Yu Zheng

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Phylogenetic detection of conserved gene clusters in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA, USA
    BMC Bioinformatics 6:243. 2005
  2. pmc Genomic functional annotation using co-evolution profiles of gene clusters
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 3:RESEARCH0060. 2002
  3. pmc Segmentally variable genes: a new perspective on adaptation
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    PLoS Biol 2:E81. 2004
  4. pmc The MspJI family of modification-dependent restriction endonucleases for epigenetic studies
    Devora Cohen-Karni
    Molecular Biology, Cell Biology, and Biochemistry Program, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 108:11040-5. 2011
  5. pmc A unique family of Mrr-like modification-dependent restriction endonucleases
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
    Nucleic Acids Res 38:5527-34. 2010
  6. pmc Characterization of two new aminopeptidases in Escherichia coli
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Massachusetts 02215, USA
    J Bacteriol 187:3671-7. 2005
  7. pmc Identification of genes with fast-evolving regions in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 32:6347-57. 2004
  8. pmc Computational identification of operons in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 12:1221-30. 2002
  9. pmc Whole-genome annotation by using evidence integration in functional-linkage networks
    Ulas Karaoz
    Bioinformatics Program, Boston University, 48 Cummington Street, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:2888-93. 2004
  10. pmc Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules
    Meni Wanunu
    Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
    J Am Chem Soc 133:486-92. 2011

Collaborators

Detail Information

Publications15

  1. pmc Phylogenetic detection of conserved gene clusters in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA, USA
    BMC Bioinformatics 6:243. 2005
    ....
  2. pmc Genomic functional annotation using co-evolution profiles of gene clusters
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 3:RESEARCH0060. 2002
    ..The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome...
  3. pmc Segmentally variable genes: a new perspective on adaptation
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    PLoS Biol 2:E81. 2004
    ..Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment...
  4. pmc The MspJI family of modification-dependent restriction endonucleases for epigenetic studies
    Devora Cohen-Karni
    Molecular Biology, Cell Biology, and Biochemistry Program, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 108:11040-5. 2011
    ..Altogether, the MspJI family of enzymes represent appealing tools of choice for method development in DNA epigenetic studies...
  5. pmc A unique family of Mrr-like modification-dependent restriction endonucleases
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
    Nucleic Acids Res 38:5527-34. 2010
    ..The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms...
  6. pmc Characterization of two new aminopeptidases in Escherichia coli
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Massachusetts 02215, USA
    J Bacteriol 187:3671-7. 2005
    ..ypdE is the immediate downstream gene of ypdF, and its start codon overlaps with the stop codon of ypdF by 1 base. YpdE is shown to be a metalloaminopeptidase and has a broad exoaminopeptidase activity...
  7. pmc Identification of genes with fast-evolving regions in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 32:6347-57. 2004
    ..Gene sets reported from our method provide a measure of the phenotypic divergence between two closely related genomes...
  8. pmc Computational identification of operons in microbial genomes
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 12:1221-30. 2002
    ..We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution...
  9. pmc Whole-genome annotation by using evidence integration in functional-linkage networks
    Ulas Karaoz
    Bioinformatics Program, Boston University, 48 Cummington Street, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:2888-93. 2004
    ..Our results contain a number of predictions and furnish strong evidence that integration of functional information is indeed a promising direction for improving the accuracy and robustness of functional genomics...
  10. pmc Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules
    Meni Wanunu
    Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
    J Am Chem Soc 133:486-92. 2011
    ..Further, the relative proportion of hmC in the sample can be determined from the electronic signature of the intact DNA fragment...
  11. ncbi request reprint STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures
    Yu Zheng
    Department of Biological Sciences and Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543
    Bioinformatics 21:2925-6. 2005
    ..STARS will facilitate assignment of ambiguous NOESY peaks, structure determination by nuclear magnetic resonance, structure validation and comparison of protein folds...
  12. ncbi request reprint [Expression of heme oxygenase-1 in rat prostate and effects of androgen and estrogen on it]
    Jian Tian
    Department of Physiology, Chengdu Military Medical College of Third Military University, Chengdu 610083, China
    Sichuan Da Xue Xue Bao Yi Xue Ban 34:234-7. 2003
    ..To investigate the influences of androgen and estrogen on expression of HO-1 gene in rat ventral prostate...
  13. ncbi request reprint NMR solution structure and dynamics of an exchangeable apolipoprotein, Locusta migratoria apolipophorin III
    Daping Fan
    Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901 4413, USA
    J Biol Chem 278:21212-20. 2003
    ..Finally, we compare the NMR structures of Manduca sexta apoLp-III and L. migratoria apoLp-III and present a united scheme for the structural basis of the reversible lipoprotein binding activity of apoLp-III...
  14. pmc Selection of restriction endonucleases using artificial cells
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 35:e83. 2007
    ..manalii. This method provides a unique tool for cloning restriction endonuclease genes and has many other potential applications...
  15. ncbi request reprint [Cloning of human brain-derived neurotrophin-6 gene and its expression in procaryotic cell]
    Chengwu Zhang
    Department of Physiology, School of Pre clinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041 P R China
    Zhonghua Yi Xue Yi Chuan Xue Za Zhi 19:475-8. 2002
    ..To clone human brain-derived neurotrophin-6(NT-6) gene and to observe its expression in the procaryotic cell...