Research Topics
Genomes and Genes | Yu ZhengSummaryAffiliation: Boston University Country: USA Publications
| Collaborators
|
Detail Information
Publications
Phylogenetic detection of conserved gene clusters in microbial genomesYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, MA, USA
BMC Bioinformatics 6:243. 2005....- 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... - 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... - 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 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... - 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... - 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... - 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... - 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
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... 
STARS: statistics on inter-atomic distances and torsion angles in protein secondary structuresYu Zheng
Department of Biological Sciences and Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543
Bioinformatics 21:2925-6. 2005..AVAILABILITY: All data, documents and execute files are freely downloadable at http://stars.zhengyuhome.com. The software works appropriately on Windows system, without any compilation or installation. CONTACT: ...- [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... - 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... - 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... - [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...