Publications

Publications

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YearTitleJournalAuthorsApplication(s)
2011Site-specific protein labeling by intein-mediated protein ligation.Methods Mol.Biol.Ghosh, I., Considine, N., Maunus, E., Sun, L., Zhang, A., Buswell, J., Evans, T.C.Jr.and Xu, M.Q.
2011T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis.BMC Biotechnol.Viollet, S., Fuchs, R.T., Munafo, D.B., Zhuang, F.and Robb, G.B.
2011Activity, specificity and structure of I-Bth03051: a representative of a new homing endonuclease familyTaylor, G.K., Heiter, D.F., Pietrokovski, S. and Stoddard, B.L.
2011Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.Nucl.Acids.Res.Vanamee, E.S., Viadiu, H., Chan, S.H., Ummat, A., Hartline, A.M., Xu, S.Y.and Aggarwal, A.K.
2011Biochemical Characterization of a Structure-Specific Resolving Enzyme from Sulfolobus Islandicus Rod-Shaped Virus 2.PLoS ONEGardner, A.F., Guan, C.and Jack, W.E.
2011A set of aspartyl protease-deficient strains for improved expression of heterologous proteins in Kluyveromyces lactis.FEMS Yeast Res.Ganatra, M.B., Vainauskus, S., Hong, J.M., Taylor, T.E., Denson, J.P., Esposito, D., Read, J.D., Schmeisser, H., Zoon, K.C., Hartley, J.L.and Taron, C.H.
2011A SNAP-tagged detivative of HIV-1 - A versatile tool to study virus-cell interactionsPLoS One Eckhardt, M. et al.
2011A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp.aureus USA300.Nucl.Acids.Res.Xu, S.Y., Corvaglia, A.R., Chan, S.H., Zheng, Y.and Linder, P.
2011Branched Intermediate Formation is the Slowest Step in th Protein Splicing Reaction of the Ala1 KbA Intein from Methanococcus jannaschiiSaleh, L., Southworth, M.W., Considine, N., O'Neill, C., Benner, J., Bollinger, J.M. and Perler, F.B.
2011Characterization of Sulfolobus islandicus rod-shaped virus 2 gp19, a single-strand specific endonuclease.ExtremophilesGardner, A.F., Prangishvili, D.and Jack.W.E.
2011Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq Genome Res. Saiful, I., Kjällquist, U., Moliner, A. et al
2011Characterization of Type II and III restriction modification systems from Bacillus cereus strains J. Bacteriol.Xu, S.Y., Nugent, R.L., Kasamkattil, J., Fomenkov, A., Gupta, Y., Aggarwal, A., Wang, X., Li, Z., Zheng, Y. and Morgan, R.
2011C.elegans galectins LEC-6 and LEC-10 interact with similar glycoconjugates in the intestine.J Biol Chem.Maduzia, L.L., Yu, E.and Zhang, Y.
2011Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI.Nucl.Acids.Res.Shen, B.W., Xu, D., Chan, S.H., Zheng, Y., Zhu, Z., Xu, S.Y.and Stoddard, B.L.
2011Characterization of MspNI (G/GWCC) and MspNII (R/GATCY), novel thermostable Type II restriction endonucleases from Meiothermus sp., isoschizomers of AvaII and BstYIMol Biol Rep.Gupta, R., Xu, S.Y., Sharma, P. and Capalash, N.
20116-Thioguanine reactivates epigenetically silenced genes in acute lymphoblastic leukemia cells by facilitating proteasome-mediated degradation of DNMT1Canc. Res.
2011A highly controllable reconstituted cell-free system--a breakthrough in protein synthesis researchCurr. Pharm. Biotechnol.Ohashi, H., Kanamori, T., Shimizu, Y. and Ueda, T.
2011A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability.Nat Struct Mol Biol.Estève, P.O., Chang, Y., Samaranayake, M., Upadhyay, A.K., Horton, J.R., Feehery, G.R., Cheng, X.and Pradhan, S.
20115-aza-2'-deoxycytidine and interleukin-1 cooperate to regulate matrix metalloproteinase-3 gene expression.Int.J.CancerCouillard, J., Estève, P.O., Pradhan, S.and St-Pierre, Y.
20115-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cellsGen. Biol.Stroud, H., et al.
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.
2011A peptide to dimerized translationally controlled tumor protein modulates allergic reactionsJ. Mol. Med.Kim, M.
2011 A reporter system for assaying influenza virus RNP functionality based on secreted Gaussia luciferase activity Virology J. Zhu, W. et al.
2011A set of aspartyl protease-deficient strains for improved expression of heterologous proteins in Kluyveromyces lactisFEMS Yeast Res.Ganatra, M.B., Rainauskas, S., Hong, J.M., Taylor, T.E., Denson, J.P.M., Esposito, D., Read, J.D., Schmeisser, H., Zoon, K.C., Hartley, J.L. and Taron, C.H.
2011A set of aspartyl protease-deficient strains for improved expression of heterologous proteins in Kluyveromyces lactisFEMS Yeast Res.Ganatra, M.B., Rainauskas, S., Hong J.M., Taylor, T.E., Denson, J.P.M., Esposito, D., Read, J.D., Schmeisser, H., Zoon, K.C., Hartley, J.L. and Taron, C.H.
2011A phage-targeting startegy for the design of spatiotemporal drug delivery from grafted matricesFibrogenesis Tissue RepairSawada, R. et al.
2011A piggyBac transposon-based mutagenesis system for the fission yeast Schizosaccharomyces pombe  Nuc. Acids Res. Li, J., Zhang, J.-M., Li, X. et al
2011A Radically Different Mechanism for S-Adenosylmethionine-Dependent Methyltransferases.Science ExpressGrove, T.L., Benner, J.S., Radle, M.I., Ahlum, J.H., Landgraf, B.J., Krebs, C.and Booker, S.J.
2011Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiationNature Ficz, G., et al.
2011Efficient in vivo selection of a novel tumor-associated peptide from a phage displayMoleculesVeleva, A.N. et al.
2011EndonucleasesCurr Protoc Mol BiolNichols, N.M.
2011Disruption of PMR1 in Kluyveromyces lactis improves secretion of calf prochymosinJ. Sci. Food Agric.Feng, Z., et al.
2011DNA LigasesCurr Protoc Mol BiolLohman, G.J., Tabor, S., Nichols, N.M.
2011 Docking-dependent ubiquitination of the interferon regulatory factor-1 tumor suppressor protein by the ubiquitin ligase CHIP J. Biol. Chem. Narayan, V., Pion, E., Landré, V., Müller, P. and Ball, K.L.
2011Engineering a waste management enzyme to overcome cancer resistance to apoptosis: adding DNase1 to the anti-cancer toolbox Cancer Gene Ther. Rosner, K., Kasprzak, M.F., Horenstein, A.C., Thurston, H.L., Abrams, J., Kerwin, L.Y., Mehregan, D.A. and Mehregan, D.R.
2011Expanding the definition of class 3 inteins and their proposed phage origin.J.Bacteriol.Tori, K.and Perler, F.B.
2011Expanding the genetic code of Escherichia coli with PhosphoserineSciencePark, H.S., Hohn, M.J., Umehara, T., Guo. L.T., Osborne, E.M., Benner, J., Noren, C.J., Rinehart, J. and Soll, D.
2011Expression of heparin sulfate sulfotransferases in Kluyveromyces lactisand preparation of PAPSGlycobiology Advance AccessZhou, X., et al.
2011Engineering BL21(DE3) derivative strains to minimize Escherichia coli protein contamination after IMAC purification.Appl. Environ. Microbiol.Robichon, C., Luo, J., Causey, T.B., Benner, J.S. and Samuelson, J.C.
2011Engineering BL21(DE3) derivative strains to minimize Escherichia coli protein contamination after IMAC purification.Appl.Environ.Microbiol.Robichon, C., Luo, J., Causey, T.B., Benner, J.S.and Samuelson, J.C.
2011ExonucleasesCurr.Protoc.Mol.Biol.McReynolds, L.A.and Nichols, N.M.
2011COMBREX – COMputational BRidges to EXperiments.Biochem.Soc.Trans.Roberts, R.J.
2011COMBREX: a project to accelerate the functional annotation of prokaryotic genomesNucleic Acids Res.Roberts, R.J., Chang, Y.C., Hu, Z., Rachlin, J.N., Anton, B.P., Pokrzywa, R.M., Choi, H.P., Faller, L.L., Guleria, J., Housman, G., Klitgord, N., Mazumdar, V., McGettrick, M.G., Osmani, L., Swaminathan, R., Tao, K.R., Letovsky, S., Vitkup, D., Segre, D., Salzberg, S.L., Delisi, C., Steffen, M. and Kasif, S.,
2011Comparative characterization of the PvuRts1I family and application in mapping genomic 5-hydroxymethylcytosine.Nucl.Acids Res.Wang, H., Guan, S., Quimby, A., Cohen-Karni, D., Pradhan, S., Wilson, G.G., Roberts, R.J., Zhu, Z.and Zheng, Y.
2011Chemical Modification of Proteins in Living CellsMethods in Protein ChemistryHanek, A.; Corrêa, I. R., Jr.
2011Chitosan but not chitin activates the inflammasome by a mechanism dependent upon phagocytosis.J Biol Chem.Bueter, C.L., Lee, C.K., Rathinam, V.A., Healy, G.J., Taron, C.H., Specht, C.A.and Levitz, S.M.
2011Cleavage of a model DNA replication fork by a methyl-specific endonuclease.Nucl.Acids.Res.Ishikawa, K., Handa, N.Sears, L., Raleigh, E.A.and Kobayashi, I.
2011Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosineNucleic Acids ResWang H, Guan S, Quimby A, Cohen-Karni D, Pradhan S, Wilson G, Roberts RJ, Zhu Z, Zheng 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.
2011Decoding a Substantial Set of Samples in Parallel by Massive SequencingPLoS ONE  Neiman, M., Lundin, S., Savolainen, P., Ahmadian, A.