Publications

Publications

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YearTitleJournalAuthorsApplication(s)
2007An improved and secreted luciferase reporter for schistosomes.Mol. Biochem. Parasitol.Cheng, G. and Davis, R.E.
2007An improved and secreted luciferase reporter for schistosomes  Mol. Biochem. Parasitol. Cheng, G. and Davis, R.E.
2007In vivo translation and stability of trans-spliced mRNAs in nematode embryos.Mol. Biochem. Parasitol.Cheng, G., Cohen, L., Mikhli, C, Jankowska-Anyszka, M., Stepinski, J., Darzynkiewicz, E. and Davis, R.E
2007In vivo translation and stability of trans-spliced mRNAs in nematode embryosMol. Biochem. Parasitol. Cheng, G., Cohen, L., Mikhli, C., Jankowska-Anyszka, M., Stepinski, J., Darzynkiewicz, E. and Davis, R.E.
1994Structure of PvuII endonuclease with cognate DNA.EMBO J.Cheng, X., Balendiran, K., Schildkraut, I., and Anderson, J.E.
1995Crystal structure of the PvuII restriction endonuclease.GeneCheng, X., Balendiran, K., Schildkraut, I., and Anderson, J.E.
1993Crystal Structure of the HhaI DNA Methyltransferase.Cheng, X., Kumar, S., Klimasauskas, S., and Roberts, R.J.
1993Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.CellCheng, X., Kumar, S., Posfai, J., Pflugrath, J.W., and Roberts, R.J.
2001AdoMet-dependent methylation, DNA methyltransferases and base flipping.Nucl.Acids Res.Cheng, X.and Roberts, R.J.
2010Base Flipping.Encyclopedia of Life SciencesCheng, X.and Roberts, R.J.
2014Traceless splicing enabled by substrate induced activation of the Nostoc punctiforme Npu DnaE intein after mutation of a catalytic cystein to serineJ Mol Biol.Cheriyan, M., Chan, S-H., Perler, F.
2013Faster Protein Splicing with the Nostoc punctiforme DnaE Intein Using Non-native Extein ResiduesJ Biol ChemCheriyan, M., Pedamallu, C.S., Tori, K. and Perler, F.
2009Protein Splicing: A Versatile Tool for Drug Discovery.Adv.Drug Deliv.Rev.Cheriyan, M.and Perler, F.B.
2015Depletion of CG-Specific Methylation in Mycoplasma hyorhinis Genomic DNA after Host Cell InvasionPLoS OneChernov AV., Reyes L., Peterson S., Strongin AY.Epigenetics, Bisulfite Conversion
2008 A designed protein for the specific and covalent heteroconjugation of biomolecules Bioconj. Chem. Chidley C. et al.
2007Automethylation of G9a and its implication in wider substrate specificity and HP1 binding.Nucl.Acids.Res.Chin, H.G., Esteve, P.O., Pradhan, M., Benner, J., Patnaik, D., Carey, M.F., and Pradhan, S.
2003Protein trans-splicing in transgenic plant chloroplast: Reconstruction of herbicide resistance from split genes.Proc.Natl.Acad.Sci.USA Chin, H.G., Kim, G.D., Marin, I., Mersha, F., Evans, T.C.Jr., Chen, L., Xu, M.-Q.and Pradhan, S.
2006Catalytic properties and kinetic mechanism of human recombinant Lys-9 histone H3 methyltransferase SUV39H1: participation of the chromodomain in enzymatic catalysis.BiochemistryChin, H.G., Patnaik, D., Esteve, P.O., Jacobsen, S.E.and Pradhan.S.
2016Transcription factor LSF-DNMT1 complex dissociation by FQI1 leads to aberrant DNA methylation and gene expression.OncotargetChin, H.G., Ponnaluri, C., Zhang, G., Esteve, P., Schaus, S.E., Hansen, U. and Pradhan, S.
2005Sequence Specificity and Role of Proximal Amino Acids of the Histone H3 Tail on Catalysis of Murine G9a Lysine 9 Histone H3 Methyltransferase.BiochemistryChin, H.G., Pradhan, M., Esteve, P., Patnaik, D., Evans, T.C.Jr.and Pradhan, S.
2014Neurospora crassa Female Development Requires the PACC and Other Signal Transduction Pathways, Transcription Factors, Chromatin Remodeling, Cell-To-Cell Fusion, and AutophagyPLoS OneChinnici JL, Fu C, Caccamise LM, Arnold JW, Free SJGibson Assembly®,
2013Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori.PLOS ONE Choi HP, Juarez S, Ciordia S, Fernandez M, Bargiela R, Albar JP, Mazumdar V, Anton BP, Kasif S, Ferrer M, Steffen M.
2014Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applicationsCurr Protoc Mol BiolChong S
1997Protein Splicing of the Saccharomyces cerevisiae VMA Intein without the Endonuclease Motifs*.J Biol.Chem.Chong, S., and Xu, M.Q.
1997Single-column purification of free recombinant proteins using a self-cleavable affinity tag derived from a protein splicing element.GeneChong, S., Mersha, F.B., Comb, D.G., Scott, M.E., Landry, D., Vence, L.M., Perler, F.B., Benner, J., Kucera, R.B., Hirvonen, C.A., Pelletier, J.J., Paulus, H., and Xu, M.Q.
1998Utilizing the C-terminal cleavage activity of a protein splicing element to purify recombinant proteins in a single chromatographic step.Nucl.Acids Res.Chong, S., Montello, G.E., Zhang, A., Cantor, E.J., Liao, W., Xu, M.-Q.and Benner, J.
1996Protein splicing involving the Saccharomyces cerevisiae VMA intein.The steps in the splicing pathway, side reactions leading to protein cleavage, and establishment of an in vitro splicing system.J.Biol.Chem.Chong, S., Shao, Y., Paulus, H., Benner, J., Perler, F.B., and Xu, M.Q.
1998Modulation of protein splicing of the saccharomyces cerevisiae vacuolar membrane ATPase intein.J.Biol.Chem.Chong, S., Williams, K.S., Wotkowicz, C.and Xu, M.Q.
2003Intein-mediated Protein PurificationMethods and Tools in Biosciences and MedicineChong, S.and Perler, F.B.
2005Harnessing Inteins for Protein Purification and Characterization.Nucleic Acids and Molecular Biology Chong, S.and Xu.M.Q.
1984DNA modification methylases: New uses in the manipulation of DNA.BioTechniquesChrist, C., and Nelson, M.
2015Selective expression of sense and antisense transcripts of the sushi-ichi-related retrotransposon - derived family during mouse placentogenesis.RetrovirologyChristine Henke, Pamela L Strissel, Maria-Theresa Schubert, Megan Mitchell, Claus C Stolt, Florian Faschingbauer, Matthias W Beckmann, Reiner StrickHigh-Fidelity PCR
2017Complete genome sequence of Kluyveromyces lactis strain GG799, a common yeast host for heterologous protein expressionGenome AnnouncementsChuzel, L., Ganatra, M.B., Schermerhorn, K.M., Gardner, A.F., Anton, B.P., Taron, C.H.
2013Targeted delivery of proapoptotic peptides to tumor-associated macrophages improves survivalProc. Natl. Acad. Sci. Cieslewicz, M. et alPhage Display
2005N-Glycans of Caenorhabditis elegans are specific to developmental stagesJ. Biol. Chem. Cipollo, J.F., Awad, A.M., Costello, C.E., Hirschberg, C.B.
2010Lighting up multiprotein complexes: lessons from GPCR oligomerizationTrends Biotechnol Ciruela F. et al.
2012Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencingNucl. Acids Res.Clark, T.A., Murray, I.A., Morgan, R.D., Kislyuk, A.O., Spittle, K.E., Boitano, M., Fomenkov, A., Roberts, R.J. and Korlach, J.
2013Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencingNucleic Acids ResearchClark, T.A., Murray, I.A., Morgan, R.D., Kislyuk, A.O., Spittle, K.E., Boitano, M., Fomenkov, A., Roberts, R.J. and Korlach, J.
2011The MspJI family of modification-dependent restriction endonucleases for epigenetic studiesProc. Natl. Acad. Sci. Cohen-Karni, D, et al.
2011The MspJI family of modification-dependent restriction endonucleases for epigenetic studies.Proc.Natl.Acad.Sci.Cohen-Karni, D., Xu, D., Apone, L., Formenkov, A., Sun, Z., Davis, P.J., Morey Kinney, S.R., Yamada-Mabuchi, M., Xu, S.-y., Davis, T., Pradhan, S.Roberts, R.J., Zheng, Y.
2008Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.NatureCokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M.and Jacobsen, S.E.
1990The identification of an Onchocerca-specific recombinant antigen containing a T cell epitope.J Immunol.Colina, K.F., Perler, F.B., Matsumura, I., Meda, M., and Nutman, T.B.
2010Cloning the human vitamin D receptor into the pTwin-1 expression vectorJ Steroid Biochem Mol BiolCollins, E. D., et. al.
2005Kluyveromyces lactis LAC4 promoter variants that lack function in bacteria but retain full function in K. lactisAppl. Environ. Microbiol.Colussi, P.A. and Taron, C.H.
2005Characterization of a nucleus-encoded chitinase from the yeast Kluyveromyces lactisAppl. Environ. Microbiol.Colussi, P.A., Specht, C.A. and Taron, C.H.
2005Characterization of a Nucleus-Encoded Chitinase from the Yeast Kluyveromyces lactis.Appl.Environ.Microbiol.Colussi, P.A., Specht, C.A.and Taron, C.H.
2005Kluyveromyces lactis LAC4 Promoter Variants That Lack Function in Bacteria but Retain Full Function in K.lactis.Appl.Environ.Microbiol.Colussi, P.A.and Taron, C.H.
2015Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.Mol Phylogenet Evol. Combosch DJ, Vollmer SV.
2014PCR amplification of a triple-repeat genetic target directly from whole blood in 15 minutes as a proof-of-principle PCR study for direct sample analysis for a clinically relevant targetBMC Med GenetConnelly CM1, Porter LR2, TerMaat JR
1997Jak1 kinase is required for cell migrations and anterior specification in zebrafish embryos.Proc.Natl.Acad.Sci.USA Conway, G., Margoliath, A., Wong-Madden, S., Roberts, R.J., and Gilbert, W.
1995Photochemically initiated protein splicing.Angew.Chem.Int.Ed.Engl.Cook, S.N., Jack, W.E., Xiong, X., Danley, L.E., Ellman, J.A., Shultz, P.G., and Noren, C.J.
2017DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureusNucl. Acids Res.Cooper, L.P., Roberts, G.A., White, J.H., Luyten, Y.A., Bower, E.K., Morgan, R.D., Roberts, R.J., Lindsay, J.A., Dryden, D.T.
2009Fluorescence in living systems: applications in chemical biology Wiley Encyc. of Chem. Biol. Cornish, V. W.
2014Live-cell reporters for fluorescence imagingCurr Opin Chem BiolCorrêa IR Jr.
2011Tuning different expression parameters to achieve soluble recombinant proteins in E. coli: Advantages of high-throughput screeningBiotechnology JournalCorrea, A. and Oppezzo, P.
2015Considerations and protocols for the synthesis of custom protein labeling probesMetholds Mol BiolCorrea, I.R. Jr.
2014Complementation of essential yeast GPI mannosyltransferase mutations suggests a novel specificity for certain Trypanosoma and Plasmodium PigB proteinsPLoS OneCortes, L.K., Scarcelli, J.J., Taron, C.H.
2000Generation of a dual-labeled fluorescence biosensor for Crk-II phosphorylation using solid-phase expressed protein ligationChem. BiolCotton, G.J. and Muir, T.W.
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.
2005Live chemical reports from the cell surfaceChem. Biol. Cravatt B.F.
1991Application of a novel chemiluminescence-based DNA detection method to single-vector and multiplex DNA sequencing.BioTechniquesCreasey, A., D'Angio, L., Dunne, T.S., Kissinger, C., O'Keefe, T., Perry-O'Keefe, H., Moran, L.S., Roskey, M., Schildkraut, I.and Sears, L.E.
2002Dirofilaria immitis encodes Di-nhr-7, a putative orthologue of the Drosophila ecdysone-regulated E78 gene.Mol.Biochem.Parasitol.Crossgrove, K., Laudet, V.and Maina, C.V.
2008Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis.Mol.Biochem.Parasitol.Crossgrove, K., Maina, C.V., Robinson-Rechavi, M.and Lochner, M.C.
2014Cofactor-Independent Phosphoglycerate Mutase from Nematodes Has Limited Druggability, as Revealed by Two High-Throughput ScreensPLoS Negl Trop Dis.Crowther, G.J., Booker, M.L., He, M., Li, T., Raverdy, S., Novelli, J.F., He, P., Dale, N.R.G., Fife, A.M., Barker, R.H., Jr., Kramer, M.L., Van Voorhis, W.C., Carlow, C.K.S. and Wang, M-W.
2016A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders.Sci RepCui, N., Zhang, H., Schneider, N., Tao, Y., Asahara, H., Sun, Z., Cai, Y., Koehler, S.A., de Greef, T.F., Abbaspourrad, A., Weitz, D.A. and Chong, S.
1999Purification and crystallization of precursors and autoprocessed enzymes of Flavobacterium glycosylasparaginase: an N-terminal nucleophile hydrolase.Acta Crystallogr.D.Biol.Crystallogr.Cui, T., Liao, P.H., Guan, C.and Guo, H.C.
2014SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolutionProtein Eng Des SelCurrin A, Swainston N, Day PJ, Kell DB
2013Evaluation of UDP-GlcN Derivatives for Selective Labeling of 5-(Hydroxymethyl)cytosineChembiochemDai N, Bitinaite J, Chin HG, Pradhan S, Corrêa IR Jr.
2002 Towards the generation of artificial O6-alkylguanine-DNA alkyltransferases: in vitro selection of antibodies with reactive cysteine residuesChemBioChem Damoiseaux, R. et al
2003Semisynthesis and application of carboxyfluorescein-labelled biologically active human interleukin-8Biol. Chem.David, R., et al.
2011High sensitivity 4-hydroxymethylcytosine detection in Balb/C brain tissue.J Vis Exp.Davis, T.and Vaisvila, R.
2009Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coliMicrobial Cell Factoriesde Marco, A.
2011Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinantsNucleic Acids Res. De Masi, F., Grove, C.A., Vedenko, A., Alibés, A., Gisselbrecht, S.S., Serrano, L., Bulyk, M.L. and Walhout, A.J.
2016Complete genome sequence of Brevibacterium linens SMQ-1335.Genome AnnouncementsDe Melo, A., Labrie, S., Dumaresq, J., Roberts, R., Tremblay, D. and Moineau, S.
2009HTRF: A technology tailored for drug discovery - a review of theoretical aspects and recent applications Curr. Chem. Genomics Degorce F. et al.
2010Targeted photoswitchable probe for nanoscopy of biological structures ChemBioChem Dellagiacoma, C. et al.
2006Profluorescent protein fragments for fast bimolecular fluorescence complementation in vitroNat. Protoc.Demidov, V.V., and Broude, N.E.
2015Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles.PLoS One. Demos TC, Kerbis Peterhans JC, Joseph TA, Robinson JD, Agwanda B, Hickerson MJ.
2005Sau421, a Bcgl-like restriction-modification system encoded by the Staphylococcus aureus quadruple-converting phage phi 42MicrobiologyDempsey, R.M., Carroll, D., Kong, H.M., Higgins, L., Keane, C.T., Coleman, D.C.
2017Highly specific imaging of mRNA in single cells by target RNA-initiated rolling circle amplificationChem SciDeng, Ruijie., Zhang, Kaixiang., Sun, Yupeng., Ren, Xiaojun., Li, Jinghong.
2007 Intein-mediated expression is an effective approach in the study of beta-defensinsBiochem Biophys Res CommunDiao, H., et. al.
2016RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas.Mol Phylogenet Evol.Díaz-Arce N, Arrizabalaga H, Murua H, Irigoien X, Rodríguez-Ezpeleta N.
2013Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systemsNucleic Acids ResDiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GMGibson Assembly®
2011Genome-wide mapping of the sixth baseGenome Biol. Diep, D. and Zhang, K.
1988Genetic dissection of the methylcytosine-specific restriction system mcrB of Escherichia coli K-12.GeneDila, D., and Raleigh, E.A.
1990Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12.J.Bacteriol.Dila, D., Sutherland, E., Moran, L., Slatko, B., and Raleigh, E.A.
2009A genomescale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity Cell Stem Cell Ding, L., Paszkowski-Rogacz, M., Nitzsche, A., Slabicki, M.M., Heninger, A.K., de Vries, I., Kittler, R., Junqueira, M., Shevchenko, A., Schulz, H., Hubner, N., Doss, M.X., Sachinidis, A., Hescheler, J., Iacone, R., Anastassiadis, K., Stewart, A.F., Pisabarro, M.T., Caldarelli, A., Poser, I., Theis, M. and Buchholz, F.
2009A genome-scale RNAi screen for Oct4 modulators defines a role of the Pafl complex for embryonic stem cell identity.Cell Stem CellDing, L., Paszkowski-Rogacz, M., Nitzsche, A., Slabicki, M.M., Heninger, A.K., de Vries, I., Kittler, R., Junqueira, M., Shevchenko, A., Schulz, H., Hubner, N., Doss, M.X., Sachinidis, A., Hescheler, J., Iacone, R., Anastassiadis, K., Stewart, A.F., Pisabarro, M.T., Caldarelli. A.. Poser, I., Theis, M. and Buchholz, F
2008Mediator links epigenetic silencing of neuronal gene expression with X-linked mental retardation.Mol.CellDing, N., Zhou, H., Esteve, P.O., Chin, H.G., Kim, S., Xu, X., Joseph, S.M., Friez, M.J., Schwartz, C.E., Pradhan, S.and Boyer, T.G.
2003Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing.J.Biol.Chem.Ding, Y., Xu, M.-Q., Ghosh, I., Chen, X., Ferrandon, S., Lesage, G., Rao, Z.
1995Differential recognition of microfilarial chitinase, a transmission-blocking vaccine candidate antigen, by sera from patients with Brigian and Bancroftian filariasis.Am.J.Trop.Med.Hyg.Dissanayake, S., Perler, F.B., Xu, M., Southworth, M.W., Yee, C.K., Wang, S., Dreyer, G., Watawana, L., Kurniawan, L., Fuhrman, J.A., and Piessens, W.F.
2006Cofactor-independent Phosphoglycerate Mutase is an essential gene in procyclic form Trypanosoma brucei.Parasitol.Res.Djikeng, A., Raverdy, S., Foster, J., Bartholomeu, D., Zhang, Y., El-Sayed, N.and Carlow, C.
2007Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei.J of Biological ChemistryDjikeng, A., Raverdy, S., Foster, J., Bartholomeu, D., Zhang, Y., El-Sayed, N.and Carlow, C.
2016Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.Genome MedicineDoan, T. et al.
2015Clinical Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of Neisseria meningitidis in Cerebrospinal Fluid.PLoS OneDoKyung Lee, Eun Jin Kim, Paul E Kilgore, Soon Ae Kim, Hideyuki Takahashi, Makoto Ohnishi, Dang Duc Anh, Bai Qing Dong, Jung Soo Kim, Jun Tomono, Shigehiko Miyamoto, Tsugunori Notomi, Dong Wook Kim, Mitsuko SekiIsothermal Amplification
2014Consequences of the disease-related L78R mutation for dimerization and activity of STAT3J Cell SciDomoszlai T, Martincuks A, Fahrenkamp D, Schmitz-Van de Leur H, Küster A, Müller-Newen GSNAP Cell, Cellular Analysis
2004Structure of the Q237W mutant of HhaI DNA methyltransferase: An insight into protein-protein interactions.Biol.Chem.Dong, A., Zhou, L., Zhang, X., Stickel, S., Roberts, R.J.and Cheng, X.
2009Characterization and subcellular localization of bacterial flotillin homologueMicrobiology Donovan C. et al.
1994Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease.Nucl.Acids.Res.Dorner, L.F., and Schildkraut, I.
1999Genetic Analysis of the Base-specific Contacts of BamHI Restriction Endonuclease.J.Mol.Biol.Dorner, L.F., Bitinaite, J., Whitaker, R.D.and Schildkraut, I.