dai Q, Lihua Li L, Liu X, Yao Y, Zhao F, Zhang MQ(2011) Integrating overlapping structures and background information of words significantly improves biological sequence comparison. PLoS ONE, 6:e26779. PMID:22102867.

Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N*, Zhang MQ*, Lucito R* (2011) Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer. PLoS ONE, 6(12):e28503. PMID:22174824.

Hu Z, Qian M, Zhang MQ (2011) Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. BMC Systems Biology. 5(Suppl 2):S8.

Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J (2011) EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 6:1505-12. PMID:22139581.

Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27:3010-6. PMID:21896509.

Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S (2011) Direct cloning of double-stranded RNAs from RNAse protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. NAR, 39:9720-30. PMID:21880592.

Cheng J, Zhu Y, He S, Lu Y, Chen J, Han B, Petrillo M, Wrzeszczynski KO, Yang S, Dai P, Zhai S, Han D, Zhang MQ, Li W, Liu X, Li H, Chen ZY, Yuan H (2011) Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64. Am J Hum Genet. 89:56-66. PMID:21722859.

Watts JA, Zhang C, Klein-SzantoAJKormish JD, Zhang MQ, Zaret K, (2011) Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development. PLoS Genet. 7:e1002277. PMID:2193553.

Zhang Z, Zhang MQ (2011) Histone modification profiles are predictive for both protein-coding and microRNA gene’s tissue.cell-type specific expression. BMC Bioinformatics. 12:155. PMID:21569556.

Yang S, Yalamanchili HK, Li X, Yao K-M, Sham PC, Zhang MQ, Wang J. (2011) Correlated evolution of transcription factors and their binding sites. Bioinformatics, 21:2972-2978 (PMID:21896508)

Qin J, Li MJ, Wang P, Zhang MQ, Wang J (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. NAR, 39:W430-6. PMID:21586587.

Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ (2011) Inferring Haplotype of Copy Number variations from High-throughput data with Uncertainty. G3 genes genomes genetics, 1:35-42.

Renault VM, Thekkat PU, Hoang KL, White JL, Brady CA, Kenzelmann Broz D, Venturelli OS, Johnson TM, Oskoui PR, Xuan Z, Santo EE, Zhang MQ, Vogel H, Attardi LD, Brunet A (2011) The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene, 30:3207-21. PMID:21423206.

Zhang MQ, (2011) Computational Promoter Prediction in a Vertebrate genome. Chap. In Handbook of Statistical Bioinformatics. Springer Handbooks of Computational Statistics. Lu H, Scholkopf B and Zhao H (Eds). pp73-85. ISBN: 978-3-642-16344-9. http://www.springer.com/statistics/book/9783642163449

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2010  

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. . (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 28:1097-105.

Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Jourdren L, Coulpier F, Triller A, Spector DL, Bessis A (2010) A long nuclear -retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J, 29:3082-93.

Bandyopadhyay S, Mitra R, Maulik U, Zhang MQ (2010) Development of the human cancer microRNA network. Silence, 1:6.

Mitra R, Bandyopadhyay S, Maulik U, Zhang MQ. (2010) SFSSClass: an integrated approach for miRNA based tumor classification.BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S22.

Chicas, A., Wang, X., Zhang, C., McCurrach, M., Zhao Z., Ozlem, M., Dickins, R., Narita, M., Zhang, M.Q ., Lowe, S.W. (2010). Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence. Cancer Cell, 17:376-87.

Wang SM, Zhang MQ (2010) The progress and challenge for transcriptome study on human CD34+ hematopoietic stem-progenitor cells. J. Cell. Physiol. Review. 223:549-552.

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2009

Zhang MQ, Waterman MS, Zhang X (2009): The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinformatics; 2009;10 Suppl 1:S1. PMID: 19208108

Smith AD, Chung W, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ (2009) Updates to the RMAP short-read mapping software. Bioinformatics. 25:2841-2842.

Hodges E*, Smith AD*, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 19:1593-605.

Kim Y-C, Wu Q, Chen J, Xuan X, Jung Y-C, Zhang, MQ, Rowley J, Wang SM. (2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. HYPERLINK "http://rulai.cshl.org/reprints/CD34Cells.pdf" PNAS. 106:8278-83.

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung, DC, Xavier RJ. (2009) An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1) target genes that form the core response to hypoxia. Nucleic Acids Res. 37:4587-602.

Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T (2009) Gene set-based module discovery in the breast cancer transcriptome BMC Bioinformatics, 10:71. PMID: 19243633.

Rosenfeld, JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ (2009) Determination of enriched histone modifications in non-genic portions of the human genome. HYPERLINK "http://rulai.cshl.org/reprints/HistoneModRosenfeld.pdf" BMC Genomics 10:143

Li T, Huang J, Jiang Y, Zeng Y, He F, Zhang MQ, Han Z, Zhang X (2009) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. HYPERLINK "http://rulai.cshl.org/reprints/Tingting_Genomics.pdf" Genomics 93(3):235-42.

Wang X, Xuan Z, Zhao X, Li Y and Zhang MQ (2009) High-resolution Human Core-promoter prediction with CoreBoost_HM. Genome Res. 22:2902.

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2008   

Castle, J.C., Zhang, C., Shah, J.K., Kulkarni, A.V., Cooper, T.A., Johnson, J.M. (2008). Differential expression of 24,426 human alternative splicing events and predicted cis-regulation in 48 tissues. Nature Genet. 40:1416-1425.

Hsieh MC, Das D, Sambandam N, Zhang MQ, Nahlé Z. (2008) HYPERLINK "http://www.ncbi.nlm.nih.gov/pubmed/18667418?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum" Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem. 2008 Oct 10;283(41):27410-7.

Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu C-I, Wang SM (2008) Poly A- Transcripts Expressed in HeLa Cells, PLoS ONE, 3:e2803.

Fan S, Zhang MQ, Zhang X (2008) Histone Methylation Marks Play Important Roles in Predicting the Methylation Status of CpG Islands. BBRC, 374:559-64.

Lin H, Zhang Z, Zhang MQ, Ma B, Li M (2008) ZOOM! Zillions of oligos mapped. HYPERLINK "http://rulai.cshl.org/reprints/ZOOMLin.pdf" Bioinformatics 24(21):2431-7.

Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer AR, Zhang MQ (2008) Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev. 22:2550-63. Erratum in: Genes Dev. 22:2902.

Zhang C, Li W-H, Krainer AR, Zhang MQ (2008) An RNA landscape of evolution for optimal exon and intron discrimination. Proc. Acad. Natl Sci. USA, 105:5797-802.

Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T (2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. Bioinformatics, 9:404.

Smith AD, Xuan Z, Zhang MQ (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9:128.

Chen G, Li W, Zhang Q-S, Regulski M, Sinha N, Barditch J, Tully T, Krainer AR, Zhang MQ, Dubnau J (2008) Identification of synaptic targets of Drosophila Pumilio. PLoS Comp Biol. (joint corresponding authors). 4(2)e1000026.

Chen J, Kim YC, Jung Y-C, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM (2008) Scanning the human genome at kilobase resolution. Genome Res. 18:751-62.

Nahle Z, Hsieh M, Pietka T, Coburn CC, Grimaldi PA, Zhang MQ, Das D, Abumrad NA. (2008) CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPARgamma/beta-mediated Adaptation to Metabolic Stress. J. Biol. Chem. 283:14317-26.

Cuddapah S, Chen X, Xuan Z, Roh T-Y, Cui K, Smith AD, Byun JS, Zhang MQ, Fuller MT, Zhao K (2008) Identification of potential human polycomb response elements in T cells. (unpublished).

Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B (2008) Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res. 18:46-59.

Wang Z*, Zang C*, Rosenfeld J*, Schones DE, Barski A, Cuddapah S, Cui K, Roh T-Y, Peng W, Zhang MQ, Zhao K (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. (*equal contributing first author), 40:897-903. PMID: 18552846, PMCID: PMC2769248

Wu X, Jiang R., Zhang MQ, Li S (2008) Network-based global inference of human disease genes. Mol. Sys. Biol. 4:189.

Wang X, Gu J, Zhang MQ, Li Y (2008) Identification of phylogenetically conserved microRNA cisregulatory elements across 12 Drosophila species. Bioinformatics, 24:165-71.

Eguchi J, Yan Q-W, Schones DE, Kamal M, Hsu C-H, Zhang MQ, Crawford GE, Rosen ED (2008) Identification of interferon-regulatory factors (IRFs) as regulators of adipocyte gene expression by mapping DNase hypersensitive sites during adipogenesis. Cell Metabolism. 7:86-94.

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Before 2008   

Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ. (2007) A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A. 104:19291-6.

Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet. 39:1522-7.

Fan S, Fang F, Zhang X, Zhang MQ (2007) Putative Zinc Finger Protein Binding Sites Are Over-represented in the Boundaries of Methylation-resistant CpG Islands in the Human Genome. PLoS ONE, 2(11):e1184.

Zhang MQ (2007) Computational analyses of eukaryotic promoters. Review proceeding of Otto Warburg International Summer School and Workshop on Networks and Regulation, Peter F Arndt & Martine Vingron eds. BMC Bioinformatics, HYPERLINK "http://www.biomedcentral.com/1471-2105/8?issue=S6" 8(Suppl 6):S2.

Wang X, Bandyopadhya S, Xuan Z, Zhao X, Zhang MQ, Zhang X (2007) PREDICTION OF TRANSCRIPTION START SITES BASED ON FEATURE SELECTION USING AMOSA. Proc. Comp. Sys. Bioinf. Conference. San Diego, Aug. 2007. World Scientific. HYPERLINK "http://eproceedings.worldscinet.com/9781860948732/9781860948732_0021.html" eProceedings.

Zhang C, Krainer AR, Zhang MQ. (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends in Genetics. 23:484-8.

Zhang C, Hastings ML Krainer AR, Zhang MQ. (2007) Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proc. Natl. Acad. Sci. USA 104, 15028-15033.

Zhang, C., Zhang MQ. 2008. Biomedical literature mining. Chapter 10 in Bioinformatics: A Concept-Based Introduction. (Mathura, V. & Kangueane, P., ed) Springer. 115-127.

Zhao X, Leotta A, Kustanovich V, Lajonchere C, Geschwind DH, Law K, Law P, Qiu S, Lord C, Sebat J, Ye K, Wigler M. (2007) A unified genetic theory for sporadic and inherited autism. Proc Natl Acad Sci U S A. 104:12831-6.

Jiang B, Zhang MQ and Zhang X. (2007) OSCAR: One-class SVM for Accurate Recognition of Cis-elements. Bioinformatics, 23:2823-8.

He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA, Hannon GJ (2007) A microRNA component of the p53 tumour suppressor network. Nature. 447, 1130-4.

Yang Z, Jiang H, Zhao F, Shankar DB, Sakamoto KM, Zhang MQ, Lin S (2007) A highly conserved distal regulatory element controls hematopoietic expression of GATA-2. BMC Developmental Biology, 7:97.

Kim TH, Abdullaev Z, Smith AD, Ching KA, Loukinow D, Green RD, Zhang MQ, Lobanenkov V, Ren B (2007) Analysis of the vertebrate insulator protein CTCF binding sites in the human genome. Cell 128(6):1231-45.

Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, Hannon GJ (2007) Critical roles for Dicer in the female germine. Gene & Dev. 21:682-93.

Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA, Gleiberman A, Zhang MQ, Enikolopov G. (2007) Neural Potential of a Stem Cell Population in the Hair Follicle. Cell Cycle 6:2161-70. (HYPERLINK "http://www.landesbioscience.com/journals/cc/article/4593"cover image!)

D. Das and M.Q. Zhang. (2007) Predictive Models of Gene Regulation: Application of Regression Methods to Microarray Data. Methods in Molecular Biology, ed. M. Korenberg. 377:95.

Zhang J, Jiang B, Li M, Tromp J, Zhang X and Zhang MQ (2007) Computing exact p-values for DNA motifs (Part I). Bioinformatics. 23:531-7.

Schones DE, Smith AD and Zhang MQ (2007) Statistical significance of cis-regulatory modules. BMC Bioinformatics 8:19.

Jiang C, Xuan Z, Zhao F, Zhang MQ (2007) TRED: A Transcriptional Regulatory Element Database, new entries and other development. Nucleic Acid Res 35: D137-D140

Zhang C, Zhao X, Zhang MQ (2007) Functional in silico analysis of gene regulatory polymorphism - Chapter 12 in: Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data, 2nd edition

(M.R. Barnes, ed.) Pp281-310 HYPERLINK "http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470026197,descCd-tableOfContents.html" Wiley-VCH

Zhao X, Xuan Z, Zhang MQ (2007) Boosting with stumps for predicting transcription start sites. Genome Biology 8:R17

Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. (2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics. 23:21-29.

Smith AD, Sumazin P and Zhang MQ (2007) Tissue-specific regulatory elements in mammalian promoters. Mol Sys Biol. 3:73.

Zhang C, Zhang X, Zhang MQ, Li Y (2007) Neighbor number, valley seeking and clustering. Pattern Recognition Letters. 28:173-180.

Zhang MQ (2007) Inferring Gene Regulatory Networks - Chapter 21 in: Bioinformatics - From Genomes to Therapies (T. Lengauer, ed.) Wiley-VCH. p807-828.

Kim YC, Jung Y-C, Xuan Z, Tong H, Zhang MQ, Wang SM (2006) Pan-genome isolation of low abundant transcripts through SAGE. FEBS Lett 580:6721-6729.

Schaffer JD, Dimitrova N, Zhang MQ (2006) Bioinformatics. Chap. 26 in Advances in Healthcare Technology: Shaping the Future of Medical Care. Spekowius G & Wendler T eds. Pp421-438. Springer.

Li J, Zhang MQ and Zhang X (2006) A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. Am. J. Hum. Genet. 79:628-639.

Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, Edwards JR, Ju J, Bestor TH, Zhang MQ (2006) Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A. 103:10713-6.

Smith PJ, Zhang C, Wang J, Chew SL, Zhang MQ, Krainer AR (2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonix splicing enhancers. Hum Mol Genet 15(16):2490-2508.

Fang F, Fan SC, Zhang X and Zhang MQ (2006) Predicting Methylation Status of CpG Islands in the Human Brain. Bioinformatics, 22:2204-2209.

Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A (2006) Characterization of RNase R-digested DNA source that consists of lariat and circular RNAs derived from pre-mRNA splicing. Nucl. Acid. Res. 34(8):e63.

Zhang C, Xuan Z, Mandel G, Zhang MQ (2006) A Clustering Property of Highly-degenerate Transcription Factor Binding Sites in the Mammalian Genome. Nucleic Acid Res 34(8):2238-2246.

Benita Y, Oosting RS, Xuan Z, Wise MJ, Zhang QM, Humphery-Smith I (2006). Challenges in the prediction of small genes in the human genome. In preparation*. Review.

Smith AD, Sumazin P, Xuan Z, Zhang MQ (2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc. Natl. Acad. Sci. USA, 103:6275-6280.

Das D, Nahle Z, Zhang MQ (2006) Adaptively Inferring Human Transcriptional Subnetworks. Mol Sys Biol. 2:2006.0029. HYPERLINK "http://www.nature.com/msb/journal/v2/n1/full/msb4100072.html" Commentary1 HYPERLINK "http://www.lbl.gov/Science-Articles/Archive/sabl/2006/Jul/05.html" Commentary2

Zhang C, Li HR, Fan JB, Fu XD and Zhang MQ (2006) Profiling alternative spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics 2006 Apr;7:202.

Rollins RA, Haghighi FG, Edwards JR, Das R, Zhang MQ, Ju J, Bester TH (2006) The Large-Scale Structure of Genomic Methylation Patterns. Genome Research, 16:157-163.

Zhang MQ (2005) Computational Molecular Biology of Genome Expression and Regulation. PReMI05 Lecture Notes in Computer Science, pp31-38, Springer-Verlag GMbH.

Prasanth KV, Prasanth SG, Xuan ZY, Sachidandam R, Hearn S, Frier SM, Bennett CF, Zhang MQ and Spector DL (2005) Regulating Gene Expression Through RNA Nuclear Retention. Cell, 123:249-263.