Research Topics
| Yu ZhengSummaryAffiliation: New England Biolabs Country: USA Publications
| Collaborators
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Detail Information
Publications
Selection of restriction endonucleases using artificial cellsYu 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...
Characterization of two new aminopeptidases in Escherichia coliYu 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...- A unique family of Mrr-like modification-dependent restriction endonucleasesYu 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... - Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosineHua 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... - Segmentally variable genes: a new perspective on adaptationYu 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... - Phylogenetic detection of conserved gene clusters in microbial genomesYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, MA, USA
BMC Bioinformatics 6:243. 2005.... - Identification of genes with fast-evolving regions in microbial genomesYu 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... - Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomesJolyon 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... - The MspJI family of modification-dependent restriction endonucleases for epigenetic studiesDevora 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... - A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300Shuang 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... - Genomic functional annotation using co-evolution profiles of gene clustersYu 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... - Using shotgun sequence data to find active restriction enzyme genesYu 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... - Computational identification of operons in microbial genomesYu 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... - Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579Shuang 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... - Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomesShannon 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... - Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonucleaseJohn R Horton
Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 and New England Biolabs, Ipswich, MA 01938, 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... - Structural bias in T4 RNA ligase-mediated 3'-adapter ligationFanglei 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... - Whole-genome annotation by using evidence integration in functional-linkage networksUlas 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... - Discrimination of methylcytosine from hydroxymethylcytosine in DNA moleculesMeni Wanunu
Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States, New England Biolabs, Ipswich, Massachusetts 01938, United States, Department of Molecular Biology, Cellular Biology, and Biochemistry, Boston University, Boston, Massachusetts 02215, United States, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, 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... 
[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..CONCLUSION: The cloning of human brain-derived NT-6 gene provides a basis for further studying the structure, function and clinical application of NT-6...- NMR solution structure and dynamics of an exchangeable apolipoprotein, Locusta migratoria apolipophorin IIIDaping 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... - [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... - [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..01). Furthermore, estrogen could increase the level of HO-1 protein expression in prostatic stroma. CONCLUSION: Carbon monoxide-heme oxygenase system might be involved in the pathologic processes of prostatic abnormal proliferation...