Yu Zheng

Summary

Affiliation: New England Biolabs
Country: USA

Publications

  1. pmc Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine
    Hua Wang
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:9294-305. 2011
  2. 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
  3. 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
  4. 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
  5. pmc High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells
    Zhiyi Sun
    New England Biolabs Inc, 240 County Road, Ipswich, MA 01938, USA
    Cell Rep 3:567-76. 2013
  6. pmc Segmentally variable genes: a new perspective on adaptation
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    PLoS Biol 2:E81. 2004
  7. 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
  8. 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
  9. pmc Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes
    Jolyon Terragni
    New England Biolabs, Inc, Ipswich, Massachusetts 01938, United States
    Biochemistry 51:1009-19. 2012
  10. 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

Collaborators

Detail Information

Publications25

  1. pmc Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine
    Hua Wang
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:9294-305. 2011
    ..Our study offers unique tools for determining more accurate hydroxymethylomes in mammalian cells...
  2. 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...
  3. 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...
  4. 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...
  5. pmc High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells
    Zhiyi Sun
    New England Biolabs Inc, 240 County Road, Ipswich, MA 01938, USA
    Cell Rep 3:567-76. 2013
    ..We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or demethylation intermediate, whereas others may suggest a locally accessible chromosomal environment for the TET enzymatic apparatus...
  6. 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...
  7. 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
    ....
  8. 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...
  9. pmc Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes
    Jolyon Terragni
    New England Biolabs, Inc, Ipswich, Massachusetts 01938, United States
    Biochemistry 51:1009-19. 2012
    ..A comparison between cancer and healthy tissue genomes suggested a lower percentage of 5-hmC in cancer, which may reflect the global hypomethylation of 5-mC observed during oncogenesis...
  10. 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...
  11. pmc A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300
    Shuang yong Xu
    New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:5597-610. 2011
    ..aureus strain SA564, and in restricting phage λ infection when the endonuclease is expressed in E. coli...
  12. 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...
  13. pmc Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes
    Shannon Morey Kinney
    New England Biolabs, Inc, Ipswich, Massachusetts 01938, USA
    J Biol Chem 286:24685-93. 2011
    ..Finally, using a quantitative PCR approach, we established that a portion of VANGL1 and EGFR gene body methylation in human tissue DNA samples is indeed hydroxymethylation...
  14. 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...
  15. pmc Using shotgun sequence data to find active restriction enzyme genes
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 37:e1. 2009
    ..Active restriction enzyme genes have been identified, and their activity demonstrated biochemically, in the sequenced genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus...
  16. pmc Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579
    Shuang yong Xu
    New England Biolabs, Inc, Ipswich, Massachusetts, USA
    J Bacteriol 194:49-60. 2012
    ..A survey of type II and III restriction-modification (R-M) system genes is presented from sequenced B. cereus, Bacillus anthracis, and Bacillus thuringiensis strains...
  17. 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...
  18. pmc Structural basis for Klf4 recognition of methylated DNA
    Yiwei Liu
    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA and Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
    Nucleic Acids Res 42:4859-67. 2014
    ....
  19. pmc Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease
    John R Horton
    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
    Nucleic Acids Res 40:9763-73. 2012
    ..Both cleavage events require binding of at least a second recognition site either in cis or in trans...
  20. pmc Structural bias in T4 RNA ligase-mediated 3'-adapter ligation
    Fanglei Zhuang
    New England Biolabs Inc, Ipswich, MA 01938, USA
    Nucleic Acids Res 40:e54. 2012
    ..We propose that using randomized adapters may improve RNA representation in experiments that include a 3'-adapter ligation step...
  21. 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...
  22. 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...
  23. 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...
  24. ncbi request reprint [The expression and activity detection of a variant N protein of SARS-CoV]
    Yang Qi
    Department of Immunology, Institute of Infectious Diseases, 302th Hospital of PLA, Beijing 100039, China
    Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 20:422-4. 2004
    ..To construct an expression vector pGEX-2T/N, and to express the fusion protein consisting of N protein of SARS-CoV and GST in E.coli...
  25. 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...