M Q Zhang

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. ncbi Computational comparison of two mouse draft genomes and the human golden path
    Zhenyu Xuan
    Cold Spring Harbor Laboratory, New York, NY 11724, USA
    Genome Biol 4:R1. 2003
  2. ncbi Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, 110 0032, Japan
    BMC Bioinformatics 9:404. 2008
  3. ncbi Gene set-based module discovery in the breast cancer transcriptome
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo, Japan
    BMC Bioinformatics 10:71. 2009
  4. ncbi Discriminant analysis and its application in DNA sequence motif recognition
    M Q Zhang
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, NY 11724, USA
    Brief Bioinform 1:331-42. 2000
  5. ncbi Identification of human gene core promoters in silico
    M Q Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 8:319-26. 1998
  6. ncbi Statistical features of human exons and their flanking regions
    M Q Zhang
    Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
    Hum Mol Genet 7:919-32. 1998
  7. ncbi Large-scale gene expression data analysis: a new challenge to computational biologists
    M Q Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 9:681-8. 1999
  8. ncbi Promoter analysis of co-regulated genes in the yeast genome
    M Q Zhang
    Cold Spring Harbor Laboratory, NY 11724, USA
    Comput Chem 23:233-50. 1999
  9. ncbi Identifying the 3'-terminal exon in human DNA
    J E Tabaska
    Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 17:602-7. 2001
  10. ncbi SCPD: a promoter database of the yeast Saccharomyces cerevisiae
    J Zhu
    Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 15:607-11. 1999

Collaborators

Detail Information

Publications15

  1. ncbi Computational comparison of two mouse draft genomes and the human golden path
    Zhenyu Xuan
    Cold Spring Harbor Laboratory, New York, NY 11724, USA
    Genome Biol 4:R1. 2003
    ..From the CSEs, we estimate the total number of human protein-coding genes to be about 40,000. This searchable publicly available online CSEdb will expedite new discoveries through comparative genomics...
  2. ncbi Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, 110 0032, Japan
    BMC Bioinformatics 9:404. 2008
    ..However, compared with the massive knowledge about the transcriptome, we have surprisingly little knowledge about regulatory mechanisms underling transcriptomic diversity...
  3. ncbi Gene set-based module discovery in the breast cancer transcriptome
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo, Japan
    BMC Bioinformatics 10:71. 2009
    ..However, such module discovery methods are not applied cancer transcriptome data...
  4. ncbi Discriminant analysis and its application in DNA sequence motif recognition
    M Q Zhang
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, NY 11724, USA
    Brief Bioinform 1:331-42. 2000
    ..This paper will review two basic parametric methods: LDA (linear discriminant analysis) and QDA (quadratic discriminant analysis). Their usage in recognition of splice sites and exons in the human genome will be demonstrated...
  5. ncbi Identification of human gene core promoters in silico
    M Q Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 8:319-26. 1998
    ..Figure 3 can be found in its entirety as an online supplement at http://www.genome.org.]..
  6. ncbi Statistical features of human exons and their flanking regions
    M Q Zhang
    Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
    Hum Mol Genet 7:919-32. 1998
    ..This information is fundamental for a quantitative view of human gene organization, and should be invaluable for individual scientists to design human molecular genetics experiments...
  7. ncbi Large-scale gene expression data analysis: a new challenge to computational biologists
    M Q Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 9:681-8. 1999
    ..In this survey I review three recent experiments related to transcriptional regulation and discuss the great challenge for computational biologists trying to extract functional information from such large-scale gene expression data...
  8. ncbi Promoter analysis of co-regulated genes in the yeast genome
    M Q Zhang
    Cold Spring Harbor Laboratory, NY 11724, USA
    Comput Chem 23:233-50. 1999
    ..Full report of the experiments and of the complete analysis will be published elsewhere when all the experiments are to be finished later in this year (Spellman, P.T., et al. 1998. Mol. Biol. Cell 9, 3273-3297)...
  9. ncbi Identifying the 3'-terminal exon in human DNA
    J E Tabaska
    Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 17:602-7. 2001
    ..AVAILABILITY: JTEF is available free for academic users on request from ftp://cshl.org/pub/science/mzhanglab/JTEF and will be made available through the World Wide Web (http://argon.cshl.org/)...
  10. ncbi SCPD: a promoter database of the yeast Saccharomyces cerevisiae
    J Zhu
    Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 15:607-11. 1999
    ..In order to facilitate a systematic study of the promoters and transcriptionally regulatory cis-elements of the yeast Saccharomyces cerevisiae on a genomic scale, we have developed a comprehensive yeast-specific promoter database, SCPD...
  11. ncbi Detection of polyadenylation signals in human DNA sequences
    J E Tabaska
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Gene 231:77-86. 1999
    ..512 in the last two exons of genes, substantially outperforming other published programs on the same data set. polyadq is also the only program that is able to consistently detect the ATTAAA variant of the polyA signal...
  12. ncbi Prediction, annotation, and analysis of human promoters
    M Q Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Cold Spring Harb Symp Quant Biol 68:217-25. 2003
  13. ncbi Computational identification of promoters and first exons in the human genome
    R V Davuluri
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Nat Genet 29:412-7. 2001
    ..Finally, we present the analysis of the predicted first exons for all of the 24 chromosomes of the human genome...
  14. ncbi TRED: a transcriptional regulatory element database, new entries and other development
    C Jiang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring, Harbor NY 11724, USA
    Nucleic Acids Res 35:D137-40. 2007
    ..Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research...
  15. ncbi A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes
    H X Liu
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Nat Genet 27:55-8. 2001
    ....