Deyou Zheng

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Trends Genet 23:219-24. 2007
  2. pmc Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:839-51. 2007
  3. 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
  4. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
  5. pmc Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 10:R2. 2009
  6. pmc Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    Olof Emanuelsson
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:886-97. 2007
  7. pmc Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity
    Yuen Jong Liu
    Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
    BMC Genomics 10:480. 2009
  8. pmc Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel
    Tatjana Coric
    Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520 8026, USA
    J Physiol 568:725-35. 2005
  9. pmc A computational approach for identifying pseudogenes in the ENCODE regions
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue, New Haven, CT 06520, USA
    Genome Biol 7:S13.1-10. 2006
  10. ncbi request reprint The real life of pseudogenes
    Mark Gerstein
    Yale University, USA
    Sci Am 295:48-55. 2006

Detail Information

Publications18

  1. ncbi request reprint The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Trends Genet 23:219-24. 2007
    ..Furthermore, we suggest a classification system to accommodate pseudogenes with various levels of functionality...
  2. pmc Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:839-51. 2007
    ..These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues...
  3. 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...
  4. pmc The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
    Joel S Rozowsky
    Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:732-45. 2007
    ..Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously...
  5. pmc Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 10:R2. 2009
    ..The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions. Conservation of pseudogenes suggests that they might have a functional role in some instances...
  6. pmc Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    Olof Emanuelsson
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 17:886-97. 2007
    ..Finally, our experiments reveal a significant amount of novel transcription outside of known genes, and an appreciable sample of this was validated by independent experiments...
  7. pmc Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity
    Yuen Jong Liu
    Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
    BMC Genomics 10:480. 2009
    ..One of the glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has already been noted to have one of the largest numbers of associated pseudogenes, among all proteins...
  8. pmc Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel
    Tatjana Coric
    Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520 8026, USA
    J Physiol 568:725-35. 2005
    ..The results also demonstrate that gating by protons is not a feature common to all ASIC1 channels. Proton sensitivity arose recently in evolution, implying that agonists different from protons activate ASIC1 in lower vertebrates...
  9. pmc A computational approach for identifying pseudogenes in the ENCODE regions
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue, New Haven, CT 06520, USA
    Genome Biol 7:S13.1-10. 2006
    ..We require alignments between duplicated pseudogenes and their parents to span intron-exon junctions, and this can be used to distinguish between true duplicated and processed pseudogenes (with insertions)...
  10. ncbi request reprint The real life of pseudogenes
    Mark Gerstein
    Yale University, USA
    Sci Am 295:48-55. 2006
  11. ncbi request reprint Integrated pseudogene annotation for human chromosome 22: evidence for transcription
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    J Mol Biol 349:27-45. 2005
    ..pseudogene.org)...
  12. pmc SPINE 2: a system for collaborative structural proteomics within a federated database framework
    Chern Sing Goh
    Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Nucleic Acids Res 31:2833-8. 2003
    ..g. crystallization LIMS local to particular laboratories) and (iii) international archival resources that SPINE links to and passes on information to (e.g. TargetDB at the PDB)...
  13. 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...
  14. ncbi request reprint PseudoPipe: an automated pseudogene identification pipeline
    Zhaolei Zhang
    Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 160 College Street, Toronto, ON M5S 3E1, Canada
    Bioinformatics 22:1437-9. 2006
    ..These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes...
  15. 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...
  16. pmc Asymmetric histone modifications between the original and derived loci of human segmental duplications
    Deyou Zheng
    Institute for Brain Disorders and Neural Regeneration, The Saul R, Korey Department of Neurology, Albert Einstein College of Medicine, Rose F, Kennedy Center 915B, 1410 Pelham Parkway South, Bronx, NY 10461, USA
    Genome Biol 9:R105. 2008
    ..However, the molecular processes involved in the evolution and regulation of duplicated sequences remain largely unexplored...
  17. pmc Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability
    Paul M Harrison
    Department of Biology, McGill University Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1B1
    Nucleic Acids Res 33:2374-83. 2005
    ..This is likely linked to well-documented extensive lineage-specific SINE/LINE activity. The list of TPPsigs is available at: http://www.biology.mcgill.ca/faculty/harrison/tppg/bppg.tov (or) http:pseudogene.org...
  18. pmc Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
    John E Karro
    Center for Comparative Genomics and Bioinformatics, 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA
    Nucleic Acids Res 35:D55-60. 2007
    ..At the present time, the database contains more than 100,000 pseudogenes spanning 64 prokaryote and 11 eukaryote genomes, including a collection of human annotations compiled from 16 sources...