Browse by CSHL Author

Paper

Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S. E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Gerstein, M., Gingeras, T. R., Gonzalez, D., Grimmond, S. M., Guigó, R., Habegger, L., Harrow, J., Hubbard, T. J., Iseli, C., Jean, G., Kahles, A., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M. H., Searle, S. M. J., Solorzano, N. D., Solovyev, V., Stanke, M., Stevenson, B. J., Stockinger, H., Valsesia, A., Weese, D., White, S., Wold, B. J., Wu, J., Wu, T. D., Zeller, G., Zerbino, D., Zhang, M. Q. (November 2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184. ISSN 15487091 (ISSN)

Rajaram, M., Zhang, J., Wang, T., Li, J., Kuscu, C., Qi, H., Kato, M., Grubor, V., Weil, R. J., Helland, A., Borrenson-Dale, A. L., Cho, K. R., Levine, D. A., Houghton, A. N., Wolchok, J. D., Myeroff, L., Markowitz, S. D., Lowe, S. W., Zhang, M., Krasnitz, A., Lucito, R., Mu, D., Powers, R. S. (June 2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8 (6). e66264. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Xing, H., Mo, Y., Liao, W., Zhang, M. Q. (July 2012) Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data. PLoS Comput Biol, 8 (7). e1002613. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Tang, M. H., Varadan, V., Kamalakaran, S., Zhang, M. Q., Dimitrova, N., Hicks, J. (2012) Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Frontiers in Oncology, 2. p. 197. ISSN 2234-943X (Electronic)2234-943X (Linking)

Rajan, P., Dalgliesh, C., Carling, P. J., Buist, T., Zhang, C. L., Grellscheid, S. N., Armstrong, K., Stockley, J., Simillion, C., Gaughan, L., Kalna, G., Zhang, M. Q., Robson, C. N., Leung, H. Y., Elliott, D. J. (December 2011) Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome. PLoS ONE, 6 (12). ISSN 1932-6203

Wrzeszczynski, K. O., Varadan, V., Byrnes, J., Lum, E., Kamalakaran, S., Levine, D. A., Dimitrova, N., Zhang, M. Q., Lucito, R. (December 2011) Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer. PLoS ONE, 6 (12). ISSN 1932-6203

Cheng, J., Zhu, Y., He, S., Lu, Y., Chen, J., Han, B., Petrillo, M., Wrzeszczynski, K. O., Yang, S., Dai, P., Zhai, S., Han, D., Zhang, M. Q., Li, W., Liu, X., Li, H., Chen, Z. Y., Yuan, H. (July 2011) Functional Mutation of SMAC/DIABLO, Encoding a Mitochondrial Proapoptotic Protein, Causes Human Progressive Hearing Loss DFNA64. The American Journal of Human Genetics, 89 (1). pp. 56-66. ISSN 0002-9297

Tang, M. H. E., Varadan, V., Kamalakaran, S., Zhang, M. Q., Dimitrova, N., Hicks, J. (2011) A method for finding novel associations between genome-wide copy number and dna methylation patterns. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). pp. 78-82.

Chicas, A., Wang, X., Zhang, C., McCurrach, M. E., Zhao, Z., Mert, O., Dickins, R. A., Narita, M., Zhang, M. Q., Lowe, S. W. (April 2010) Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence. Cancer Cell, 17 (4). pp. 376-387.

Wang, S. M., Zhang, M. Q. (February 2010) Transcriptome Study for Early Hematopoiesis-Achievement, Challenge and New Opportunity. Journal of Cellular Physiology, 223 (3). pp. 549-552. ISSN 0021-9541

Mitra, R., Bandyopadhyay, S., Maulik, U., Zhang, M. Q. (January 2010) SFSSClass: an integrated approach for miRNA based tumor classification. BMC Bioinformatics, 11(S1). S22. ISSN 1471-2105

Zhang, M. Q., Smith, A. D. (2010) Challenges in understanding genome-wide DNA methylation. Journal of Computer Science and Technology, 25 (1). pp. 26-34.

Harris, R. A., Wang, T., Coarfa, C., Nagarajan, R. P., Hong, C., Downey, S. L., Johnson, B. E., Fouse, S. D., Delaney, A., Zhao, Y., Olshen, A., Ballinger, T., Zhou, X., Forsberg, K. J., Gu, J., Echipare, L., O'Geen, H., Lister, R., Pelizzola, M., Xi, Y., Epstein, C. B., Bernstein, B. E., Hawkins, R. D., Ren, B., Chung, W. Y., Gu, H., Bock, C., Gnirke, A., Zhang, M. Q., Haussler, D., Ecker, J. R., Li, W., Farnham, P. J., Waterland, R. A., Meissner, A., Marra, M. A., Hirst, M., Milosavljevic, A., Costello, J. F. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology, 28 (10). pp. 1097-1105.

Bandyopadhyay, S., Mitra, R., Maulik, U., Zhang, M. Q. (2010) Development of the human cancer microRNA network. Silence, 1 (1). p. 6. ISSN 1758-907x

Bernard, D., Prasanth, K. V. , Tripathi, V., Colasse, S., Nakamura, T., Xuan, Z., Zhang, M. Q. , Sedel, F., Jourdren, L., Coulpier, F., Triller, A., Spector, D. L., Bessis, A. (2010) A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO Journal, 29 (18). pp. 3082-3093.

Smith, A. D., Chung, W. Y., Hodges, E., Kendall, Jude T., Hannon, G. J., Hicks, J. B., Xuan, Z., Zhang, M. Q. (November 2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25 (21). pp. 2841-2842.

Hodges, E., Smith, A. D., Kendall, J. T., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M. H., Hannon, G. J., Hicks, J. B. (September 2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research, 19 (9). pp. 1593-1605. ISSN 1088-9051

Benita, Y., Kikuchi, H., Smith, A. D., Zhang, M. Q., Chung, D. C., Xavier, R. J. (August 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 (14). 4587–4602.

Kim, Y. C., Wu, Q., Chen, J., Xuan, Z., Jung, Y.-C., Zhang, M. Q., Rowley, J. D., Wang, S. M. (May 2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A, 106 (20). pp. 8278-8283.

Rosenfeld, J. A., Wang, Z., Schones, D. E., Zhao, K., DeSalle, R., Zhang, M. Q. (March 2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics, 10 (1). p. 143. ISSN 1471-2164

Li, T., Huang, J., Jiang, Y., Zeng, Y., He, F., Zhang, M. Q., Han, Z., Zhang, X. (March 2009) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics, 93 (3). pp. 235-242.

Niida, A., Smith, A. D., Imoto, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (February 2009) Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics, 10. p. 71. ISSN 1471-2105

Wang, X., Xuan, Z., Zhao, X., Li, Y., Zhang, M. Q. (February 2009) High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res, 19 (2). pp. 266-75.

Zhang, M. Q., Waterman, M. S., Zhang, X. (January 2009) The seventh Asia Pacific bioinformatics conference (APBC2009). BMC Bioinformatics, 10 (SUPPL.).

Lin, H., Zhang, Z., Zhang, M. Q., Ma, B., Li, M. (November 2008) ZOOM! Zillions of oligos mapped. Bioinformatics, 24 (21). pp. 2431-7.

Hsieh, M. C., Das, D., Sambandam, N., Zhang, M. Q., Nahle, Z. (October 2008) Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem, 283 (41). pp. 27410-7.

Niida, A., Smith, A. D., Imoto, S., Tsutsumi, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (September 2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics, 9. p. 404.

Zhang, C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A. R., Zhang, M. Q. (September 2008) Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev, 22 (18). pp. 2550-63.

Wu, Q., Kim, Y. C., Lu, J., Xuan, Z. Y., Chen, J., Zheng, Y., Zhou, T., Zhang, M. Q., Wu, C. I., Wang, S. M. (July 2008) Poly A- transcripts expressed in HeLa cells. PLoS ONE, 3 (7). e2803.

Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Peng, W., Zhang, M. Q., Zhao, K. (July 2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet, 40 (7). pp. 897-903.

Maulik, U., Mukhopadhyay, A., Bandyopadhyay, S., Zhang, M. Q., Zhang, X. (June 2008) Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure. IEEE Congress on Evolutionary Computation. pp. 1536-1543.

Nahle, Z., Hsieh, M., Pietka, T., Coburn, C. T., Grimaldi, P. A., Zhang, M. Q., Das, D., Abumrad, N. A. (May 2008) CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPAR{delta}/{beta}-mediated Adaptation to Metabolic Stress. J Biol Chem, 283 (21). pp. 14317-26.

Zhang, C., Li, W. H., Krainer, A. R., Zhang, M. Q. (April 2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A, 105 (15). 5797-5802 .

Chen, G., Li, W., Zhang, Q. S. , Regulski, M. R., Sinha, N., Barditch, J., Tully, T. , Krainer, A. R., Zhang, M. Q., Dubnau, J. T. (February 2008) Identification of Synaptic Targets of Drosophila Pumilio. PLoS Computational Biology, 4 (2). e1000026. ISSN 1553734X

Smith, A. D., Xuan, Z. Y., Zhang, M. Q. (February 2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. Bmc Bioinformatics, 9 (128). ISSN 1471-2105

Wang, X. W., Gu, J., Zhang, M. Q., Li, Y. D. (January 2008) Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics, 24 (2). pp. 165-171. ISSN 1367-4803

Fan, S., Zhang, M. Q., Zhang, X. (2008) Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochemical and Biophysical Research Communications, 374 (3). pp. 559-564. ISSN 0006291X

Eguchi, J., Yan, Q. W., Schones, D. E., Karnal, M., Hsu, C. H., Zhang, M. Q., Crawford, G. E., Rosen, E. D. (2008) Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metabolism, 7 (1). pp. 86-94. ISSN 1550-4131

Wu, X., Jiang, R., Zhang, M. Q., Li, S. (2008) Network-based global inference of human disease genes. Mol Syst Biol, 4. p. 189.

Chen, J., Kim, Y. C., Jung, Y. C., Xuan, Z. Y., Dworkin, G., Zhang, Y. M., Zhang, M. Q., Wang, S. M. (2008) Scanning the human genome at kilobase resolution. Genome Res, 18 (5). pp. 751-762. ISSN 1088-9051

Jiang, B., Zhang, M. Q., Zhang, X. (November 2007) OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics, 23 (21). pp. 2823-8. ISSN 1460-2059 (Electronic)

Zhang, C., Krainer, A. R., Zhang, M. Q. (October 2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet, 23 (10). pp. 484-488. ISSN 0168-9525 (Print)

Zhang, M. Q. (September 2007) Computational analyses of eukaryotic promoters. Bmc Bioinformatics, 8 Supp (6). S3. ISSN 1471-2105 (Electronic)

Mignone, J. L., Roig-Lopez, J. L., Fedtsova, N., Schones, D. E., Manganas, L. N., Maletic-Savatic, M., Keyes, W. M., Mills, A. A., Gleiberman, A., Zhang, M. Q., Enikolopov, G. N. (September 2007) Neural Potential of a Stem Cell Population in the Hair Follicle. Cell Cycle, 6 (17). 2161 - 2170 . ISSN 1551-4005 (Electronic)

Zhang, C. L., Hastings, M. L., Krainer, A. R., Zhang, M. Q. (September 2007) Dual-specificity splice sites function alternatively as 5 ' and 3 ' splice sites. Proceedings of the National Academy of Sciences of the United States of America, 104 (38). pp. 15028-15033. ISSN 0027-8424

Yang, Z., Jiang, H., Zhao, F., Shankar, D. B., Sakamoto, K. M., Zhang, M. Q., Lin, S. (August 2007) A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish. Bmc Developmental Biology, 7. p. 97. ISSN 1471-213X

Murchison, E. P., Stein, P., Xuan, Z. Y., Pan, H., Zhang, M. Q., Schultz, R. M., Hannon, G. J. (March 2007) Critical roles for Dicer in the female germline. Genes Dev, 21 (6). pp. 682-93. ISSN 0890-9369 (Print)

Kim, T. H., Abdullaev, Z. K., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., Ren, B. (March 2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell, 128 (6). pp. 1231-1245. ISSN 0092-8674

Zhang, J., Jiang, B., Li, M., Tromp, J., Zhang, X. G., Zhang, M. Q. (March 2007) Computing exact P-values for DNA motifs. Bioinformatics, 23 (5). pp. 531-537. ISSN 1367-4803

Zhao, Xi., Xuan, Z. Y., Zhang, M. Q. (February 2007) Boosting with stumps for predicting transcription start sites. Genome Biol, 8 (2). R17. ISSN 1465-6914 (Electronic)

Martinez, M. J., Smith, A. D., Li, B. L., Zhang, M. Q., Harrod, K. S. (January 2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics, 23 (1). pp. 21-29. ISSN 1367-4803

Zhang, C., Zhang, X., Zhang, M. Q., Li, Y. (January 2007) Neighbor number, valley seeking and clustering. Pattern Recognition Letters, 28 (2). pp. 173-180. ISSN 0167-8655

Schones, D. E., Smith, A. D., Zhang, M. Q. (January 2007) Statistical significance of cis-regulatory modules. Bmc Bioinformatics, 8. p. 16. ISSN 1471-2105

Jiang, C., Xuan, Z. Y., Zhao, F., Zhang, M. Q. (January 2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res, 35 (Databa). D137-D140. ISSN 0305-1048

Smith, A. D., Sumazin, P., Zhang, M. Q. (January 2007) Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology, 3. ISSN 1744-4292

Das, D., Zhang, M. Q. (2007) Predictive models in gene regulation. Methods Mol Biol, 377. pp. 95-110. ISSN 978-1-59745-390-5

Kim, Y. C., Jung, Y. C., Xuan, Z., Dong, H., Zhang, M. Q., Wang, S. M. (December 2006) Pan-genome isolation of low abundance transcripts using SAGE tag. Febs Letters, 580 (28-29). pp. 6721-6729. ISSN 0014-5793

Smith, P. J., Zhang, C., Wang, J., Chew, S. L., Zhang, M. Q., Krainer, A. R. (August 2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet, 15 (16). pp. 2490-508. ISSN 0964-6906 (Print)

Das, R., Dimitrova, N., Xuan, Z. Y., Rollins, R. A., Haghighi, F., Edwards, J. R., Ju, J. Y., Bestor, T. H., Zhang, M. Q. (July 2006) Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A, 103 (28). pp. 10713-6. ISSN 0027-8424 (Print)

Das, D , Nahlé, Z , Zhang, M. Q. (June 2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol, 2. pp. 2006-2029. ISSN 1744-4292 (Electronic)

Smith, A. D., Sumazin, P., Xuan, Z., Zhang, M. Q. (April 2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A, 103 (16). pp. 6275-80. ISSN 0027-8424 (Print)

Suzuki, H., Zuo, Y., Wang, J., Zhang, M. Q., Malhotra, A., Mayeda, A. (2006) Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Research, 34 (8). ISSN 03051048

Rollins, R. A., Haghighi, F., Edwards, J. R., Das, Rajdeep, Zhang, M. Q., Ju, J., Bestor, T. H. (2006) Large-scale structure of genomic methylation patterns. Genome Research, 16 (2). pp. 157-163. ISSN 10889051

Fang, F., Fan, S., Zhang, X., Zhang, M. Q. (2006) Predicting methylation status of CpG islands in the human brain. Bioinformatics, 22 (18). pp. 2204-2209. ISSN 13674803

Zhang, C., Li, H. R., Fan, J. B., Wang-Rodriguez, J., Downs, T., Fu, X. D., Zhang, M. Q. (2006) Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics, 7. p. 202. ISSN 1471-2105 (Electronic)

Zhang, C., Xuan, Z., Otto, S., Hover, J. R., McCorkle, S. R., Mandel, G., Zhang, M. Q. (2006) A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res, 34 (8). pp. 2238-46. ISSN 1362-4962 (Electronic)

Li, J., Zhang, M. Q., Zhang, X. (2006) A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. American Journal of Human Genetics, 79 (4). pp. 628-639. ISSN 00029297

Prasanth, K. V. , Prasanth, S. G., Xuan, Z. Y., Hearn, S., Freier, S. M., Bennett, C. F., Zhang, M. Q., Spector, D. L. (October 2005) Regulating gene expression through RNA nuclear retention. Cell, 123 (2). pp. 249-263. ISSN 0092-8674

Zhang, M. Q. (July 2005) Using CorePromoter to find human core promoters. Curr Protoc Bioinformatics, Chapte. Unit 2.9. ISSN 1934-340X (Electronic)

Smith, A. D., Sumazin, P., Das, D., Zhang, M. Q. (June 2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics, 21 Sup. i403-12. ISSN 1367-4803 (Print)

Enikolopov, G. N., Hoffman, R., Li, L. N., Maletic-Savatic, M., Manganas, L. N., Mignone, J. L., Roig, J. L., Schones, D. E., Zhang, M. Q. (March 2005) Neural potential of stem cells in the hair follicle. Faseb Journal, 19 (4). A765-A765. ISSN 0892-6638

Smith, A. D., Sumazin, P., Zhang, M. Q. (February 2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A, 102 (5). pp. 1560-5. ISSN 0027-8424 (Print)

Schones, D. E., Sumazin, P., Zhang, M. Q. (February 2005) Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics, 21 (3). pp. 307-13. ISSN 1367-4803 (Print)

Sumazin, P., Chen, G., Hata, N., Smith, A. D., Zhang, T., Zhang, M. Q. (January 2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)

Zhao, F., Xuan, Z., Liu, L., Zhang, M. Q. (January 2005) TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res, 33 (Databa). D103-107. ISSN 1362-4962 (Electronic)

Xuan, Z., Zhang, M. Q. (January 2005) From worm to human: bioinformatics approaches to identify FOXO target genes. Mech Ageing Dev, 126 (1). pp. 209-15. ISSN 0047-6374 (Print)

Wang, J., Smith, P. J., Krainer, A. R., Zhang, M. Q. (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res, 33 (16). pp. 5053-62. ISSN 1362-4962 (Electronic)

Xuan, Z. Y., Zhao, F., Wang, J., Chen, G., Zhang, M. Q. (2005) Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biology, 6 (8). R72. ISSN 1465-6906

Dike, S., Balija, V. S., Nascimento, L. U., Xuan, Z. Y., Ou, J., Zutavern, T., Palmer, L. E., Hannon, G. J., Zhang, M. Q., McCombie, W. R. (December 2004) The mouse genome: experimental examination of gene predictions and transcriptional start sites. Genome Res, 14 (12). pp. 2424-9. ISSN 1088-9051 (Print)

Das, D., Banerjee, N., Zhang, M. Q. (November 2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A, 101 (46). pp. 16234-9. ISSN 0027-8424 (Print)

Zhang, J., Li, F., Li, J., Zhang, M. Q., Zhang, X. G. (November 2004) Evidence and characteristics of putative human alpha recombination hotspots. Human Molecular Genetics, 13 (22). pp. 2823-2828. ISSN 0964-6906

Kato, M., Hata, N., Banerjee, N., Futcher, B., Zhang, M. Q. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology, 5 (8). ISSN 1465-6914

Chen, G., Hata, N., Zhang, M. Q. (2004) Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res, 32 (8). pp. 2362-71. ISSN 1362-4962 (Electronic)

Banerjee, N., Zhang, M. Q. (December 2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Research, 31 (23). pp. 7024-7031. ISSN 0305-1048

Cartegni, L., Wang, J. H., Zhu, Z. W., Zhang, M. Q., Krainer, A. R. (July 2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Research, 31 (13). pp. 3568-3571. ISSN 0305-1048

Li, Z. R., Van Calcar, S., Qu, C. X., Cavenee, W. K., Zhang, M. Q., Ren, B. (July 2003) A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proceedings of the National Academy of Sciences of the United States of America, 100 (14). pp. 8164-8169. ISSN 0027-8424

Xuan, Z., Wang, J., Zhang, M. Q. (2003) Computational comparison of two mouse draft genomes and the human golden path. Genome Biology, 4 (1). R1. ISSN 1474-7596

Zhang, M. Q. (2003) Prediction, annotation, and analysis of human promoters. Cold Spring Harbor Symposia on Quantitative Biology, 68. pp. 217-25. ISSN 0091-7451 (Print)

Zhang, M. Q. (October 2002) Extracting functional information from microarrays: A challenge for functional genomics. Proceedings of the National Academy of Sciences of the United States of America, 99 (20). pp. 12509-12511. ISSN 0027-8424

Zhang, Y., Mei, P. C., Lou, R., Zhang, M. Q., Wu, G. Y., Qiang, B. Q., Zhang, Z. G., Shen, Y. (October 2002) Gene expression profiling in developing human hippocampus. Journal of Neuroscience Research, 70 (2). pp. 200-208. ISSN 0360-4012

Zhang, M. Q. (September 2002) Computational prediction of eukaryotic protein-coding genes. Nature Reviews Genetics, 3 (9). pp. 698-709. ISSN 1471-0056

Banerjee, N., Zhang, M. Q. (June 2002) Functional genomics as applied to mapping transcription regulatory networks. Current Opinion in Microbiology, 5 (3). pp. 313-317. ISSN 1369-5274

Chen, G. X., Jaradat, S. A., Banerjee, N., Tanaka, T. S., Ko, M. S. H., Zhang, M. Q. (January 2002) Evaluation and comparison of clustering algorithms in analyzing es cell gene expression data. Statistica Sinica, 12 (1). pp. 241-262. ISSN 1017-0405

Carmell, M. A., Xuan, Z., Zhang, M. Q., Hannon, G. J. (2002) The Argonaute family: Tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes and Development, 16 (21). pp. 2733-2742. ISSN 08909369 (ISSN)

Nahle, Zaher, Polakoff, Julia, Davuluri, Ramana V., McCurrach, Mila E., Jacobson, Matthew D., Narita, Masashi, Zhang, Michael Q., Lazebnik, Yuri, Bar-Sagi, Dafna, Lowe, Scott W. (2002) Direct coupling of the cell cycle and cell death machinery by E2F. Nature Cell Biology, 4 (11). pp. 859-864. ISSN 1465-7392

Xuan, Z., McCombie, W. R., Zhang, M. Q. (2002) GFScan: A gene family search tool at genomic DNA level. Genome Research, 12 (7). pp. 1142-1149. ISSN 10889051 (ISSN)

Zhang, M. Q. (2002) Using MZEF to find internal coding exons. Current Protocols in Bioinformatics , 4. Unit 4.2 .

Davuluri, R. V., Grosse, I., Zhang, M. Q. (December 2001) Computational identification of promoters and first exons in the human genome. Nature Genetics, 29 (4). pp. 412-417. ISSN 1061-4036

Zhang, T., Zhang, M. (December 2001) Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinformatics, 17 (12). pp. 1232-1233. ISSN 1367-4803

Weinmann, A. S., Bartley, S. M., Zhang, T., Zhang, M. Q., Farnham, P. J. (October 2001) Use of chromatin immunoprecipitation to clone novel E2F target promoters. Molecular and Cellular Biology, 21 (20). pp. 6820-6832. ISSN 0270-7306

Ando, S., Sarlis, N. J., Krishnan, J., Feng, X., Refetoff, S., Zhang, M. Q., Oldfield, E. H., Yen, P. M. (September 2001) Aberrant alternative splicing of thyroid hormone receptor in a TSH-secreting pituitary tumor is a mechanism for hormone resistance. Molecular Endocrinology, 15 (9). pp. 1529-1538. ISSN 0888-8809

Tabaska, J. E., Davuluri, R. V., Zhang, M. Q. (July 2001) Identifying the 3 '-terminal exon human DNA. Bioinformatics, 17 (7). pp. 602-607. ISSN 1367-4803

Kel, A. E., Kel-Margoulis, O. V., Farnham, P. J., Bartley, S. M., Wingender, E., Zhang, M. Q. (May 2001) Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology, 309 (1). pp. 99-120. ISSN 0022-2836

Wu, Q., Zhang, T., Cheng, J. F., Kim, Y., Grimwood, J., Schmutz, J., Dickson, M., Noonan, J. P., Zhang, M. Q., Myers, R. M., Maniatis, T. (March 2001) Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Research, 11 (3). pp. 389-404. ISSN 1088-9051

Liu, H. X., Cartegni, L., Zhang, M. Q., Krainer, A. R. (January 2001) A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nature Genetics, 27 (1). pp. 55-58. ISSN 1061-4036

Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O., Zhang, M. Q. (December 2000) An alternative-exon database and its statistical analysis. DNA and Cell Biology, 19 (12). pp. 739-756. ISSN 1044-5498

Davuluri, R. V., Suzuki, Y., Sugano, S., Zhang, M. Q. (November 2000) CART classification of human 5 ' UTR sequences. Genome Research, 10 (11). pp. 1807-1816. ISSN 1088-9051

Zhang, M. Q. (November 2000) Discriminant analysis and its application in DNA sequence motif recognition. Brief Bioinform, 1 (4). pp. 331-42. ISSN 1467-5463 (Print)

Ioshikhes, I. P., Zhang, M. Q. (September 2000) Large-scale human promoter mapping using CpG islands. Nature Genetics, 26 (1). pp. 61-63. ISSN 1061-4036

Getz, G., Levine, E., Domany, E., Zhang, M. Q. (May 2000) Super-paramagnetic clustering of yeast gene expression profiles. Physica A: Statistical Mechanics and its Applications, 279 (1-4). pp. 457-464. ISSN 03784371 (ISSN)

Liu, H. X., Chew, S. L., Cartegni, L., Zhang, M. Q., Krainer, A. R. (February 2000) Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Molecular and Cellular Biology, 20 (3). pp. 1063-1071. ISSN 0270-7306

Machida, M., Yamazaki, S., Kunihiro, S., Tanaka, T., Kushida, N., Jinno, K., Haikawa, Y., Yamazaki, J., Yamamoto, S., Sekine, M., Oguchi, A., Nagai, Y., Sakai, M., Aoki, K., Ogura, K., Kudoh, Y., Kikuchi, H., Zhang, M. Q., Yanagida, M. (January 2000) A 38 kb segment containing the 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). pp. 71-80. ISSN 0749-503X

Zhang, M. Q. (August 1999) Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Research, 9 (8). pp. 681-8. ISSN 1088-9051 (Print)

Mayeda, A., Badolato, J., Kobayashi, R., Zhang, M. Q., Gardiner, E. M., Krainer, A. R. (August 1999) Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. EMBO Journal, 18 (16). pp. 4560-4570. ISSN 0261-4189

Zhu, J., Zhang, M. Q. (July 1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15 (7-8). pp. 607-11. ISSN 1367-4803 (Print)

Zhang, M. Q. (June 1999) Promoter analysis of co-regulated genes in the yeast genome. Computers & Chemistry, 23 (3-4). pp. 233-50. ISSN 0097-8485 (Print)

Tabaska, J. E., Zhang, M. Q. (April 1999) Detection of polyadenylation signals in human DNA sequences. Gene, 231 (1-2). pp. 77-86. ISSN 0378-1119 (Print)

Ioshikhes, I., Trifonov, E. N., Zhang, M. Q. (March 1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proceedings of the National Academy of Sciences, 96 (6). pp. 2891-5. ISSN 0027-8424 (Print)

Liu, H. X., Zhang, M., Krainer, A. R. (July 1998) Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Development, 12 (13). pp. 1998-2012. ISSN 0890-9369

Zhang, M. Q. (July 1998) Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis. Plant Molecular Biology, 37 (5). pp. 803-6. ISSN 0167-4412 (Print)

Zhang, M. Q. (May 1998) Statistical features of human exons and their flanking regions. Human Molecular Genetics, 7 (5). pp. 919-32. ISSN 0964-6906 (Print)

Zhang, M. Q. (March 1998) Identification of human gene core promoters in silico. Genome Research, 8 (3). pp. 319-26. ISSN 1088-9051 (Print)

Zhang, M. Q. (1998) A discrimination study of human core-promoters. Pacific Symposium on Biocomputing. pp. 240-51.

Zhang, M. Q. (January 1997) Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proceedings of the National Academy of Sciences, 94 (2). pp. 565-8. ISSN 0027-8424 (Print)

Zhang, M. Q., Marr, T. G. (May 1995) Alignment of molecular sequences seen as random path analysis. Journal of Theoretical Biology, 174 (2). pp. 119-29. ISSN 0022-5193 (Print)

Zhang, M. Q., Marr, T. G. (May 1994) Fission yeast gene structure and recognition. Nucleic Acids Res, 22 (9). pp. 1750-9. ISSN 0305-1048 (Print)

Stamm, S., Zhang, M. Q., Marr, T. G., Helfman, D. M. (May 1994) A sequence compilation and comparison of exons that are alternatively spliced in neurons. Nucleic Acids Res, 22 (9). pp. 1515-26. ISSN 0305-1048 (Print)

Zhang, M. Q., Marr, T. G. (November 1993) Genome Mapping by Random Anchoring - a Discrete Theoretical-Analysis. Journal of Statistical Physics, 73 (3-4). pp. 611-623. ISSN 0022-4715

Zhang, M. Q., Marr, T. G. (October 1993) A weight array method for splicing signal analysis. Comput Appl Biosci, 9 (5). pp. 499-509. ISSN 0266-7061 (Print)

Zhang, M. Q., Marr, T. G. (January 1993) Genome mapping by nonrandom anchoring: a discrete theoretical analysis. Proc Natl Acad Sci U S A, 90 (2). pp. 600-4. ISSN 0027-8424 (Print)0027-8424 (Linking)

Conference or Workshop Item

Zhu, J., Zhang, M. Q. (January 2000) Cluster, function and promoter: analysis of yeast expression array. In: Pacific Symposium on Biocomputing.