Publications by years



2014    | 2013    | 2012    | 2011    | 2010    | Before 2010   

2014   [top]

  • 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, Jahanbanian F, Kasowski M, Zhang MQ, Snyder MP (2014). Genome-wide map of regulatory interactions in the human genome. Genome Res. pii: gr.176586.114. [Epub ahead of print], PMID:25228660.
  • Sephton CF, Tang AA, Kulkarni A, Brooks M, Stubblefield J, Liu Y, Zhang MQ, Green CB, Huber KM, Huang J, Herz J, Yu G (2014) Activity-Dependent FUS Dysregulation Disrupts Synaptic Homeostasis. PNAS, in press
  • 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. In press. PMID:25227905.
  • 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. SCLS in press.
  • Ouyang W, Liao W, Zhang MQ, Li M (2014) Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes. Genomics Data, in press.
  • 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. JHG In press.
  • 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.
  • 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 (2014) Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut. doi: 10.1136/gutjnl-2013-305715. PMID:24572141.
  • 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 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.


  • 2013   [top]

  • 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, Chung, W-Y, Qian, M, Pellegrini, M, Zhang MQ (2013). Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. NAR. 42:3009-16. PMID:24343027.
  • 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.


  • 2012   [top]

  • 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. 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. In press.
  • 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.



  • 2011   [top]

  • 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-SzantoAJ,Kormish 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). In press. ISBN: 978-3-642-16344-9. HYPERLINK "http://www.springer.com/statistics/book/978-3-642-16344-9" http://www.springer.com/statistics/book/978-3-642-16344-9



  • 2010   [top]

  • 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.



  • 2009   [top]

  • 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.



  • 2008   [top]

  • 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) Genome-wide correlation analysis of histone acetylation and methylation in human T cells. Nat. Genet. (*equal contributing first author), 40:897-903.
  • 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.


  • Before 2008   [top]

  • 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. (2007) Biomedical literature mining. Chap 10. in Introduction to Bioinformatics: A workbook approach. Mathura V ed. Elsevier. In press.
  • 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.
  • Wang J, Smith PH, Krainer AR, Zhang MQ (2005) Distribution of SR Protein Exonic Splicing Enhancer Motifs in Human Protein-Coding Genes. Nucl Acid Res, 33:5053-5062.
  • Xuan ZY, Zhao F, Wang JH, Chen GX and Zhang MQ (2005) Genome-Wide Promoter Extraction and Analysis in Human, Mouse and Rat. Genome Biology, 6:R74.
  • Zhang MQ (2005) Finding Human Core Promoter Regions. in: Current Protocols in Bioinformatics. (A. D. Baxevanis & D. B. Davison, Eds.), John Wiley & Sons.
  • Smith AD, Sumazin P, Das D and Zhang MQ (2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Accepted talk, ISMB2005. Bioinformatics. 21 Suppl 1:i403-i412
  • Zhao F, Xuan ZY, Liu Lihua and Zhang MQ (2005) TRED: a Transcription Regulatory Element Database and a platform for in silico gene regulation studies. Nucl Acid Res, 33:D103-107.
  • Xuan ZY and Zhang MQ (2005) From worm to human:Bioinformatics approaches to identify FOXO target genes. Special issue on Functional Genomics of Ageing 2004. Mech. Ageing Dev. 126:209-215.
  • Smith AD, Sumazin P and Zhang MQ (2005) Identifying tissue-specific transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci USA, 102:1560-1565.
  • Schones DE, Sumazin P and Zhang MQ (2005) Similarity of Position Frequency Matrices for Transcription Factor Binding Sites. Bioinformatics, 21:307-313.
  • Sumazin P, Chen GX, Hata N, Smith AD and Zhang MQ (2005) DWE: Discriminant Word Enumerator. Bioinformatics, 21:31-38.
  • Zhang J, Li F, Li J, Zhang MQ and Zhang XG (2004) Evidence and Characteristics of Putative Human α Recombination Hotspots. Hum. Mol. Genet. 13:2823-2828.
  • Long F, Liu H, Hahn C, Sumazin P, Zhang MQ and Zilberstein A (2004) Genome-wide Prediction and Analysis of Function-Specific Transcription Factor Binding Sites. HYPERLINK "http://www.bioinfo.de/isb/2004/04/0033/" In Silico Biology, 4:0033.
  • Banerjee N and Zhang MQ (2005) Transcription Regulatory Networks in Yeast Cell Cycle. A chapter in Microarray expression profiling and transcriptional regulatory networks, Shannon F and Rao S eds. In press.
  • Guigo R and Zhang MQ (2005) Gene predictions and annotations, Chap17 in Mammalian Genomics, eds. A. Ruvinsky and J.A. Marshall Graves. Pp 429 Wallingford:CAB International.
  • Das D, Banerjee N and Zhang MQ (2004) Interacting Models of Cooperative Gene Regulation. Proc. Natl Acad Sci. USA, 101:16234-16239.
  • Chen J, Lee S, Sun M, X ZY, Zhou G, Zhang RS, Rowley JD, Zhang MQ and Wang SM (2004) Exhaustive identification of novel transcription units in the human genome using novel SAGE tags. Unpublished.
  • Dike S, Vivekanand S. Balija, Lidia Gnoj, Zhenyu Xuan, Jacqueline Ou, Theresa Zutavern, Lance E. Palmer, Greg Hannon, Michael Q. Zhang, W. Richard McCombie (2004). The Mouse Genome: Experimental examination of gene predictions and transcriptional start sites. Genome Res 14:2424-2429..
  • Guigo R, Birney E, Brent M, Dermitzakis E, Pachter L, Roest Crollius H, Solovyev V and Zhang M (2004) Completion of the catalog of protein coding genes in the human genome. Quantitative Biology. Online, HYPERLINK "http://arxiv.org/abs/q-bio.GN/0410008" http://arxiv.org/abs/q-bio.GN/0410008
  • Wang JH, Hata N, Fu XD and Zhang MQ (2004). Searching for tissue specific splicing cis-elements in human alternatively spliced genes. Unpublished.
  • Kato M, Hata N, Banerjee B and Zhang MQ (2004). Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology 5:R56.
  • Chen GX, Hata N and Zhang MQ (2004). Transcription factor binding element detection using functional clustering of mutant expression data. Nucl. Acid Res. 32:2362-2371.
  • Banerjee N and Zhang MQ (2003) Identification of cooperativity among transcription factors controlling cell cycle in yeast. Nucl. Acid Res. 31:7024-7031.
  • Wang, JH, Xuan ZY, Fu XD and Zhang, MQ (2004). Cross-species comparison of alternative splicing between human and mouse. Unpublished.
  • Zhang MQ (2003) Prediction, Annotation and Analysis of Human Promoters. Cold Spring Harbor Symposium Quantitative Biology 68:217-225, Cold Spring Harbor Press.
  • Davuluri R and Zhang MQ (2003) Computer software to find genes in plant genomic DNA.
  • Methods Mol Biol. 236:87-108.
  • Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ and Ren B (2003) A global transcriptional Regulatory role for c-myc in Burkitt’s lymphoma cells. Proc. Natl. Acad. Sci. USA 100:8164-8169.
  • Cartegni L, Wang JH, Zhu ZW, Zhang MQ and Krainer AR (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucl. Acid. Res. 31:3568-3571.
  • Davuluri R, Grosse I and Zhang MQ (2003) Annotation of promoters and first exons in the human genome. unpublished.
  • Carmell M, Xuan ZY, Zhang MQ and Hannon GJ (2002) Argonaute proteins : tentacles that reach into RNAi, stem cell maintenance and tumorigenesis. G&D, 16:2733-2742.
  • Xuan ZY, Wang JH and Zhang MQ (2002) Computational comparison of two mouse draft genomes and the human goldenpath. Genome Biology, 4(1):R1.
  • Zhang MQ (2002) Extracting functional information from microarrays: A challenge for functional genomics.
  • Proc Natl Acad Sci U S A 99:12509-12511.
  • Nahle Z, Polyakoff J, Davuluri RV, Jacobson MD, McCurrach ME, Narita M, Zhang MQ, Lazebnik Y, Bar-Sagi D and Lowe SW (2002) Direct coupling of the cell cycle and cell death machinery by E2F. Nat. Cell Biol. 4:859-864.
  • Zhang MQ (2002) Computational prediction of eukaryotic protein-coding genes. Nat. Rev Genet. 3:698-709.
  • Grosse I, Zhang MQ and Herzel H (2002) On the dynamic origin of isochores. (presented at the CSHL Genome Meeting in May 2001) Unpublished.
  • Saied A. Jaradat, Tetsuya S. Tanaka, Lydia O'Neill, G. Chen, N. Banerjee, Kevin G. Becker, Michael Q. Zhang , Kenneth R. Boheler and Minoru S.H. Ko (2002) Dynamic genetic reprogramming of pluripotent embryonic stem cells during differentiation. Unpublished.
  • Zhang Y, Mei PC, Lou R, Zhang MQ, Wu G, Qiang B, Zhang ZG and Shen Y(2002). Gene expression profiling in developing human hippocampus. J. Neurosci. Res. 70:200-208.
  • Zhang MQ (2003) Using MZEF to Find Internal Coding Exons. In Current Protocols in Bioinformatics, Baxevanis A et al. eds. John Wiley & Sons.
  • Zhang MQ (2002) Predicting full-length transcripts. Trends Biotechnol. 20:275.
  • Xuan ZY, McCombie WR and Zhang MQ (2002) GFScan: a gene family search tool at genomic DNA sequence level. Genome Res. 12:1142-1149.
  • Banerjee N and Zhang MQ (2002) Functional genomics as applied to mapping transcription regulatory networks. Curr. Op. Microbiol. 5:313-317.
  • Weinmann AS, Bartley SM, Zhang T, Zhang MQ and Farnham PJ (2001). Use of chromatin immunoprecipitation to clone novel e2f target promoters. Mol. Cell Biol. 21:6820-6832.
  • Davuluri R, Grosse I and Zhang MQ. (2001). Computational identification of promoters and first exons in the human genome. Nat. Genet. 29:412-417.
  • Zhang T and Zhang MQ (2001). Promoter extraction from GenBank (PEG): automatic extraction of promoter sequences in large sets of genes. Bioinformatics, 12:1232-1233.
  • Chen G, Jaradat SA, Banerjee N, Tanaka TS, Ko MSH and Zhang MQ (2002). Cluster analysis of microarray gene expression data: application to and evaluation with NIA mouse 15K array on ES cell differentiation. Statistica Sinica, 12:241-262.
  • Kel AE, Kel-Margoulis OV, Farnham PJ, Stephanie MB, Wingender E and Zhang MQ (2001). Computer-assisted identification of cell cycle-related genes - new targets for E2F transcription factors. J. Mol. Biol. 309:99-120.
  • Zhang MQ (2001). Computational methods for promoter recognition. Chapter 10 in Current Topics in Computational Biology (Jiang T, Smith T, Xu Y and Zhang MQ eds). pp249-268. MIT Press and TUP.
  • Wu Q, Zhang T, Cheng J-F, Kim Y, Grimwood J, Schmulz J, Dickson M, Noonan JP, Zhang MQ, Myers RM and Maniatis T. (2001) Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 11:389-404.
  • Tabaska JE, Davuluri R and Zhang MQ (2001). A novel 3'-Terminal exon recognition algorithm. (Result was presented at CSHL Computational Biology Workshop 9/99). Bioinformatics 17:602-607.
  • Liu H-X, Cartegni L, Zhang MQ and Krainer AR. (2001) Mechanism of exon skipping caused by a nonsense mutation in the BRCA1 gene. Nature Genetics, 27:55-58.
  • Zhang MQ (2001). Discriminant analysis and its application in DNA sequence motif recognition. Based on a lecture given at the EBI Symposium: Genome Based Gene Structure Determination.(Jun 1-2,2000, Cambridge, UK) Briefings in Bioinformatics, 1(4)331-342.
  • Ando S, Sarlis N, Krishnan J, Feng X, Refetoff S, Zhang MQ, Oldfield EH and Yen PM (2001). Brief report: A berrant alternative-splicing of thyroid hormone receptor is a mechanism for thyroid hormone resistance in a thyrotropin-producing pituitary tumor. Molecular Endocrinology, 15:1529-1538.
  • Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O and Zhang MQ. (2000) A database and statistical analysis of aternative exons. DNA & Cell Biol., 19:739-756.
  • Davuluri R, Suzuki Y, Sugano S and Zhang MQ. (2000) CART classification of human 5'UTR sequences. Genome Res. 10:1807-1816.
  • Ioshikhes I and Zhang MQ (2000). Large-scale human promoter mapping using CpG islands. discrimination. Nature Genetics, 26:61-63.
  • Zhu J and Zhang MQ (2000). Cluster, function and promoter: analysis of yeast expression array. In Proceedings of Pacific Symposium on Biocomputing 2000. R.B. Altman et al. eds., 5:476-487.
  • Liu, H-X, Chew SL, Cartegni L, Zhang MQ and Krainer AR, (2000). Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. MCB, 20:1063-1071.
  • Getz G, Levine E, Domany E and Zhang MQ (2000). Super-paramagnetic clustering of yeast gene expression profiles. Physica A. 279:457-464.
  • Mayeda A, Badolato J, Kobayashi R, Zhang MQ, Gardiner EM and Krainer AR.(1999) Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing, EMBL 18:4560-4570.
  • Machida M, Yamazaki S, Kunihiro S, Tanaka T, Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S, Sekine M, Ogudhi A, Nagai Y, Sakai M, Aoki K, Ogura K, Kudoh Y, Kikuchi H, Zhang MQ and Yanagida M.(2000) A. 38 kb segment containing cdc2 gene from the left arm of fission yeast chromosome II: sequence analys is and characterization of the genomic DNA and cDNAs encoded on the segment, Yeast, 16:71-80.
  • Zhang, M.Q .(1999) Large scale gene expression data analysis: a new challenge to computational biologists, Genome Res. 9:681-688.
  • Tabaska, J.E. and Zhang, M.Q .(1999), Detection of polyadenylation signals in human DNA sequences. Gene, 231:77-86.
  • Ioshikhes, I., Trifonov, E.N. and Zhang, M.Q . (1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc. Natl. Acad. Sci. USA, 96:2891-2895.
  • Zhang, M.Q ., (1999) Promoter Analysis of Co-regulated Genes in the Yeast Genome. Computers and Chemistry, 23:233-250.
  • Zhu, J. and Zhang, M.Q ., (1999) SCPD: A Promoter Database of Yeast Saccharomyces cerevisiae, Bioinformatics, 15:607-611.
  • Spellman, P.T., Sherlock, G., Zhang, M.Q ., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998). Comprehensive Identification of Cell Cycle Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol. Biol. Cell. 9:3273-3297.
  • Liu, H.-X., Zhang, M.Q . and Krainer, A.R., (1998). Identification of Functional Exonic Splicing Enhancer Motifs Recognized by Individual SR Proteins. Gene & Dev. 12:1998-2012.
  • Zhang, M.Q ., (1998). Identification of Protein Coding Regions in Arabidopsis thaliana Genome Based on Quadratic Discriminant Analysis. Mol. Plant. Biol., 37:803-806.
  • Zhang, M.Q ., (1998). Identification of Human Gene Core-promoters In Silico. Genome Res., 8:319-326.
  • Zhang, M.Q ., (1998). Statistical Features of Human Exons and Their Flanking Regions. Hum. Mol. Genet., 7:919-932.
  • Zhang, M.Q .,(1998). A Discrimination Study of Human Core-promoters, in Proceedings of Pacific Symposium on Biocomputing 1998. R.B. Altman et al. eds. pp240-251, World Scientific, Singapore.
  • Chen, T., and Zhang, M.Q . (1998). POMBE: A Fission Yeast Gene-finding and Exon-intron Structure Prediction System. Yeast, 14:701-710.
  • Zhang, M.Q . (1997). Identification of Protein Coding Regions in the Human Genome Based on Quadratic Discriminant Analysis. Proc. Natl. Acad. Sci. USA, 94:565-568.
  • N.Kaplan, M.Lodhi, A.Johnson, M.Q.Zhang, T.G.Marr and W.R.McCombie (1995), The Schizosaccharomyces Pombe Genome Project, Cold Spring Harb. Symp., Genome Mapping and Sequencing.
  • M.Q.Zhang and T.G.Marr (1995), Molecular Sequence Alignment Seen as Random Path Analysis, J. Theor. Biol., 174:119-130.
  • M.Q.Zhang and T.G.Marr (1995), Exploratory Analysis of Long Genomic DNA Sequences using the Wavelet Transform: Examples using Polyomavirus Genomes, Genome Sequencing and Analysis Conference VI, Hilton Head, NC, pp.72, Mary Ann Liebert, Inc..
  • S.Stamm, M.Q.Zhang, T.G.Marr and D.M.Helfman (1994), A Sequence Compilation and Comparison of Exons That Are Alternatively Spliced in Neurons, Nucl. Acid. Res., 22:1515-1526.
  • M.Q.Zhang and T.G.Marr (1994), Statistical Analysis of the fission yeast genomic DNA sequences and gene recognition, Nucl. Acid. Res., 22:1750-1759.
  • M.Q.Zhang and T.G.Marr (1994), Genome Mapping with Random Anchored Clones: A Discrete Theoretical Analysis, J. Stat. Phys., 73:611-623.
  • M.Q.Zhang and T.G.Marr (1993), Large-scale Structure of Yeast Chromosome III: Implications in Genome Evolution, Cold Spring Harb. Symp., Genome Mapping and Sequencing.
  • M.Q.Zhang and T.G.Marr (1993), A Weight Array Method for Splicing Signal Analysis, CABIOS 9:499-509.
  • M.Q.Zhang and T.G.Marr (1993),Genome Mapping by Nonrandom Anchored Clones: A Discrete Theoretical Analysis, Proc. Natl. Acad. Sci. USA, 90:600-604.
  • M.Q.Zhang (1991), How to Find the Lax Pairs from the Yang-Baxter Equations, Comm. Math. Phys.141:523.
  • M.Q.Zhang (1991), The Nonuniform Hard Rod Fluids Revisited, J. Stat. Phys.342:1191.
  • M.Q.Zhang (1991), Exact Response Functions of a 2D Fermion Fluid, J. Math. Phys. 32:1344.
  • M.Q.Zhang (1991), Crystallization of One-dimensional Hard Rods with a Periodic Interaction, J. Phys. A24:3949.
  • M.Q.Zhang (1990), Zero-thickness Membrane Interface and Schrodinger Equation, {\em Phys. Rev.,A42:4588.
  • M.Q.Zhang and J.K.Percus (1990), A Recursive Density Functional Formalism of Nonuniform Fluids, J. Chem. Phys. 92:6779.
  • M.Q.Zhang (1990), Entropy Functional of a Nonuniform Ising Model on a Two Row Lattice, J. Phys., A23:1.
  • J.K.Percus and M.Q.Zhang (1989), The Quasi-One Dimensional Hard Square Gas, Mol. Phys.,69:347.
  • M.Q.Zhang (1989). Inhomogeneous Ising Model on a Multiconnected Networks, J.Stat.Phys., 56:695.
  • M.Q.Zhang and J.K.Percus (1989), Direct Correlations of the Capillary Wave Model and Construction of Free Energy Density Functional for the Liquid-Vapor Interface System, J. Chem. Physics, 90:3795.
  • M.Q.Zhang (1989), A Fast Vectorized Multispin Coding Algorithm for 3D Monte Carlo Simulations Using Kawasaki Spin-exchange Dynamics, J.Stat.Phys., 56:939.
  • M.Q.Zhang and J.K.Percus (1988), 1-D Inhomogeneous Ising Model with Periodic Boundary Condition, Phys.Rev., B38:11737.
  • G.Ord, J.K.Percus and M.Q.Zhang (1988), Energetics of a Discrete Interface, Nucl.Phys., B305[FS23]:271.
  • M.Q.Zhang (1988), Exact Pair Correlation Function for Ising Spins with Competing Dynamics,J.Stat.Phys., 53:1217.
  • M.Q.Zhang , J.S.Wang, J.L.Lebowitz and J.L.Valles (1988), Power Law Decay of Correlations in Stationary Nonequilibrium Lattice Gases with Conservative Dynamics, J.Stat.Phys., 52:1461.
  • M.Q.Zhang (1988), Nonequilibrium Steady States of Some Stochastic Lattice Gas Models, Nucl.Phys.,B(Proc.Suppl.)5A:278.
  • M.Q.Zhang (1987), Supersymmetrical Approach to Critical Dynamics of Relaxational Models, Phys.Rev., B36:3824.
  • M.Q.Zhang (1987), Exact Results on the Steady State of a Hopping Model,Phys.Rev., A35:2266.
  • J.Krug,J.L.Lebowitz, H.Spohn and M.Q.Zhang (1986), The Fast Rate Limit of Diffusive System, J.Stat.Phys., 44:535