Zhang Lab:

Computational Biology and Bioinformatics

 

 

Home

 

 

 

People

 

 

 

Databases and Software Tools

 

 

 

Collaborations

 

 

 

Courses

 

Seminars

 

Meetings and Workshops

 

 

 

Publications

 

 

 

Links

 

 

 

Positions Available

 

 

 

 

 

Publications

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.

Watts JA, Zhang C, Kormish JD, Zhang MQ, Zaret K (2009) “Cryptic pathway of genetic regulation of Cdx2 revealed by genome location analysis of FoxA2 at silent genes.” Submitted.

   
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.

 

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung, DC, Xavier RJ. (2009) An integrative genomics approach identifies Hyposix Inducible Factor-1 (HIF-1) target genes that form the core response to hypoxia. Nucleic Acids Res (14):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(1):71

 

Wang X, Xuan Z, Zhao X, Li Y and Zhang MQ (2009) High-resolution Human Core-promoter prediction with CoreBoost_HM. Genome Res 19(2):266-75

 

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 CpG Islands. BBRC 374(3):559-64

 

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, Nahlé 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, Krainer AR, Zhang MQ (2008) An RNA landscape of evolution for optimal exon and intron discrimination. PNAS 105:5797-802. PDF

 

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.

 

Zhao X, Yoon S, Zhang MQ, Ye K, Geschwind DH, Sebat J, Iakoucheva LM (2008) High Connectivity among Autism Gene Candidates in Biological Networks: Evidence for Common Pathways. Submitted.

 

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, 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. eProceedings. PDF

 

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

 

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. 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, 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, 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.

Cuddapah S, Chen X, Xuan Z, Roh T-Y, Cui K, Smith AD, Byun JS, Zhang MQ, Fuller MT, Zhao K (2007) Identification of potential human polycomb response elements in T cells. Submitted.

Bernard D, Prasanth KV, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Triller A, Spector DL, Bessis A (2007) A nuclear retained non-coding RNA regulates synaptogenesis. Submitted.

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

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 Wiley-VCH PDF

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

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

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

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

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 HTML PDF

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 HTML PDF

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(16):6275-6280 PDF, Supplemental Data

Das D, Nahle Z, Zhang MQ (2006) Adaptively Inferring Human Transcriptional Subnetworks. Mol Sys Biol. 2:2006.0029. Epub 2006 Jun 6. PDF Commentary1 Commentary2

Grosse I, Zhang MQ, Herzel H (2006) On the dynamic origin of large-scale GC variations in warmblooded vertebrate genomes. Submitted.

Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu, Michael Q Zhang (2006) Profiling alternatively spliced mRNA isoforms for prostate cancer classification BMC Bioinformatics 2006 Apr;7:202 PDF

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, Zhao F, Wang J, Chen G, Zhang MQ (2005) Genome-Wide Promoter Extraction and Analysis in Human, Mouse and Rat - Genome Biol 6(8):R72   HTML   PDF

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

Zhao F, Xuan Z, Liu L, Zhang MQ (2005) TRED: A Transcription Regulatory Element Database and a Platform for in silico Gene Regulation Studies - Nucl Acid Res 33:D103-107   HTML    PDF

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.

Schones DE, Sumazin P, Zhang MQ (2005) Similarity of Position Frequency Matrices for Transcription Factor Binding Sites - Bioinformatics 21(3):307-313   HTML   PDF, MatCompare 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 S Rao, eds.) In Press.   PDF

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, Cambridge, UK) - Brief Bioinform 1(4):331-342    PDF

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 CpG Islands - Nat Genet 26(1):61-63    HTML   PDF

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