Michael Zhang

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. pmc TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
    Fang Zhao
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 33:D103-7. 2005
  2. pmc Tissue-specific regulatory elements in mammalian promoters
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Mol Syst Biol 3:73. 2007
  3. pmc Adaptively inferring human transcriptional subnetworks
    Debopriya Das
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11274, USA
    Mol Syst Biol 2:2006.0029. 2006
  4. pmc A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome
    Chaolin Zhang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 34:2238-46. 2006
  5. pmc Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome
    Shicai Fan
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China
    PLoS ONE 2:e1184. 2007
  6. pmc Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes
    Jinhua Wang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 33:5053-62. 2005
  7. pmc Identification of synaptic targets of Drosophila pumilio
    Gengxin Chen
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Comput Biol 4:e1000026. 2008
  8. pmc 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
  9. pmc Development of the human cancer microRNA network
    Sanghamitra Bandyopadhyay
    Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
    Silence 1:6. 2010
  10. pmc Identifying combinatorial regulation of transcription factors and binding motifs
    Mamoru Kato
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Genome Biol 5:R56. 2004

Collaborators

Detail Information

Publications72

  1. pmc TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
    Fang Zhao
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 33:D103-7. 2005
    ..TRED can provide good training datasets for further genome-wide cis-regulatory element prediction and annotation, assist detailed functional studies and facilitate the decipher of gene regulatory networks (http://rulai.cshl.edu/TRED)...
  2. pmc Tissue-specific regulatory elements in mammalian promoters
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Mol Syst Biol 3:73. 2007
    ..In a broader context, methods used to construct the catalog provide a model for the analysis of genomic regions that regulate differentially expressed genes...
  3. pmc Adaptively inferring human transcriptional subnetworks
    Debopriya Das
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11274, USA
    Mol Syst Biol 2:2006.0029. 2006
    ....
  4. pmc A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome
    Chaolin Zhang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 34:2238-46. 2006
    ..We propose that this arrangement provides a favorable genomic landscape for functional target site selection...
  5. pmc Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome
    Shicai Fan
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China
    PLoS ONE 2:e1184. 2007
    ..Understanding about mechanisms that may lead to the methylation resistance of CpG islands is still very poor...
  6. pmc Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes
    Jinhua Wang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 33:5053-62. 2005
    ..Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing...
  7. pmc Identification of synaptic targets of Drosophila pumilio
    Gengxin Chen
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Comput Biol 4:e1000026. 2008
    ..Finally, we show that the endogenous dlg1 mRNA can be regulated by Pumilio in a neuronal context, the adult mushroom bodies (MB), which is an anatomical site of memory storage...
  8. pmc 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...
  9. pmc Development of the human cancer microRNA network
    Sanghamitra Bandyopadhyay
    Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
    Silence 1:6. 2010
    ..However limited attempt has been made to collate this multitude of information and obtain a global perspective of miRNA dysregulation in multiple cancer types...
  10. pmc Identifying combinatorial regulation of transcription factors and binding motifs
    Mamoru Kato
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Genome Biol 5:R56. 2004
    ..Although various genomic datasets are relevant to this issue, each dataset provides relatively weak evidence on its own. Developing methods that can integrate different sequence, expression and localization data have become important...
  11. pmc Genome-wide promoter extraction and analysis in human, mouse, and rat
    Zhenyu Xuan
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Genome Biol 6:R72. 2005
    ....
  12. pmc Boosting with stumps for predicting transcription start sites
    Xiaoyue Zhao
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Genome Biol 8:R17. 2007
    ..CoreBoost improves greatly on locating transcription start sites. We also demonstrate that by further utilizing some tissue-specific information, better accuracy can be achieved...
  13. pmc Determination of enriched histone modifications in non-genic portions of the human genome
    Jeffrey A Rosenfeld
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Genomics 10:143. 2009
    ..Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers...
  14. pmc A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish
    Zhongan Yang
    Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095 1606, USA
    BMC Dev Biol 7:97. 2007
    ..Identification and characterization of these elements should help elucidating transcription regulatory mechanisms of GATA-2 expression in hematopoietic lineage...
  15. pmc SFSSClass: an integrated approach for miRNA based tumor classification
    Ramkrishna Mitra
    Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
    BMC Bioinformatics 11:S22. 2010
    ..A judicious integration of such knowledge with effective miRNA and sample selection through a biclustering approach could be an important step in improving the accuracy of tumor classification...
  16. pmc Using quality scores and longer reads improves accuracy of Solexa read mapping
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11274, USA
    BMC Bioinformatics 9:128. 2008
    ..Two sources of information that are often ignored when mapping reads from the Solexa technology are the 3' ends of longer reads, which contain a much higher frequency of sequencing errors, and the base-call quality scores...
  17. pmc Statistical significance of cis-regulatory modules
    Dustin E Schones
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 8:19. 2007
    ..While various algorithms for this purpose have been introduced, most are not well suited for rapid, genome scale scanning...
  18. pmc Profiling alternatively spliced mRNA isoforms for prostate cancer classification
    Chaolin Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 7:202. 2006
    ..Here, we investigate the advantage of using splice isoforms, which couple transcriptional and splicing regulation, for cancer classification...
  19. ncbi request reprint Predicting methylation status of CpG islands in the human brain
    Fang Fang
    Bioinformatics Division, TNLIST, Department of Automation, Tsinghua University 100084 China
    Bioinformatics 22:2204-9. 2006
    ..Large-scale experimental detection of DNA methylation is still both labor-intensive and time-consuming. Therefore, it is necessary to develop in silico approaches for predicting methylation status of CpG islands...
  20. ncbi request reprint Computational prediction of eukaryotic protein-coding genes
    Michael Q Zhang
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, New York 11724, USA
    Nat Rev Genet 3:698-709. 2002
    ..Here, I discuss these approaches and explain why they have become essential for the analyses of newly sequenced genomes...
  21. pmc Extracting functional information from microarrays: a challenge for functional genomics
    Michael Q Zhang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 99:12509-11. 2002
  22. ncbi request reprint DWE: discriminating word enumerator
    Pavel Sumazin
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 21:31-8. 2005
    ..Tissue-specific transcription factor binding sites give insight into tissue-specific transcription regulation...
  23. pmc Interacting models of cooperative gene regulation
    Debopriya Das
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 101:16234-9. 2004
    ..We believe our multivariate adaptive regression splines-based approach will become more significant when applied to higher eukaryotes, especially mammals, where cooperative control of gene regulation is absolutely essential...
  24. pmc Transcription factor binding element detection using functional clustering of mutant expression data
    Gengxin Chen
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 32:2362-71. 2004
    ..Functional clustering included in our approach may also provide new insights into the function of the relevant transcription factor...
  25. pmc GFScan: a gene family search tool at genomic DNA level
    Zhenyu Xuan
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 12:1142-9. 2002
    ..We also showed that motifs constructed based on human genes could be used to search the mouse genome to identify orthologous family members in mouse. This program is available at http://www.cshl.org/mzhanglab/...
  26. pmc 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
    ..The two available mouse genome assemblies, from the public mouse genome sequencing consortium and Celera Genomics, were obtained using different clone libraries and different assembly methods...
  27. pmc High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
    Emily Hodges
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 19:1593-605. 2009
    ..Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs...
  28. doi request reprint Using CorePromoter to find human core promoters
    Michael Q Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Curr Protoc Bioinformatics . 2005
    ..The protocols in this unit introduce its basic methodology and discuss how to apply it to a sample problem in conjunction with other gene-finding programs...
  29. pmc Computational analyses of eukaryotic promoters
    Michael Q Zhang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 8:S3. 2007
    ..More details may be found in the extended references. This review is based on a summer lecture given at Max Planck Institute at Berlin in 2005...
  30. pmc The mouse genome: experimental examination of gene predictions and transcriptional start sites
    Sujit Dike
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 14:2424-9. 2004
    ..This approach can be a useful tool in the ongoing efforts to increase the quality of gene annotations, especially transcriptional start sites, in complex genomes...
  31. pmc Identifying cooperativity among transcription factors controlling the cell cycle in yeast
    Nilanjana Banerjee
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 31:7024-31. 2003
    ..This study is an example of how systematic combination of diverse data types along with new functional genomic approaches can provide a rigorous platform to map TF interactions more efficiently...
  32. ncbi request reprint Similarity of position frequency matrices for transcription factor binding sites
    Dustin E Schones
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 21:307-13. 2005
    ..The ability to compare PFMs representing binding sites is especially important for de novo sequence motif discovery, where it is desirable to compare putative matrices to one another and to known matrices...
  33. ncbi request reprint Mining ChIP-chip data for transcription factor and cofactor binding sites
    Andrew D Smith
    Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 21:i403-12. 2005
    ..Identification of single motifs and motif pairs that can be used to predict transcription factor localization in ChIP-chip data, and gene expression in tissue-specific microarray data...
  34. ncbi request reprint An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers
    Philip J Smith
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Hum Mol Genet 15:2490-508. 2006
    ..Finally, we have derived an increased specificity score matrix that incorporates information from both of our SF2/ASF-specific matrices and that accurately predicts the exon-skipping phenotypes of deleterious point mutations...
  35. ncbi request reprint From worm to human: bioinformatics approaches to identify FOXO target genes
    Zhenyu Xuan
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mech Ageing Dev 126:209-15. 2005
    ..Here we demonstrate how to identify FOXO target genes and their potential cis-regulatory binding sites in the promoters via bioinformatics approaches. These results provide new testable hypotheses for further experimental verifications...
  36. ncbi request reprint Evolutionary impact of limited splicing fidelity in mammalian genes
    Chaolin Zhang
    Cold Spring Harbor Laboratory, NY 11724, USA
    Trends Genet 23:484-8. 2007
    ..These results suggest AS events introducing mild changes are generally favored during evolution and explain the excess of shorter, frame-preserving cassette exons in present mammalian genomes...
  37. ncbi request reprint Regulating gene expression through RNA nuclear retention
    Kannanganattu V Prasanth
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Cell 123:249-63. 2005
    ..This mechanism of action highlights an important paradigm for the role of a nuclear-retained stable RNA transcript in regulating gene expression...
  38. pmc Identifying tissue-selective transcription factor binding sites in vertebrate promoters
    Andrew D Smith
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11274, USA
    Proc Natl Acad Sci U S A 102:1560-5. 2005
    ....
  39. pmc ESEfinder: A web resource to identify exonic splicing enhancers
    Luca Cartegni
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 31:3568-71. 2003
    ....
  40. pmc Computational prediction of methylation status in human genomic sequences
    Rajdeep Das
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 103:10713-6. 2006
    ..Using hdfinder, we have depicted the entire genomic methylation patterns for all 22 human autosomes...
  41. ncbi request reprint Direct coupling of the cell cycle and cell death machinery by E2F
    Zaher Nahle
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nat Cell Biol 4:859-64. 2002
    ..The data also underscore how cell cycle progression can be coupled to the apoptotic machinery...
  42. pmc DNA motifs in human and mouse proximal promoters predict tissue-specific expression
    Andrew D Smith
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 103:6275-80. 2006
    ..The identification in proximal promoters of cis-regulatory modules with tissue-specific activity lays the groundwork for complete characterization and deciphering of cis-regulatory DNA code in mammalian genomes...
  43. ncbi request reprint Functional genomics as applied to mapping transcription regulatory networks
    Nila Banerjee
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Curr Opin Microbiol 5:313-7. 2002
    ..We focus in particular on the budding yeast Saccharomyces cerevisiae...
  44. pmc Neural potential of a stem cell population in the hair follicle
    John L Mignone
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Cell Cycle 6:2161-70. 2007
    ..Our results show that nestin-expressing cells in the bulge region of the hair follicle have stem cell-like properties, are multipotent, and can effectively generate cells of neural lineage in vitro and in vivo...
  45. pmc Dual-specificity splice sites function alternatively as 5' and 3' splice sites
    Chaolin Zhang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 104:15028-33. 2007
    ..We discuss the implications of this unusual splicing pattern for the diverse mechanisms of exon recognition and for gene evolution...
  46. pmc Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2
    Chaolin Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genes Dev 22:2550-63. 2008
    ..We also identified instances of binding site creation or loss in different vertebrate lineages and human populations, which likely reflect fine-tuning of gene expression regulation during evolution...
  47. pmc RNA landscape of evolution for optimal exon and intron discrimination
    Chaolin Zhang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 105:5797-802. 2008
    ..Our results suggest that human genes have been optimized for exon and intron discrimination through an RNA landscape shaped during evolution...
  48. pmc Critical roles for Dicer in the female germline
    Elizabeth P Murchison
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA
    Genes Dev 21:682-93. 2007
    ..Our studies identify Dicer as central to a regulatory network that controls oocyte gene expression programs and that promotes genomic integrity in a cell type notoriously susceptible to aneuploidy...
  49. pmc Combinatorial patterns of histone acetylations and methylations in the human genome
    Zhibin Wang
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Genet 40:897-903. 2008
    ..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...
  50. ncbi request reprint Evidence and characteristics of putative human alpha recombination hotspots
    Jing Zhang
    MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Bejing, China
    Hum Mol Genet 13:2823-8. 2004
    ..These long-sought putative human alpha recombination hotspots should deserve further experimental investigations...
  51. pmc Histone methylation marks play important roles in predicting the methylation status of CpG islands
    Shicai Fan
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua University, FIT Building 1 107, Beijing 100084, China
    Biochem Biophys Res Commun 374:559-64. 2008
    ..And the established open environment may be a prerequisite for or a consequence of the function implementation of zinc finger proteins that could protect CpG islands from DNA methylation...
  52. pmc Poly A- transcripts expressed in HeLa cells
    Qingfa Wu
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
    PLoS ONE 3:e2803. 2008
    ..Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown...
  53. pmc ZOOM! Zillions of oligos mapped
    Hao Lin
    Institute for Computing Technology, Chinese Academy of Sciences, Beijing, China
    Bioinformatics 24:2431-7. 2008
    ..Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts...
  54. pmc A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data
    Jun Li
    Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing 100084, China
    Am J Hum Genet 79:628-39. 2006
    ..In particular, we observed that DNaseI-hypersensitive sites are enriched in hotspots, suggesting the existence of human beta hotspots similar to those found in yeast...
  55. pmc A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
    Zirong Li
    Ludwig Institute for Cancer Research, University of California at San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093 0653, USA
    Proc Natl Acad Sci U S A 100:8164-9. 2003
    ..Taken together, these results suggest a general role for overexpressed c-Myc in global transcriptional regulation in some cancer cells and point toward molecular mechanisms for c-Myc function in malignant transformation...
  56. ncbi request reprint Gene expression profiling in developing human hippocampus
    Yan Zhang
    Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People s Republic of China
    J Neurosci Res 70:200-8. 2002
    ....
  57. pmc Network-based global inference of human disease genes
    Xuebing Wu
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua University, Beijing, China
    Mol Syst Biol 4:189. 2008
    ....
  58. ncbi request reprint Genome-wide prediction and analysis of function-specific transcription factor binding sites
    Fan Long
    Aventis Pharmaceuticals Inc, Route 202 206, Bridgewater, NJ 08807, USA
    In Silico Biol 4:395-410. 2004
    ..Our tools and analysis provide a new resource for deciphering transcription regulation in different biological paradigms...
  59. ncbi request reprint Computational prediction of novel components of lung transcriptional networks
    M Juanita Martinez
    Lovelace Respiratory Research Institute, 2425 Ridgecrest Dr SE, Albuquerque, NM 87108, USA
    Bioinformatics 23:21-9. 2007
    ..Little is known regarding the transcriptional mechanisms involved in forming and maintaining epithelial cell lineages of the mammalian respiratory tract...
  60. pmc Pan-genome isolation of low abundance transcripts using SAGE tag
    Yeong Cheol Kim
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, IL 60201, USA
    FEBS Lett 580:6721-9. 2006
    ..Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through SAGE tags mis-priming...
  61. ncbi request reprint Computing exact P-values for DNA motifs
    Jing Zhang
    State Key Laboratory of Intelligent Technology and System, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
    Bioinformatics 23:531-7. 2007
    ..They often significantly deviate from the true P-value by orders of magnitude. Exact P-value computation is needed for ranking the motifs. Furthermore, surprisingly, the complexity of the problem is unknown...
  62. pmc Large-scale structure of genomic methylation patterns
    Robert A Rollins
    Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, Columbia University, New York, NY 10032, USA
    Genome Res 16:157-63. 2006
    ..This suggestion is compatible with the finding that cytosine methylation is universal among large-genome eukaryotes, while many eukaryotes with genome sizes <5 x 10(8) bp do not methylate their DNA...
  63. pmc Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    Tae Hoon Kim
    Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093 0653, USA
    Cell 128:1231-45. 2007
    ..In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites...
  64. ncbi request reprint Predictive models of gene regulation: application of regression methods to microarray data
    Debopriya Das
    Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    Methods Mol Biol 377:95-110. 2007
    ..Periodic regulation of the cell cycle, connection with underlying energetics, and the inference of combinatorial logic are also discussed. An implementation based on regression splines is discussed in detail...
  65. ncbi request reprint OSCAR: one-class SVM for accurate recognition of cis-elements
    Bo Jiang
    MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    Bioinformatics 23:2823-8. 2007
    ..Recent biological and computational researches, however, suggest that there exist not only locational preferences of binding, but also correlations between transcription factors...
  66. ncbi request reprint Prediction of transcription start sites based on feature selection using AMOSA
    Xi Wang
    Bioinformatics Division, TNLIST and Department of Automation, Tsinghua Univ, Beijing 100084, China
    Comput Syst Bioinformatics Conf 6:183-93. 2007
    ..This system is found to be comparable to, often better than, several existing methods in terms of different quantitative performance measures...
  67. ncbi request reprint Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species
    Xiaowo Wang
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    Bioinformatics 24:165-71. 2008
    ..MicroRNAs are a class of endogenous small RNAs that play regulatory roles. Intergenic miRNAs are believed to be transcribed independently, but the transcriptional control of these crucial regulators is still poorly understood...
  68. pmc Interferon regulatory factors are transcriptional regulators of adipogenesis
    Jun Eguchi
    Division of Endocrinology and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
    Cell Metab 7:86-94. 2008
    ..This analysis suggests an important role for IRF proteins in adipocyte biology and demonstrates the utility of this approach in identifying cis- and trans-acting factors not previously suspected to participate in adipogenesis...
  69. pmc Scanning the human genome at kilobase resolution
    Jun Chen
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, Illinois 60201, USA
    Genome Res 18:751-62. 2008
    ....
  70. pmc Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
    Leah O Barrera
    Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093 0653, USA
    Genome Res 18:46-59. 2008
    ..Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals...

Research Grants19

  1. Computational and experimental modeling of RNA Splicing
    Michael Zhang; Fiscal Year: 2009
    ....
  2. Computational Modeling of Mammalian Promoters
    Michael Zhang; Fiscal Year: 2009
    ..Such models are likely to offer new insights into mechanisms of gene regulation or mis-regulation, and will generate many hypotheses for further functional studies on global regulation of gene expression. ..
  3. Computational and experimental modeling of RNA Splicing
    Michael Zhang; Fiscal Year: 2007
    ....
  4. IDENTIFICATION OF PROTEIN CODING GENES IN HUMAN GENOMES
    Michael Zhang; Fiscal Year: 2005
    ..The methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structures/functions more efficiently and more accurately. ..
  5. IDENTIFICATION OF PROTEIN CODING GENES IN HUMAN GENOMES
    Michael Zhang; Fiscal Year: 2004
    ..The methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structures/functions more efficiently and more accurately. ..
  6. IDENTIFICATION OF PROTEIN CODING GENES IN HUMAN GENOMES
    Michael Zhang; Fiscal Year: 2003
    ..The methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structures/functions more efficiently and more accurately. ..
  7. IDENTIFICATION OF PROTEIN CODING GENES IN HUMAN GENOMES
    Michael Zhang; Fiscal Year: 2002
    ..The investigators predict that methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structures/functions more efficiently and more accurately. ..
  8. COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATA
    Michael Zhang; Fiscal Year: 2002
    ..abstract_text> ..
  9. IDENTIFICATION OF PROTEIN CODING GENES IN HUMAN GENOMES
    Michael Zhang; Fiscal Year: 2001
    ..The investigators predict that methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structures/functions more efficiently and more accurately. ..
  10. IDENTIFICATION OF PROTEIN CODING GENES IN HUMAN GENOMES
    Michael Zhang; Fiscal Year: 2001
    ..The investigators predict that methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structures/functions more efficiently and more accurately. ..
  11. COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATA
    Michael Zhang; Fiscal Year: 2001
    ..abstract_text> ..
  12. IDENTIFICATION OF PROTEIN CODING GENES IN HUMAN GENOMES
    Michael Zhang; Fiscal Year: 2000
    ..The investigators predict that methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structures/functions more efficiently and more accurately. ..
  13. COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATA
    Michael Zhang; Fiscal Year: 2000
    ..abstract_text> ..
  14. PROTEIN CODING GENES IN THE HUMAN GENOME
    Michael Zhang; Fiscal Year: 1999
    ..The methods and tools resulting from this project will help molecular biologists to find human genes and to interpret the structure/functions more quickly and accurately. ..
  15. Computational and experimental modeling of RNA Splicing
    Michael Zhang; Fiscal Year: 2009
    ....