Research Topics
| Zhengdong D ZhangSummaryAffiliation: Yale University Country: USA Publications
| Collaborators
|
Detail Information
Publications
Microbial identification by mass catalogingZhengdong 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...- Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genomeJia 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... - PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing dataJan 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... 
Rapid in vivo exploration of a 5S rRNA neutral networkZhengdong 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...- Tilescope: online analysis pipeline for high-density tiling microarray dataZhengdong 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... - Modeling ChIP sequencing in silico with applicationsZhengdong 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... 
Divergence of transcription factor binding sites across related yeast speciesAnthony 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...- Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variantsJiang 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... - PeakSeq enables systematic scoring of ChIP-seq experiments relative to controlsJoel 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... - Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regionsZhengdong 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... - Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platformsAnthony 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... - Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologiesGhia 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... - A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledgeJiang Du
Department of Computer Science, Yale University, New Haven, CT 06520, USA
Bioinformatics 22:3016-24. 2006..This latter result has strong implications for the optimum way medium-scale validation experiments should be carried out to verify the results of the genome-scale tiling array experiments... - Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primatesZhengdong 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... - 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... - Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primatesZhengdong 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... - EBNA1 regulates cellular gene expression by binding cellular promotersAllon 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... - Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their storiesZhengdong 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... - Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence datasetZhengdong Zhang
Department of Biology and Biochemistry, University of Houston, Houston, TX 77204 5001, USA
Bioinformatics 18:244-50. 2002..Over 16,000 15mers were identified that might be useful as signatures. Signature oligonucleotides are available for over 80% of the nodes in the representative tree... - NCIR: a database of non-canonical interactions in known RNA structuresUma 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... - 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...