Michael Q Zhang

Summary

Affiliation: University of Texas at Dallas
Country: USA

Publications

  1. pmc Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming
    Zhirui Hu
    MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    BMC Syst Biol 5:S8. 2011
  2. pmc Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes
    Zhihua Zhang
    Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
    BMC Bioinformatics 12:155. 2011
  3. pmc High-resolution human core-promoter prediction with CoreBoost_HM
    Xiaowo Wang
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    Genome Res 19:266-75. 2009
  4. pmc Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation
    Ruijuan Li
    MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    Genomics 100:297-302. 2012
  5. 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
  6. 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
  7. pmc ZOOM! Zillions of oligos mapped
    Hao Lin
    Institute for Computing Technology, Chinese Academy of Sciences, Beijing, China
    Bioinformatics 24:2431-7. 2008
  8. 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
  9. pmc Regulatory elements of Caenorhabditis elegans ribosomal protein genes
    Monica C Sleumer
    Bioinformatics Division, Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, China
    BMC Genomics 13:433. 2012
  10. 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

Research Grants

  1. Computational and experimental modeling of RNA Splicing
    Michael Q Zhang; Fiscal Year: 2010
  2. Computational Modeling of Mammalian Promoters
    Michael Q Zhang; Fiscal Year: 2010

Collaborators

Detail Information

Publications15

  1. pmc Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming
    Zhirui Hu
    MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    BMC Syst Biol 5:S8. 2011
    ..However, the mechanism of induced pluripotency is still unknown...
  2. pmc Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes
    Zhihua Zhang
    Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
    BMC Bioinformatics 12:155. 2011
    ..However, the effect of chromatin on tissue/cell-type specific gene regulation (TCSR) is largely unknown. In this paper, we present a method to elucidate the relationship between histone modification/variation (HMV) and TCSR...
  3. pmc High-resolution human core-promoter prediction with CoreBoost_HM
    Xiaowo Wang
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    Genome Res 19:266-75. 2009
    ..We also identified a few intronic microRNAs that may have their own promoters. This result suggests that our new method can help to identify and characterize the core-promoters of both coding and noncoding genes...
  4. pmc Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation
    Ruijuan Li
    MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China
    Genomics 100:297-302. 2012
    ..Our observations suggested that the different gene expression patterns upon external stimulus were regulated by a combination of multi-layer regulators...
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. pmc Regulatory elements of Caenorhabditis elegans ribosomal protein genes
    Monica C Sleumer
    Bioinformatics Division, Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, China
    BMC Genomics 13:433. 2012
    ..elegans RPGs, providing a new insight regarding the regulation of these genes in C. elegans...
  10. 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...
  11. 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
    ....
  12. pmc Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development
    Tingting Li
    TNLIST Department of Automation, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua University, Beijing, China
    Genomics 93:235-42. 2009
    ..A group of uncharacterized genes which might be involved in the fetal hematopoiesis were detected...
  13. 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...
  14. 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...
  15. pmc FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer
    Dingming Wu
    Bioinformatics Division Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology TNLIST, Department of Automation, Tsinghua University, Beijing, China
    PLoS ONE 8:e74275. 2013
    ..FastDMA can benefit the data analyses of large-scale DNA methylation studies with an integrative pipeline and a high computational efficiency. The software is freely available via http://bioinfo.au.tsinghua.edu.cn/software/fastdma/. ..

Research Grants2

  1. Computational and experimental modeling of RNA Splicing
    Michael Q Zhang; Fiscal Year: 2010
    ....
  2. Computational Modeling of Mammalian Promoters
    Michael Q Zhang; Fiscal Year: 2010
    ..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. ..