Zhengdong D Zhang

Summary

Publications

  1. pmc Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 11:R26. 2010
  2. ncbi Divergence of transcription factor binding sites across related yeast species
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Science 317:815-9. 2007
  3. pmc Modeling ChIP sequencing in silico with applications
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS Comput Biol 4:e1000158. 2008
  4. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
  5. doi Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Evol 66:446-56. 2008
  6. pmc Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants
    Jiang Du
    Department of Computer Science, Yale University, New Haven, Connecticut, USA
    PLoS Comput Biol 5:e1000432. 2009
  7. ncbi Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
    Mol Biol Evol 25:131-43. 2008
  8. ncbi Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Funct Integr Genomics 7:335-45. 2007
  9. doi Rapid in vivo exploration of a 5S rRNA neutral network
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Microbiol Methods 76:181-7. 2009

Detail Information

Publications9

  1. pmc Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 11:R26. 2010
    ..They constitute only a small fraction of annotated pseudogenes in the human genome. However, as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution...
  2. ncbi Divergence of transcription factor binding sites across related yeast species
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Science 317:815-9. 2007
    ..Transcription factor binding sites have therefore diverged substantially faster than ortholog content. Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species...
  3. pmc Modeling ChIP sequencing in silico with applications
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS Comput Biol 4:e1000158. 2008
    ..This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion...
  4. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information...
  5. doi Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Evol 66:446-56. 2008
    ..Thus, positive selection on CD4 among primates may reflect forces driven by SIV infection and could provide a link between changes in sequence and structure of CD4 during evolution and the interaction with the immunodeficiency virus...
  6. pmc Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants
    Jiang Du
    Department of Computer Science, Yale University, New Haven, Connecticut, USA
    PLoS Comput Biol 5:e1000432. 2009
    ..Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost...
  7. ncbi Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
    Mol Biol Evol 25:131-43. 2008
    ..By comparing orthologous sequences, we dated the FXR-FXRbeta duplication and the nonfunctionalization of FXRbeta in primates...
  8. ncbi Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms
    Anthony R Borneman
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
    Funct Integr Genomics 7:335-45. 2007
    ..The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available...
  9. doi Rapid in vivo exploration of a 5S rRNA neutral network
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Microbiol Methods 76:181-7. 2009
    ..Unlike a complete knockout system, the method allows recovery of both deleterious and functional variants.. The method can be used to study variants of any 5S rRNA in the E. coli context including those of E. coli...