Research Topics
| Deyou ZhengSummaryAffiliation: Albert Einstein College of Medicine Country: USA Publications
| Collaborators
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Detail Information
Publications
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... - 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... - Profiling RE1/REST-mediated histone modifications in the human genomeDeyou Zheng
Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Rose F Kennedy Center for the Study of Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Genome Biol 10:R9. 2009.... - Differential deployment of REST and CoREST promotes glial subtype specification and oligodendrocyte lineage maturationJoseph J Abrajano
Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, United States of America
PLoS ONE 4:e7665. 2009..Despite their involvement in multiple aspects of neuronal development, REST and CoREST are not believed to have any direct modulatory roles in glial cell maturation... - Corepressor for element-1-silencing transcription factor preferentially mediates gene networks underlying neural stem cell fate decisionsJoseph J Abrajano
Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Proc Natl Acad Sci U S A 107:16685-90. 2010..Clonal NSC REST and CoREST gene manipulation paradigms further revealed that CoREST has largely independent and previously uncharacterized roles in promoting NSC multilineage potential and modulating early neural fate decisions... - Development of patient-specific neurons in schizophrenia using induced pluripotent stem cellsErika Pedrosa
Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York 10416, USA
J Neurogenet 25:88-103. 2011..2 deletions towards a differentiated state may be marked by subtle changes in expression of pluripotency-associated genes... - RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disordersMingyan Lin
Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
PLoS ONE 6:e23356. 2011.... - A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1Sandeep N Wontakal
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
PLoS Genet 7:e1001392. 2011..1 also regulates many of the same genes and pathways in other blood cells, leading us to propose that PU.1 is a multifaceted factor with overlapping, as well as distinct, functions in several hematopoietic lineages... - A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiationSandeep N Wontakal
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Proc Natl Acad Sci U S A 109:3832-7. 2012.... - ?-catenin promoter ChIP-chip reveals potential schizophrenia and bipolar disorder gene networkErika Pedrosa
Department of Psychiatry and Behavioral Sciences, Division of Basic Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA
J Neurogenet 24:182-93. 2010..In addition, the finding that a putative lithium-responsive pathway may influence a subgroup of SZ and ASD candidate genes could have therapeutic implications... - Characterization of the past and current duplication activities in the human 22q11.2 regionXingyi Guo
Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
BMC Genomics 12:71. 2011..Segmental duplications (SDs) on 22q11.2 (LCR22), serve as substrates for meiotic non-allelic homologous recombination (NAHR) events resulting in several clinically significant genomic disorders... - REST and CoREST modulate neuronal subtype specification, maturation and maintenanceJoseph J Abrajano
Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, United States of America
PLoS ONE 4:e7936. 2009.... - Small RNAs originated from pseudogenes: cis- or trans-acting?Xingyi Guo
Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Albert Einstein College of Medicine, New York, New York, United States of America
PLoS Comput Biol 5:e1000449. 2009..Our findings suggest that pseudogenes of exapted functions may be a phenomenon ubiquitous in eukaryotic organisms... - 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... - 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... - The real life of pseudogenesMark Gerstein
Yale University, USA
Sci Am 295:48-55. 2006 - 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... - 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... - 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)... - 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... - 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.... - 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... - 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... - 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... - 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... - 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...