Research Topics
Species | Deyou ZhengSummaryAffiliation: Yale University Country: USA Publications
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Publications
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...
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolutionDeyou 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...- What is a gene, post-ENCODE? History and updated definitionMark 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... - The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel lociJoel 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... - Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomesSuganthi 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... - Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activityYuen 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... - A computational approach for identifying pseudogenes in the ENCODE regionsDeyou Zheng
Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue, New Haven, CT 06520, USA
Genome Biol 7:S13.1-10. 2006.... - 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 channelTatjana 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... - The real life of pseudogenesMark Gerstein
Yale University, USA
Sci Am 295:48-55. 2006 - Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genomeOlof 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... - Integrated pseudogene annotation for human chromosome 22: evidence for transcriptionDeyou 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)... - SPINE 2: a system for collaborative structural proteomics within a federated database frameworkChern-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)... - PseudoPipe: an automated pseudogene identification pipelineZhaolei 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..Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts... - Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genomeNathan 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... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Asymmetric histone modifications between the original and derived loci of human segmental duplicationsDeyou 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... - Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding abilityPaul 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... - Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotationJohn 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...