Publications by years
| 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | Before 2005
Xiaotu Ma, Ashwinikumar Kulkarni, Zhihua Zhang, Zhenyu Xuan, Robert Serfling and Michael Q. Zhang.
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Research, 2012, 1–1.
Zhang M Q. Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data.
Chapter in Bioinformatics for High Throughput Sequencing.
Rodríguez-Ezpeleta, Naiara; Hackenberg, Michael; Aransay, Ana M. (Eds.) 2012, p209.
Zhang MQ. Computational Promoter Prediction in a Vertebrate genome.
Chapter in "Handbook of Statistical Bioinformatics". Springer Handbooks of Computational Statistics.
Lu H, Scholkopf B and Zhao H (Eds). (2011) ISBN: 978-3-642-16344-9.
Rajan P, Dalgliesh C, Carling PJ, Buist T, Zhang C, Grellscheid SN, Armstrong K, Stockley J, Simillion C, Gaughan L, Kalna G, Zhang MQ, Robson CN, Leung HY, Elliott DJ. Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome. PLoS One. 2011;6(12):e29088. Epub 2011 Dec 14. PubMed PMID: 22194994; PubMed Central PMCID: PMC3237596.
Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R. Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One. 2011;6(12):e28503. Epub 2011 Dec 8. PubMed PMID: 22174824; PubMed Central PMCID: PMC3234280.
Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 2011 Dec 1;6(12):1505-12. PubMed PMID: 22139581.
Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S. 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. Nucleic Acids Res. 2011 Dec 1;39(22):9720-9730. Epub 2011 Aug 31. PubMed PMID: 21880592; PubMed Central PMCID: PMC3239178.
Watts JA, Zhang C, Klein-Szanto AJ, Kormish JD, Fu J, Zhang MQ, Zaret KS. Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. PLoS Genet. 2011 Sep;7(9):e1002277. Epub 2011 Sep 15. PubMed PMID: 21935353; PubMed Central PMCID: PMC3174211.
Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics. 2011 Nov 1;27(21):3010-6. Epub 2011 Sep 6. PubMed PMID: 21896509; PubMed Central PMCID: PMC3198574.
Yang S, Yalamanchili HK, Li X, Yao KM, Sham PC, Zhang MQ, Wang J. Correlated evolution of transcription factors and their binding sites. Bioinformatics. 2011 Nov 1;27(21):2972-8. Epub 2011 Sep 6. PubMed PMID: 21896508.
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. Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64. Am J Hum Genet. 2011 Jul 15;89(1):56-66. Epub 2011 Jun 30. PubMed PMID: 21722859; PubMed Central PMCID: PMC3135809.
Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T and Zhang MQ. Inferring Haplotypes of Copy Number Variations From High-Throughput Data With Uncertainty. G3 Genes Genomes Genetics (2011) Jun; 1:35-42.
Qin J, Li MJ, Wang P, Zhang MQ, Wang J. ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W430-6. Epub 2011 May 17. PubMed PMID: 21586587; PubMed Central PMCID: PMC3125757.
Zhang Z, Zhang MQ (2011) Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics. (Accepted)
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.
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. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. 2010 Oct;28(10):1097-105. Epub 2010 Sep 19. PDF
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.
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.
Kinney JB, Murugan A, Callan CG Jr, Cox EC. (2010) "Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence." PNAS May 3. [Epub ahead of print]
Wang SM, Zhang MQ. (2010) "Transcriptome study for early hematopoiesis - achievement, challenge and new opportunity." J Cell Physiol 223(3):549-52.
Chicas A, Wang X, Zhang C, McCurrach M, Zhao Z, Mert O, Dickins RA, Narita M, Zhang M, Lowe SW. (2010) "Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence." Cancer Cell 17(4):376-87. Bandyopadhyay S, Mitra R, Maulik U, Zhang MQ. (2010) "Development of the human micorRNA network." Silence 1(1):6.
Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. (2009) "Updates to the RMAP short-read mapping software" Bioinformatics 25(21):2841-2.
*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 JB. (2009) "High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing" Genome Res 19(9):1593-605. (*joint corresponding authors)
Zhang MQ, Waterman MS, Zhang X. (2009) "The Seventh Asia Pacific Bioinformatics Conference (APBC2009)" BMC Bioinformatics 10 Suppl 1:S1.
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" Genomics 93(3):235-42.
Kim Y-C, Wu Q, Chen J, Xuan X, Jung Y-C, Zhang MQ, Rowley J, Wang SM. The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A 106(20):8278-83.
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(1):71
Wang X, Xuan Z, Z
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. BMC Genomics 10:143
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. [PubMed][PDF]
Lin H, Zhang Z, Zhang MQ, Ma B, Li M (2008) ZOOM! Zillions of oligos mapped. Bioinformatics 24(21):2431-7
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(7):e2803
Fan S, Zhang MQ, Zhang X (2008) Histone Methylation Marks Play Important Roles in Predicting the Methylation Status of
Li T, Huang J, Jiang Y, Zeng Y, He F, Zhang MQ, Han Z, Zhang X (2008) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics 93(3):235-42.
Hsieh MC, Das D, Sambandam N, Zhang MQ, Nahl. Z (2008) Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem 283(41):27410-7.
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.
Zhang C, Li W-H,
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. MBC Bioinformatics, 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. PDF.
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(21):14317-26. PDF
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. PDF,
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), Nat Genet, 40:897-903.,
Wu X, Jiang R, Zhang MQ, Li S (2008) Large-scale network-based prediction of human disease genes. Mol. Sys. Biol. 4:189. PDF.
Wang X, Gu J, Zhang MQ, Li Y (2008) Identification of phylogenetically conserved microRNA cis-regulatory 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
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, 2007; 2(11): e1184. PDF
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, 8(Suppl 6):S2.,
Wang X, Bandyopadhya
S, Xuan Z, Z
Zhang C,
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 PDF
Zhang C, Zhang MQ. (2007) Biomedical
literature mining. Chap 10. in Introduction to Bioinformatics: A workbook approach.
Z
Jiang B, Zhang MQ and Zhang X. (2007) OSCAR: One-class SVM for Accurate Recognition of Cis-elements. Bioinformatics, PDF 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, Z
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. PDF
Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, Hannon GJ (2007) Critical roles for Dicer in the female germline. 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. (cover image!),
Das D and Zhang MQ. (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. PDF
Schones DE, Smith AD and Zhang MQ (2007) Statistical significance of cis-regulatory modules. BMC Bioinformatics 8:19 PDF
Jiang C, Xuan Z, Z
Zhang C,
Z
(M.R. Barnes, ed.) Pp281-310 Wiley-VCHPDF
Z
Smith AD, Sumazin P and Zhang MQ (2007) Tissue-specific regulatory elements in mammalian promoters. Mol Sys Biol. 3:73 PDF
Zhang C, Zhang X, Zhang MQ, Li Y (2007) Neighbor number, valley seeking and clustering. Pattern Recognition Letters. 28:173-180. PDF,
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 PDF (equal contributing first author)
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. PDF
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. PDF
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. PDF
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. 2006 Jul 3; 103:10713-6. PDF
Fang F, Fan SC, Zhang X and Zhang
MQ (2006) Predicting Methylation Status of CpG Islands in the Human
Brain. Bioinformatics, 22:2204-2209. PDF
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. Nucleic Acids Res 34(8):e63 HTMLPDF
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 HTMLPDF
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
Das D, Nahle Z, Zhang MQ (2006) Adaptively Inferring Human Transcriptional Subnetworks. Mol Sys Biol. 2:2006.0029. Epub 2006 Jun 6. PDFCommentary1 Commentary2 ,
Rollins RA, Haghighi FG, Edwards JR, Das R, Zhang MQ, Ju J, Bester TH (2006) Large-scale structure of genomic methylation patterns.Genome Res. 2006 Feb;16(2):157-63 PDF,
Zhang MQ (2005) Using Core Promoters to Find Human Core Promoter Regions - Chapter 2 in Current Protocols in Bioinformatics (AD Baxevanis & DB Davison, eds.) pp.2.9.1-2.9.10 John Wiley & Sons, Inc. PDF,
Zhang MQ (2005) Computational Molecular Biology of Genome Expression and Regulation. PReMI05 Lecture Notes in Computer Science, pp31-38, Springer-Verlag GMbH. PDF ,
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. 2005 Oct 21;123(2):249-63 PDF,
Wang J, Smith PH, Krainer AR, Zhang MQ (2005) Distribution of SR Protein Exonic Splicing Enhancer Motifs in Human Protein-Coding Genes - Nucleic Acids Research 2005 33(16):5053-5062 HTML PDF,
Xuan Z, Z
Smith AD, Sumazin P, Das D, Zhang MQ (2005) Mining ChIP-chip Data for Transcription Factor and CoFactor Binding Sites - Bioinformatics 21:Suppl 1:i403-i412 PDF,
Z
Xuan Z, Zhang MQ (2005) From Worm to Human: Bioinformatics Approaches to Identify FOXO Target Genes - Mech Ageing Dev 126(1):209-215 HTML PDF,
Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ (2005) DWE: Discriminating Word Enumerator - Bioinformatics 21(1):31-38 HTML PDF,
Smith AD, Sumazin P, Zhang MQ (2005) Identifying Tissue-Specific Transcription Factor Binding Sites in Vertebrate Promoters - Proc Natl Acad Sci USA - 102(5):1560-1565 HTML PDF, DME License.,
Wang JH, Hata N, Fu XD, Zhang MQ (2005) Searching for Tissue Specific Splicing cis-Elements in Human Alternatively Spliced Genes - Unpublished,
Banerjee N and Zhang MQ (2005) Transcription Regulatory Networks in
Yeast Cell Cycle - Chapter in: Microarray Expression Profiling
and Transcriptional Regulatory Networks (F Shannon and
Guigo R, Zhang MQ (2005) Gene Predictions and Annotations - Chapter 17 in Mammalian Genomics (A Ruvinsky and JA Marshall Graves, eds.) pp429 Wallingford:CAB International PDF,
Zhang J, Li F, Li J, Zhang MQ, Zhang X (2004) Evidence and Characteristics of Putative Human alpha Recombination Hotspots - Hum Mol Genet 13(22):2823-2828 HTML PDF,
Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A (2004) Genome-Wide Prediction and Analysis of Function-Specific Transcription Factor Binding Sites - In Silico Biology, 4(3):0033 HTML,
Das D, Banerjee N, Zhang MQ (2004) Interacting Models of Cooperative Gene Regulation - Proc Natl Acad Sci USA 101(46):16234-16239 HTML PDF, MARSMotif License.,
Chen J, Lee S, Sun M, Xu ZY, Zhou G, Zhang RS, Rowley JD, Zhang MQ, Wang SM (2004) Exhaustive Identification of Novel Transcription Units in the Human Genome Using Novel SAGE Tags - Unpublished,
Dike S, Balija VS, Gnoj L, Xuan Z, Ou J, Zutavern T, Palmer LE, Hannon G, Zhang MQ, McCombie WR (2004) The Mouse Genome: Experimental Examination of Gene Predictions and Transcriptional Start Sites - Genome Res 14(12):2424-2429 HTML PDF,
Chen G, Hata N, Zhang MQ (2004) Transcription Factor Binding Element Detection Using Functional Clustering of Mutant Expression Data - Nucl Acid Res 32(8):2362-2371 HTML PDF,
Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ (2004) Identifying Combinatorial Regulation of Transcription Factors and Binding Motifs - Genome Biol 5(8):R56 HTML PDF,
Wang JH, Xuan ZY, Fu XD and Zhang MQ (2004) Cross-Species Comparison of Alternative Splicing and Cross-Species Comparison Between Human and Mouse - Unpublished,
Davuluri R, Gross I, Zhang MQ (2004) Annotation of Promoters and First Exons in the Human Genome - Unpublished,
Zhang MQ (2003) Prediction, Annotation and Analysis of Human Promoters - CSHL Quantitative Biology Symposium 68. pp217-225 Cold Spring Harb Symp Quant Biol 2003;68:217-225 PDF,
Banerjee N, Zhang MQ (2003) Identifying Cooperativity Among Transcription Factors Controlling the Cell Cycle in Yeast - Nucl Acid Res 31(23):7024-7031 HTML PDF,
Davuluri R, Zhang MQ (2003) Computer Software to Find Genes in Plant Genomic DNA - Chapter 6, Methods Mol Biol 236:87-108, Plant Functional Genomics Methods and Protocols HTML PDF,
Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B (2003) A Global Transcriptional Regulatory Role for c-Myc in Burkitt’s Lymphoma Cells - Proc Natl Acad Sci USA 100(14):8164-8169 HTML PDF,
Cartegni L, Wang J, Zhu A, Zhang MQ, Krainer AR (2003) ESEfinder: A Web Resource to Identify Exonic Enhancers - Nucl Acid Res 31(13)3568-3571 HTML PDF,
Xuan Z, Wang J, Zhang MQ (2003) Computational Comparison of Two Mouse Draft Genomes and the Human Golden Path - Genome Biol 4(1):R1 HTML PDF,
Zhang MQ (2003) Using MZEF to Find Internal Coding Exons - Current Protocols in Bioinformatics (AD Baxevanis & DB Davison, eds.) John Wiley & Sons, Inc. 1,4.2.1-18 PDF,
Carmell M, Xuan Z, Zhang MQ, Hannon GJ (2002) The Argonaute Family: Tentacles that Reach into RNAi, Developmental Control, Stem Cell Maintenance, and Tumorigenesis - Genes Dev 16(21):2733-2742 HTML PDF,
Zhang MQ (2002) Extracting Functional Information from Microarrays: A Challenge for Functional Genomics - Proc Natl Acad Sci USA 99(20):12509-12511 HTML PDF,
Nahle Z, Polakoff J, Davuluri RV, McCurrach ME, Jacobson MD, 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(11):859-864 HTML PDF,
Zhang MQ (2002) Computational Prediction of Eukaryotic Protein-Coding Genes - Nat Rev Genet 3(9):698-709 HTML PDF,
Zhang MQ (2002) Predicting Full-Length Transcripts (discussion) - Trends Biotechnol 20(7):273-275, discussion 275 HTML PDF,
Banerjee N, Zhang MQ (2002) Functional Genomics as Applied to Mapping Transcription Regulatory Networks - Curr Opin Microbiol 5(3):313-317 HTML PDF,
Herzel H, Grosse I, Zhang MQ (2002) On the Dynamic Origin of Isochores - (Presented at the CSHL Genome Meeting, May 2001) Unpublished,
Xuan Z, McCombie WR, Zhang MQ (2002) GFScan: A Gene Family Search Tool at Genomic DNA Level - Genome Res 12(7):1142-1149 HTML PDF,
Zhang MQ (2002) Computational Methods for Promoter Recognition - Chapter 10, Current Topics in Computational Molecular Biology (Jiang T, Xu Y & Zhang MQ, eds.) pp249-268 MIT Press, Cambridge, Massachusetts PDF,
Jaradat SA, Tanaka TS, O'Neill L, Chen G, Banerjee N, Becker KG, Zhang MQ, Boheler KR, Ko MSH (2002) Dynamic Genetic Reprogramming of Pluripotent Embryonic Stem Cells During Differentiation - Unpublished,
Zhang Y, Mei P, Lou R, Zhang MQ, Wu G, Qiang B, Zhang Z, Shen Y (2002) Gene Expression Profiling in Developing Human Hippocampus - J Neurosci Res 70(2):200-208 HTML PDF,
Chen G, Jaradat SA, Banerjee N, Tanaka TS, Ko MSH, 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 PDF,
Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ (2001) Use of Chromatin Immunoprecipitation to Clone Novel E2F Target Promoters - Mol Cell Biol 21(20):6820-6832 HTML PDF,
Davuluri RV, Grosse I, Zhang MQ (2001) Computational Identification of Promoters and First Exons in the Human Genome - Nat Genet 29(4):412-417 HTML PDF,
Zhang T, Zhang M (2001) Promoter Extraction from GenBank (PEG): Automatic Extraction of Eukaryotic Promoter Sequences in Large Sets of Genes - Bioinformatics 17(12):1232-1233 HTML PDF,
Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ (2001) Computer-Assisted Identification of Cell Cycle-Related Genes: New Targets for E2F Transcription Factors - J Mol Biol 309(1):99-120 HTML PDF,
Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J, Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T (2001) Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters - Genome Res 11(3):389-404 HTML PDF,
Tabaska JE, Davuluri RV, Zhang MQ (2001) Identifying the 3'-Terminal in Human DNA (Presented at CSHL Computational Biology Workshop, Sept. 1999) - Bioinformatics 17(7):602-607 HTML PDF,
Liu HX, Cartegni L, Zhang MQ, Krainer AR (2001) A Mechanism of Exon Skipping Caused by Nonsense or Missense Mutations in the BRCA1 and other Genes - Nat Genet 27(1):55-58 HTML PDF,
Ando S, Sarlis NJ, Krishnan J, Feng X, Refetoff S, Zhang MQ, Oldfield EH, Yen PM (2001) Aberrant Alternative Splicing of Thyroid Hormone Receptor in a TSH-Secreting Pituitary Tumor is a Mechanism for Hormone Resistance - Mol Endocrinol 15(9):1529-1538 HTML PDF,
Zhang MQ (2000) Discriminant Analysis and its Application in DNA
Sequence Motif Recognition (Based on a lecture given at EBI
Symposium: Genome Based Gene Structure Determination; Jun 1-2, 2000,
Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O, Zhang MQ (2000) An Alternative-Exon Database and its Statistical Analysis - DNA Cell Biol 19(12):739-756,
Davuluri RV, Suzuki Y, Sugano S, Zhang MQ (2000) CART Classification of Human 5'UTR Sequences - Genome Res 10(11):1807-1816 HTML PDF,
Ioshikhes IP, Zhang MQ (2000) Large-Scale Human
Promoter Mapping Using
Getz G, Levine E, Domany E, Zhang MQ (2000) Super-Paramagnetic Clustering of Yeast Gene Expression Profiles - Physica A 279:457-464 PDF Clusters,
Liu, HX, Chew SL, Cartegni L, Zhang MQ, Krainer AR (2000) Exonic Splicing Enhancer Motif Recognized by Human SC35 Under Splicing Conditions - Mol Cell Biol 20(3):1063-1071 HTML PDF,
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, Yanagida M (2000) - A 38 kb Segment Containing cdc2 Gene from the Left Arm of Fission Yeast Chromosome II: Sequence Analysis and Characterization of the Genomic DNA and cDNAs Encoded on the Segment - Yeast 16(1):71-80 HTML PDF,
Zhu J, Zhang MQ (1999) Cluster, Function and Promoter: Analysis of Yeast Expression Array - Proceedings of Pacific Symposium on Biocomputing 2000 (RB Altman, et al, eds.) 5:476-487 PDF,
Mayeda A, Badolato J, Kobayashi R, Zhang MQ, Gardiner EM, Krainer AR (1999) Purification and Characterization of Human RNPS1: A General Activator of Pre-mRNA Splicing - EMBO J 18(16):4560-4570 HTML PDF,
Zhang MQ (1999) Large Scale Gene Expression Data Analysis: A New Challenge to Computational Biologists - Genome Res 9(8):681-688 HTML PDF,
Tabaska JE, Zhang MQ (1999) Detection of Polyadenylation Signals in Human DNA Sequences - Gene 231(1-2):77-86 PDF,
Ioshikhes I, Trifonov EN, Zhang MQ (1999) Periodical Distribution of Transcription Factor Sites in Promoter Regions and Connection with Chromatin Structure - Proc Natl Acad Sci USA 96(6):2891-2895 HTML PDF,
Zhang MQ (1999) Promoter Analysis of Co-Regulated Genes in the Yeast Genome - Comput Chem 23(3-4):233-250 PDF,
Zhu J and Zhang MQ (1999) SCPD: A Promoter Database of Yeast Saccharomyces cerevisiae - Bioinformatics 15:607-611 HTML PDF,
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization - Mol Biol Cell 9(12):3273-3297 HTML PDF,
Liu HX, Zhang MQ and Krainer AR (1998) Identification of Functional Exonic Splicing Enhancer Motifs Recognized by Individual SR Proteins - Gene Dev 12(13):1998-2012 HTML PDF,
Zhang MQ (1998) Identification of Protein Coding Regions in Arabidopsis thaliana Genome Based on Quadratic Discriminant Analysis - Mol Plant Biol 37(5):803-806 HTML PDF,
Zhang MQ (1998) Identification of Human Gene Core Promoters in Silico - Genome Res 8(1):319-326 HTML PDF,
Zhang MQ (1998) Statistical Features of Human Exons and Their Flanking Regions - Hum Mol Genet 7(5):919-932 HTML PDF,
Zhang MQ (1998) A Discrimination Study of Human Core Promoters - Proceedings of Pacific Symposium on Biocomputing (RB Altman, et al, eds.) Pac Symp Biocomput 1998;:240-51 PDF,
Chen T and Zhang MQ (1998) POMBE: A Fission Yeast Gene-Finding and Exon-Intron Structure Prediction System for Fission Yeast- Yeast 14(8):701-710 HTML PDF,
Zhang MQ (1997) Identification of Protein Coding Regions in the Human Genome by Quadratic Discriminant Analysis - Proc Natl Acad Sci USA 94(2):565-568 PDF Erratum,