Zhengdong D Zhang

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Microbial identification by mass cataloging
    Zhengdong Zhang
    Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204 5001, USA
    BMC Bioinformatics 7:117. 2006
  2. pmc Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome
    Jia Qian Wu
    Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA
    Genome Biol 9:R3. 2008
  3. pmc PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    Jan O Korbel
    Gene Expression Unit, European Molecular Biology Laboratory EMBL, Meyerhofstr, Heidelberg, 69117, Germany
    Genome Biol 10:R23. 2009
  4. doi request reprint 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
  5. pmc Tilescope: online analysis pipeline for high-density tiling microarray data
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 8:R81. 2007
  6. 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
  7. ncbi request reprint 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
  8. 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
  9. 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
  10. pmc Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:787-97. 2007

Detail Information

Publications22

  1. pmc Microbial identification by mass cataloging
    Zhengdong Zhang
    Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Avenue, Houston, TX 77204 5001, USA
    BMC Bioinformatics 7:117. 2006
    ..Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms...
  2. pmc Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome
    Jia Qian Wu
    Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA
    Genome Biol 9:R3. 2008
    ..However, there is still much uncertainty regarding precisely what portion of the genome is transcribed, the exact structures of these novel transcripts, and the levels of the transcripts produced...
  3. pmc PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    Jan O Korbel
    Gene Expression Unit, European Molecular Biology Laboratory EMBL, Meyerhofstr, Heidelberg, 69117, Germany
    Genome Biol 10:R23. 2009
    ..The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors...
  4. doi request reprint 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...
  5. pmc Tilescope: online analysis pipeline for high-density tiling microarray data
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 8:R81. 2007
    ..The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis...
  6. 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...
  7. ncbi request reprint 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...
  8. 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...
  9. 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...
  10. pmc Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:787-97. 2007
    ..Data sets associated with histone modifications have particularly strong correlations. Finally, we show how the correlations between factors change when only regulatory elements far from the transcription start sites are considered...
  11. ncbi request reprint 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...
  12. pmc Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies
    Ghia M Euskirchen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    Genome Res 17:898-909. 2007
    ..Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies...
  13. ncbi request reprint A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
    Jiang Du
    Department of Computer Science, Yale University, New Haven, CT 06520, USA
    Bioinformatics 22:3016-24. 2006
    ..Here we propose a supervised framework for doing this. It has the advantage of explicitly incorporating validated biological knowledge into the model and allowing for formal training and testing...
  14. 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...
  15. ncbi request reprint What is a gene, post-ENCODE? History and updated definition
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
    Genome Res 17:669-81. 2007
    ..It also manifests how integral the concept of biological function is in defining genes...
  16. doi request reprint 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...
  17. pmc EBNA1 regulates cellular gene expression by binding cellular promoters
    Allon Canaan
    Department of Genetics, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 106:22421-6. 2009
    ..We have correlated EBNA1 bound promoters with changes in gene expression. Sequence analysis of the 100 promoters most enriched revealed a DNA motif that differs from the EBNA1 binding site in the EBV genome...
  18. ncbi request reprint 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...
  19. ncbi request reprint Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset
    Zhengdong Zhang
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204 5001, USA
    Bioinformatics 18:244-50. 2002
    ....
  20. pmc NCIR: a database of non-canonical interactions in known RNA structures
    Uma Nagaswamy
    Department of Biology and Biochemistry, University of Houston, 369 Science and Research Building 2, Houston, TX 77204 5001, USA
    Nucleic Acids Res 30:395-7. 2002
    ..The most frequent triple interaction connects N3 of an A with the amino of a G that is also involved in a standard Watson-Crick pair...
  21. pmc Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
    Nathan D Trinklein
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 17:720-31. 2007
    ..Our results suggest that there are at least 35% more functional promoters in the human genome than currently annotated...
  22. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...