Publications

Publications

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YearTitleJournalAuthorsApplication(s)
1998The Maltoxe-Binding Protein as a Scaffold for Monovalent Display of Peptides Derived from Phage Libraries.Anal.Biochem.Zwick, M.B., Bonnycastle, L.L.C., Noren, K.A., Venturini, S., Leong, E., Barbas, C.F., Noren, C.J.and Scott, J.K.
2003Phosphorylation of eIF4E attenuates its interaction with mRNA 5' cap analogs by electrostatic repulsion: intein-mediated protein ligation strategy to obtain phosphorylated proteinRNAZuberek, J., et al.
2007Identification and evaluation of a new tumor cell-binding peptideJ. Nucl. Med.Zitzman, S. et al.
2008DNA damage in preserved specimens and tissue samples: a molecular assessment.Frontiers in Zoology Zimmermann, J., Hajibabaei, M., Blackburn, D.C., Hanken, J., Cantin, E., Posfai, J.and Evans, T.C.
2008Sialylation of beta1 integrins blocks cell adhesion to galectin-3 and protects cells against galectin-3-induced apoptosisJ. Biol. Chem. Zhuo, Y., Chammas, R., Bellis, S.L.
2014Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIIIProtein CellZhuo W, Lai X, Zhang L, Chan SH, Li F, Zhu Z, Yang M, Sun D
2012Structural bias in T4 RNA ligase-mediated 3'-adapter ligationNucleic Acids Res.Zhuang, F., Fuchs, R.T., Sun, Z., Zheng, Y. and Robb, G.B.
2012Review: Small RNA expression profiling by high-throughput sequencing: Implications of enzymatic manipulationJournal of Nucleic AcidsZhuang, F., Fuchs, R.T. and Robb, G.B.
2003Isolation of BsoBI restriction endonuclease variants with altered substrate specificity.J.Mol.Biol.Zhu, Z., Zhou, J., Friedman, A.M.and Xu, S.-Y.
2004Engineering Strand-specific DNA Nicking Enzymes fro the Type IIS Restriction Endonucleases BsaI, BsmBI and BsmAI.J.Mol.Biol.Zhu, Z., Samuelson, J.C., Zhou, J., Dore, A.and Xu, S.-Y.
2010Cloning of NruI and Sbo13I restriction and modification sstems in E.coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases.BMC Res NotesZhu, Z., Pedamallu, C.S., Fomenkov, A., Benner, J.and Xu, S.Y.
2014Characterization of cleavage intermediate and star sites of RM.Tth111II.Sci RepZhu, Z., Guan, S., Robinson, D., El Fezzazi, H., Quimby, A. and Xu, S-Y.
2011 A reporter system for assaying influenza virus RNP functionality based on secreted Gaussia luciferase activity Virology J. Zhu, W. et al.
2015An IL-27/NFIL3 signalling axis drives Tim-3 and IL-10 expression and T-cell dysfunctionNat Commun Zhu, C., Sakuishi, K., Xiao, S., Sun, Z., Zaghouani, S., Gu, G., Wang, C., Tan, D.J., Wu, C., Rangachari, M., Pertel, T., Jin, H.T., Ahmed, R., Anderson, A.C., Kuchroo, V.K.
2012Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components Nucleic Acids Res.Zhou, Y., Asahara, H. and Chong, S.
2011Expression of heparin sulfate sulfotransferases in Kluyveromyces lactisand preparation of PAPSGlycobiology Advance AccessZhou, X., et al.
2002Cloning, Expression and Immunization of the new antigen gene Sj-Ts4 of Schistosoma japonicum.Acta Biochimica et Biophysica Sinica Zhou, D.-M., Yi, X.-Y., Zeng, X.-F., Wang, M., Cai, C., Wang, Q.-L., Zhang, S.-K., McReynolds, L.
2007Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferasesACS Chemical Biology Zhou Z. et al.
2015High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing.PLoS One. Zhou Z, Liu S, Dong Y, Gao S, Chen Z, Jiang J, Yang A, Sun H, Guan X, Jiang B, Wang B.
2014Engineering Bacterial Transcription Regulation To Create a Synthetic in Vitro Two-Hybrid System for Protein Interaction AssaysJ Am Chem SocZhou Y, Asahara H, Schneider N, Dranchak P, Inglese J, Chong S
2002Endosomal localization and function of sortingProc. Natl. Acad. Sci. USAZhong, Q., et al.
2012Characterization of Transcription Factors That Regulate the Type IV Secretion System and Riboflavin Biosynthesis in Wolbachia and Brugia malayiPLoS OneZhiru, Li and Carlow, C.K.S.
2011Screening of specific binding peptide targeting blood vessel of human esophageal cancer in vivo in miceChin. Med. J. Zhi, M. et al.
2007Selection of restriction endonucleases using artificial cells.Nucl.Acids.Res.Zheng, Y.and Roberts, R.
2002Computational Identification of Operons in Microbial Genomes.Genome Res.Zheng, Y., Szustakowski, J.D., Fortnow, L., Roberts, R.J.and Kasif, S.
2002Genomic functional annotation using co-evolution profiles of gene clusters.Genome Biol.Zheng, Y., Roberts, R.J.and Kasif, S.
2005Characterization of Two New Aminopeptidases in Escherichia coli.BMC BioinformaticsZheng, Y., Roberts, R.J., Kasif, S.and Guan, C.
2004Segmentally Variable Genes: A new perspective on adaptation.PLoS BiologyZheng, Y., Roberts, R.J., and Kasif, S.
2009Using shotgun sequence data to find active restriction enzyme genesNuc. Acid. Res. Zheng, Y., Posfai, J., Morgan, R. D., Vincze, T., and Roberts, R.J.
2005Phylogenetic detection of conserved gene clusters in microbial genomes.BMC Bioinformatics Zheng, Y., Anton, B.P., Roberts, R.J.and Kasif, S.
2010A unique family of Mrr-like modification-dependent restriction endonucleasesNucl. Acids Res.Zheng, Y. et al.
2015TALEN-mediated targeting of HPV oncogenes ameliorates HPV-related cervical malignancy.J Clin InvestZheng Hu, Wencheng Ding, Da Zhu, Lan Yu, Xiaohui Jiang, Xiaoli Wang, Changlin Zhang, Liming Wang, Teng Ji, Dan Liu, Dan He, Xi Xia, Tao Zhu, Juncheng Wei, Peng Wu, Changyu Wang, Ling Xi, Qinglei Gao, Gang Chen, Rong Liu, Kezhen Li, Shuang Li, Shixuan Wang, Jianfeng Zhou, Ding Ma, Hui Wang Genome Editing
2011Simple and efficient synthesis of 5′ pre-adenylated DNA using thermostable RNA ligase.Nucl.Acids Res.Zhelkovsky, A.M.and McReynolds, L.A.
2012Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase - engineering a thermostable ATP independent enzymeBMC Mol Biol.Zhelkovsky, A.M. and McReynolds, L.A.
2008Purification of green fluorescent protein using a two-intein systemAppl. Microbiol. Biotechnol.Zhao, Z., et. al.
2008An efficient on-column expressed protein ligation strategy: application to segmental triple labeling of human apolipoprotein E3Protein Sci. Zhao, W. et al.
2010Isolation and initial application of a novel peptide that specifically recognizes the neural stem cells derived from rhesus monkey embryonic stem cellsJ. Biomol. Screen.Zhao, W. et al.
2010Novel peptide ligands that bind specifically to mouse embryonic stem cellsPeptidesZhao, S. et al.
2007Circumventing the heterogeneity and instability of human serum albumin-interferon-_2b fusion protein by altering its orientationJ. Biotech. Zhao, H.L., et al.
2014Gene and protein sequence optimization for high-level production of fully active and aglycosylated lysostaphin in Pichia pastorisAppl Environ MicrobiolZhao H, Blazanovic K, Choi Y, Bailey-Kellogg C, Griswold KEGlycobiology
2014Boronic acid-mediated polymerase chain reaction for gene- and fragment-specific detection of 5-hydroxymethylcytosineNucleic Acids ResZhao C, Wang H, Zhao B, Li C, Yin R, Song M, Liu B, Liu Z, Jiang G
2003The role of C-terminal tyrosine phosphorylation in the regulation of SHP-1 explored via expressed protein ligationJ. Biol. Chem.Zhang, Z., et al.
2005The chitin synthase genes chs-1 and chs-2 are essential for C.elegans development and responsible for chitin deposition in the eggshell and pharynx, respectively.Dev.Biol.Zhang, Y., Foster, J.M., Nelson, L.S., Ma, D.and Carlow C.K.S.
2004Cofactor-independent Phosphoglycerate Mutase Has an Essential Role in Caenorhabditis elegans and Is Conserved in Parasitic Nematodes.J.Biol.Chem.Zhang, Y., Foster, J.M., Kumar, S., Fougere, M.and Carlow C.K.S.
2010Mutations in the Caenorhabditis elegans eIF2{beta} Permit Translation Initiation From Non-AUG Start Codons.GeneticsZhang, Y, Maduzia, L.L.
2010Transmembrane delivery and biological effect of human growth hormone via a phage displayed peptide in vivo and in vitroJ. Pharm. Sci.Zhang, T. et al.
2009Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.Protein Expr.Purif.Zhang, P., Too, P.H., Samuelson, J.C., Chan, S.H., Vincze, T., Doucette, S., Backstrom, S., Potamousis, K.D., Schramm, T.M., Forrest, D., Schwartz, D.C.and Xu, S.Y.
2007Rational design of a chimeric endonuclease targeted to NotI recognition site.Protein Eng Des Sel Zhang, P., Bao, Y., Higgins, L.and Xu, S-Y.
2011Cyclophosphamide Perturbs Cytosine Methylation in Jurkat-T Cells through LSD1-Mediated Stabilization of DNMT1 Protein.Chem.Res.Toxicol.Zhang, J., Yuan, B., Zhang, F., Xiong, L., Pradhan, S.and Wang, Y.
2011Cyclophosphamide perturbs cytosine methylation in jurkat-T Cells through LSD1-mediated stabilization of DNMT1 ProteinChem. Res. Toxicol.Zhang, J. et al.
2015Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylationNucleic Acids ResZhang, G., Esteve, P.O., Chin, H.G., Terragni, J., Dai, N., Correa, I.R. Jr. and Pradhan, S.
2015Mammalian DNA (cytosine-5) methyltransferase mechanisms and RNA-mediated inhibition for future therapies.Epigenetics Diagnostic TherapyZhang, G., Esteve, P.O., Chin, H.G. and Pradhan, S
2015Mammalian DNA (cytosine-5) methyltransferase mechanisms and RNA-mediated inhibition for future therapies.Epigenetics Diagnostic TherapyZhang, G., Esteve, P.O., Chin, H.G. and Pradhan, S
1993The M.AluI DNA-(cytosine C5)-methyltransferse has an unusually large, partially dispensable, variable region.Nucl.Acids Res.Zhang, B., Tao, T., Wilson, G.G., and Blumenthal, R.M.
2011Fluorescent site-specific labeling of Escherichia coli expressed proteins with Sfp phosphopantetheinyl transferaseMethods Mol.Biol.Zhang, A., Sun, L., Buswell, J., Considine, N., Ghosh, I., Masharina, A., Noren, C.and Xu, M.Q.
2001Construction of a mini-intein fusion system to allow both direct monitoring of soluble protein expression and rapid purification of target proteins.GeneZhang, A., Gonzales, S.M., Cantor, E.J.and Chong, S.
2005Productive interaction of chaperones with substrate protein domains allows correct folding of the downstream GFP domain.GeneZhang, A., Cantor, E.J., Barshevsky, T.and Chong, S.
2015High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers.DNA Res. Zhang Q, Liu C, Liu Y, VanBuren R, Yao X, Zhong C, Huang H.
2015Identification of a Conserved Linear B-Cell Epitope of Streptococcus dysgalactiae GapC Protein by Screening Phage-Displayed Random Peptide LibraryPLoS OneZhang L., Zhang H., Fan Z., Zhou X., Yu L., Sun H., Wu Z., Yu Y., Song B., Ma J., Tong C., Wang X., Zhu Z., Cui Y.
2010 Covalent quantum dot receptor linkage via the acyl carrier protein for single-molecule tracking, internalization, and trafficking studiesBioTechniques Zelman-Femiak, M. et al.
1989Use of Degenerate Oligonucleotides for Amplification of the nifH Gene from the Marine Cyanobacterium Trichodesmium thiebautii.Appl.Environ.Microbiol.,Zehr, J.P., and McReynolds, L.A.
2002Inhibition of poly(ADP-ribosyl)ation induces DNA hypermethylation: a possible molecular mechanism.FASEB J.Zardo, G., Reale, A., Passananti, C., Pradhan, S., Bountempo, S., DeMatteis, G., Adams, R.L.P.and Caiafa, P.
Identification of a cardiac specific protein transduction domain by in vivo biopanning using a M13 phage peptide display library in micePLoS OneZahid, M. et al.
2008Template-Independent DNA Polymerases.Curr.Protoc.Mol.Biol.Yue, D., Tabor, S.and Nichols, N.M.
2000One step purification of recombinant human Neurotrophic factor-3 with the splicing function of intein.Chin.J.Biochem.Mol.Biol.Yuan, J.M., Li, Z.Y., Wang, Y.M.and Xu., M.-Q.
20116-Thioguanine Reactivates Epigenetically Silenced Genes in Acute Lymphoblastic Leukemia Cells by Facilitating Proteasome-mediated Degradation of DNMT1Cancer Res.Yuan, B., Zhang, J., Wang, H., Xiong, L., Cai, Q., Wang, T., Jacobsen, S., Pradhan, S. andd Wang, Y.
2011High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing Nuc. Acids Res. Yuan, B., Wang, J., Cao, H. et al
2015The RpoE Stress Response Pathway Mediates Reduction of the Virulence of Enteropathogenic Escherichia coli by Zinc.Appl Environ MicrobiolYuan Xue, Jossef Osborn, Anand Panchal, Jay L MelliesHigh-Fidelity PCR
2010Gene synthesis of the bovine prochymosin gene and high-level expression in Kluyvermyces lactisSheng Wu Gong Cheng Xue BaoYuan W, et al.
2010Expressed protein ligation for the preparation of fusion proteins with cell penetrating peptides for endotoxin removal and intracellular deliveryBiochim Biophys Acta Yu, H. H., et. al.
2010Secretory production of recombinant proteins in Escherichia coliRecent Patents on BiotechnologyYoon, S.H., Kim, S.K., and Kim J.F.
2015Activation and enhancement of Fredericamycin A production in deepsea-derived Streptomyces somaliensis SCSIO ZH66 by using ribosome engineering and response surface methodology.Microb Cell FactYonghe Zhang, Huiming Huang, Shanshan Xu, Bo Wang, Jianhua Ju, Huarong Tan, Wenli LiHigh-Fidelity PCR
2014Structural basis for Klf4 recognition of methylated DNANucleic Acids ResearchYiwei Liu, Yusuf Olatunde Olanrewaju, Yu Zheng, Hideharu Hashimoto, Robert M. Blumenthal, Xing Zhang, Xiaodong Cheng
2005Co-translational involvement of the chaperonin GroEL in the folding of newly translated polypeptidesJ. Biol. Chem.Ying, B.W., Taguchi, H., Kondo, M. and Ueda, T.
2014A restriction enzyme-powered autonomous DNA walking machine: its application for a highly sensitive electrochemiluminescence assay of DNANanoscaleYing Chen, Yun Xiang, Ruo Yuan, Yaqin Chai
2005Labeling proteins with small molecules by site-specific posttranslational modificationJ Am Chem SocYin J. et al.
2005Single-cell FRET imaging of transferrin receptor trafficking dynamics by Sfp-catalyzed, site-specific protein labelingChem. Biol Yin J. et al.
2003Generation of the R2 subunit of ribonucleotide reductase by intein chemistry: insertion of 3-nitrotyrosine at residue 356 as a probe of the radical initiation process BiochemistryYee, C.S., et al.
2016Complete genome and methylome sequences of two SalmonellaGenome AnnouncementsYao, K., Muruvanda, T., Roberts, R.J., Payne, J., Allard, M.W., Hoffmann, M.
2016Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar Sloterdijk (ATCC 15791).Genome Announc.Yao, K., Muruvanda, T., Roberts, R.J., Payne, J., Allard, M.W. and Hoffmann, M.
2004Structural characterization and comparative phylogenetic analysis of E.coli HemK, a protein (N5)-glutamine methyltransferase.Mol.Microbiol.Yang, Z., Shipman, L., Zhang, M., Anton, B., Roberts, R.J.and Cheng, X.
2005Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.Nucl.Acids.Res.Yang, Z., Horton, J.R., Maunus, R., Wilson, G.G., Roberts, R.R.and Cheng, X.
2009The Kruppel-like zinc finger protein Glis3 directly and indirectly activates insulin gene transcriptionNucleic Acids Res.Yang, Y., Chang, B.H., Samson, S.L., Li, M.V., Chan, L.
2009The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).PLoS ONEYang, J.C., Madupu, R., Durkin, A.S., Ekborg, N.A., Pedamallu, C.S., Hostetler, J.B., Radune, D., Toms, B.S., Henrissat, B., Coutinho, P.M., Schwarz, S., Field, L., Trindade-Silva, A.E., Soares, C.A., Elshahawi, S., Hanora, A., Schmidt, E.W., Haygood, M.G., Posfai, J., Benner, J., Madinger, C., Nove, J., Anton, B., Chaudhary, K., Foster, J., Holman, A., Kumar, S., Lessard, P.A., Luyten, Y.A., Slatko, B., Wood, N., Wu, B., Teplitski, M., Mougous, J.D., Ward, N., Eisen, J.A., Badger, J.H.and Distel, D.L.
2015TonEBP modulates the protective effect of taurine in ischemia-induced cytotoxicity in cardiomyocytesCell Death Dis.Yang YJ, Han YY, Chen K, Zhang Y, Liu X, Li S, Wang KQ, Ge JB, Liu W, Zuo J.
2015Production of a Highly Protease-Resistant Fungal α-Galactosidase in Transgenic Maize Seeds for Simplified Feed ProcessingPLoS OneYang W., Zhang Y., Zhou X., Zhang W., Xu X., Chen R., Meng Q., Yuan J., Yang P., Yao B.
2016Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing.PLoS One. Yang H, Wei CL, Liu HW, Wu JL, Li ZG, Zhang L, Jian JB, Li YY, Tai YL, Zhang J, Zhang ZZ, Jiang CJ, Xia T, Wan XC.
2016Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants.Plant Methods. Yang GQ, Chen YM, Wang JP, Guo C, Zhao L, Wang XY, Guo Y, Li L, Li DZ, Guo ZH.
2012RNAi triggered by specialized machinery silences developmental genes and retrotransposonsNatureYamanaka, S., Mehta, S., Reyes-Turcu, F.E., Zhuang, F., Fuchs, R.T., Rong, Y., Robb, G.B. and Grewal, S.I.
2013RNAi triggered by specialized machinery silences developmental genes and retrotransposonsNatureYamanaka, S., Mehta, S., Reyes-Turcu, F.E., Zhuang, F., Fuchs, R.T., Rong, Y., Robb, G.B. and Grewal, S.I.
2011Identification of a chitin-induced small RNA that regulates translation of the tfoX gene, encoding a positive regulator of natural competence in Vibrio cholerae J Bacteriol. Yamamoto, S., Izumiya, H., Mitobe, J., Morita, M., Arakawa, E., Ohnishi, M. and Watanabe, H.
2015Iron-induced Local Complement Component 3 (C3) Up-regulation via Non-canonical Transforming Growth Factor (TGF)-β Signaling in the Retinal Pigment Epithelium.J Biol ChemYafeng Li, Delu Song, Ying Song, Liangliang Zhao, Natalie Wolkow, John W Tobias, Wenchao Song, Joshua L DunaiefHigh-Fidelity PCR, Site Directed Mutagenesis
2012Dual binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants.CellXuehua Zhong, X., Du, J., Bernatavichute, Y.V., Stroud, H., Feng, S., Caro, E., Vashisht, A.A., Chin, H.G., Terragni, J., Tu, A., Hetzel, J., Wohlschlegel, J.A., Pradhan, S., Patel, D.J. and Jacobsen, S.E.
2016Redox pathway sensing bile salts activates virulence gene expression in Vibrio cholerae.Mol Microbiol.Xue, Y., Tue, F., Shi, M., Wu, C.Q., Ren, G., Wang, X., Fang, W., Song, H. and Yang, M.
2001Engineering a Nicking Endonuclease N.AlwI by Domain SwappingProc.Natl.Acad.Sci.USA Xu, Y., Lunnen, K.and Kong, H.
2006Simultaneous amplification and screening of whole plasmids using the T7 bacteriophage replisome.Nucl.Acids.Res.Xu, Y., Kim, H-J., Kays, A., Rice, J.and Kong, H.
2015 Sequence-specific DNA nicking endonucleasesBiomol conceptsXu, S-Y
2007Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI.Nucl.Acids.Res.Xu, S.Y.,  Zhu, Z., Zhang, P., Chan, S.H., Samuelson, J., Xiao, J., Ingalls D.and Wilson, G.
1997Cloning of the BssHII restriction-modification system in Escherichia coli: BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs.Nucl.Acids Res.Xu, S.Y., Xiao, J.P., Posfai, J., Maunus, R., and Benner, J
1998Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI and SapI restriction-modification systems in Escherichia coliMol.Gen.Genet.Xu, S.Y., Xiao, Ettwiller L., holden, M., Aliotta, J., Poh, C.L., Dalton, M., Robinson, D.P., Petronzio, T.R., Moran, L., Ganatra, M., Ware, J., Slatko, B.and Benner, J.