Publications

Publications

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YearTitleJournalAuthorsApplication(s)
2012Drugs and targets to perturb the symbiosis of Wolbachia and filarial nematodesParasitic Helminths: Targets, Screens, Drugs and VaccinesTaylor, M.J., Ford, L, Ford, Hoerauf, A., Pfarr, K., Foster, J.M., Kumar, S. and Slatko, B.E.
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.
2004Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with Chromomethylase3.EMBO J.Lindroth, A.M., Shultis, D., Jasencakova, Z., Fuchs, J., Johnson, L., Scubert, D., Patnaik, D., Pradhan, S., Goodrich, J., Schubert, Il, Jenuwein, T., Khorasanizadeh, S.and Jacobsen, S.E
2007Dual-reporter assay using two secreted luciferase genes Biotechniques Wu, C., Suzuki-Ogoh, C. and Ohmiya, Y.
2007Dual-reporter assay using two secreted luciferase genesBiotechniquesWu, C., Suzuki-Ogoh, C., Ohmiya, Y.
2015Dynamic caveolae exclude bulk membrane proteins and are required for sorting of excess glycosphingolipidsNat CommunElena Shvets, Vassilis Bitsikas, Gillian Howard, Carsten Gram Hansen, Benjamin J NicholsSNAP Surface
2007Dynamic developmental elaboration of N-linked glycan complexity in the Drosophila melanogaster embryoJ. Biol. Chem. Aoki, K., Perlman, M., Lim, J.M., Cantu, R., Wells, L., Tiemeyer, M.
2011Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiationNature Ficz, G., et al.
2009E.coli RNase III(E38A) generates discrete-sized products from long dsRNA.RNAXiao, J., Feehery, C.E., Tzertzinis, G.and Maina, C.V.
1988EarI, a restriction endonuclease from Enterobacter aerogenes which recognizes 5'CTCTTC3'.Nucl.Acids Res.Polisson, C., and Morgan, R.D.
2009EcR-B1 and Usp nuclear hormone receptors regulate expression of the VM32E eggshell gene during Drosophila  oogenesis.Dev.Biol.Bernardi, F., Romani, P., Tzertzinis, G., Gargiulo, G.and Cavaliere V.
2009Educational Outreach - Discover the Microbes Within!BioTechniquesWeiner, M.P.and Slatko, B.(eds.)
2009Educational Outreach - Give Students a Taste for Molecular Biology and Tasting PTC: A New Lab with an Old Flavor.BioTechniquesWeiner, M.P.and Slatko, B.(eds.)
1999Effect of CWG methylation on expression of plant genes.Biochem J.Pradhan, S., Urwin, N.A., Jenkins, G.I.and Adams, R.L.
2009Effect of temperature-shift strategy on recombinat chymosin of Kluyveromyces LactisHeilongjiang Animal Science and Veterinary MedicineFeng, Z., et al
2012Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet.Proc. Natl. Acad. Sci. USAMalyshev, D.A., Dhami, K., Quach, H.T., Lavergne, T., Ordoukhanian, P., Torkamani, A. and Romesberg, F.E.
2013Efficient and specific gene knockdown by small interfering RNAs produced in bacteriaNat Biotechnol.Huang, L., Jin, J., Deighan, P., Liner, E., McReynolds, L. and Lieberman, J.
Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella
2014Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligaseNucleic Acids ResearchGregory J. S. Lohman, Yinhua Zhang, Alexander M. Zhelkovsky, Eric J. Cantor, Thomas C. Evans Jr.
2015Efficient expression of full-length antibodies in the cytoplasm of engineered bacteriaNat Commun.Robinson MP, Ke N, Lobstein J, Peterson C, Szkodny A, Mansell TJ, Tuckey C, Riggs PD, Colussi PA, Noren CJ, Taron CH, DeLisa MP, Berkmen M.
2015Efficient expression of full-length antibodies in the cytoplasm of engineered bacteriaNature Communications Robinson, M.-P., Ke, N., Lobstein, J., Peterson, C., Szkodny, A., Mansell, T.J., Tuckey, C., Riggs, P.D., Colussi, P.A., Noren, C.J., Taron, C.H., Delisa, M.P., Berkmen, M.
2013Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombinationNucleic Acids ResChen C, Fenk LA, de Bono MGibson Assembly®
2016Efficient In Situ Detection of mRNAs using the Chlorella virus DNA ligase for Padlock Probe LigationRNASchneider, N and Meier, M.
2011Efficient in vivo selection of a novel tumor-associated peptide from a phage displayMoleculesVeleva, A.N. et al.
2008Efficient interval partitioning approach for global optimization.Journal of Global OptimizationPedamallu, C.S., Ozdamar, L., Csendes, T.and Vinko, T.
2002Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR.Nucl.Acids.Res.Wei, A., Yuan, A., Fawcett, G., Butler, A., Davis, T., Xu, S.Y.and Salkoff, 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
2016Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria.ISME J.Seth-Smith, M.B.P. et al.
2006Enabling Glycosyltransferase Evolution: A Facile Substrate-Attachment Strategy for Phage-Display Enzyme Evolution.Chembiochem.Love K.R., Swoboda J.G., Noren C.J.and Walker, S.
2011EndonucleasesCurr Protoc Mol BiolNichols, N.M.
2002Endosomal localization and function of sortingProc. Natl. Acad. Sci. USAZhong, Q., et al.
2010Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer.PLoS ONEMcNulty, S.N., Foster, J.M., Mitreva, M., Dunning-Hotopp, J.C., Martin, J., Fischer, K., Wu, B., Davis, P.J., Kumar, S., Brattig, N.W., Slatko, B.E., Weil, G.J.and Fischer, P.U.
2008Endothelial nitric oxide synthase gene expression during murine embryogenesis: commencement of expression in the embryo occurs with the establishment of a unidirectional circulatory system.Circ Res.Teichert, A.M., Scott, J.A., Robb, G.B., Zhou, Y.Q., Zhu, S.N., Lem, M., Keightley, A., Steer, B.M., Schuh, A.C., Adamson, S.L., Cybulsky, M.I.and Marsden, P.A.
2012Engineered derivatives of maltose-binding proteinProtein EngineeringRiggs, P.D.
2001Engineering a Nicking Endonuclease N.AlwI by Domain SwappingProc.Natl.Acad.Sci.USA Xu, Y., Lunnen, K.and Kong, H.
2006Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants.NAR Samuelson, J.C., Morgan, R.D., Benner, J.S., Claus, T.E., Packard, S.L.and Xu, S.Y.
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.
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
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.
2010Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA Protein Exp PurifZhang, P., Too, P.H., Samuelson, J.C., Chan, S.H., Vincze, T., Doucete, S., Backstrom, S., Potamousis, K.D., Schramm, T.M., Forrest, D., Schwartz, D.C., Xu, S.Y.
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.
2012Engineering Escherichia coli for soluble expression and single step purification of active human lysozymeJournal of BiotechnologyLamppa, J.W., Tanyos, S.A., and Griswold, K.E.
2014Engineering hydrogen gas production from formate in a hyperthermophile by heterologous production of an 18-subunit membrane-bound complexJ Biol ChemLipscomb GL, Schut GJ, Thorgersen MP, Nixon WJ, Kelly RM, Adams MWGibson Assembly®
2014Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNANucleic Acids ResGutjahr A, Xu SYGibson Assembly®
2010Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.Nucl.Acids.Res.Too, P.H., Zhu, Z., Chan, S.H.and Xu, S.Y.
2010Engineering of a synthetic electron conduit in living cellsProc. Natl. Acad. Sci. USAJensen, H.M., et al.
2007Engineering of the yeast Yarrowia lipolytica for the production of glycoproteins lacking the outer-chain mannose residues of N-glycansAppl. Environ. Microbiol.  Song, Y., Choi, M.H., Park, J.N., Kim, M.W., Kim, E.J., Kang, H.A., Kim, J.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.
2005Engineering substrate specificity of O6-alkylguanine-DNA alkyltransferase for specific protein labeling in living cellsChemBioChem Juillerat A. et al.
2014Enhanced gene disruption by programmable nucleases delivered by a minicircle vector.Gene TherA-Bk Dad, S Ramakrishna, M Song, H KimGenome Editing
2015Enhanced production of secretory glycoprotein VSTM1-v2 with mouse IgGκ signal peptide in optimized HEK293F transient transfectionJ Biosci BioengLiu H., Zou X., Li T., Wang X., Yuan W., Chen Y., Han W.
1987Enhancement of the apparent cleavage specificities of restriction endonucleases: applications to megabase mapping of chromosomes.McClelland, M., and Nelson, M.
2015Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp.Sci Rep.Katharios, P. et al.
1996Enzymatic C5-Cytosine Methylation Of DNA - Mechanistic Implications Of New Crystal-Structures For HhaI Methyltransferase-DNA-Adohcy Complexes.J.Mol.Biol.O'Gara, M., Klimasauskas, S., Roberts, R., and Cheng, X.D.
2016Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencingSex. Transm. InfectGraham, R.M.A. et al.
2009Epigenetic mechanisms in mammalsCell Mol Life SciKim, J.K., Samaranayake, M., Pradhan, S
2008Epigenetic mechanisms in mammals.Cell Mol.Life Sci.Kim JK, Samaranayake M, Pradhan S.
2014Epigenetic silencing of apoptosis-inducing gene expression can be efficiently overcome by combined SAHA and TRAIL treatment in uterine sarcoma cellsPLoS OneFröhlich LF, Mrakovcic M, Smole C, Lahiri P, Zatloukal K
2016Erratum to: SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm.Microb Cell Fact. Lobstein, J., Emrich, C.A., Jeans, C., Faulkner, M., Riggs, P. and Berkmen, M.
1986Escherichia coli K-12 restricts DNA containing 5-methylcytosine.Proc.Natl.Acad.Sci.USA Raleigh, E.A., and Wilson, G.
2014Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cellsAppl Microbiol BiotechnolWippermann A, Klausing S, Rupp O, Albaum SP, Büntemeyer H, Noll T, Hoffrogge R
2014Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cellsBosch PJ, Corrêa IR Jr, Sonntag MH, Ibach J, Brunsveld L, Kanger JS, Subramaniam V
1998Evaluation of the ASSURE/FH Antibody Assay for the Detection of Feline Heartworm Infection.Proc.Amer.Heartworm Symp.Bestul, K.J., McCall, J.W., Supakorndej, N., Ma, D., Carlow, C.K.S.
2006Evaluation of two novel tag-based labeling technologies for site-specific modification of proteinsInt. J. Biol. Macromol.Tirat A. et al.
2013Evaluation of UDP-GlcN Derivatives for Selective Labeling of 5-(Hydroxymethyl)cytosineChembiochemDai N, Bitinaite J, Chin HG, Pradhan S, Corrêa IR Jr.
2006Evidence supporting a cisi-enedio-based mechanism for Pyrococcus furiousus phophoglucose isomerase.J Mol Biol.Berrisford, J.M., Hounslow, A.M., Akerboom, J., Hagen, W.R., Brouns, S.J., van der Oost, J., Murray, I.A., Michael Blackburn, G., Waltho, J.P., Rice, D.W.and Baker, P.J.
2010Evolution of Bacterial Phosphoglycerate Mutases: Non-homologous Isofunctional Enzymes Undergoing Gene Losses, Gains and Lateral Transfers.PLoS ONEFoster, J.M., Davis, P.J., Raverdy, S., Sibley, M.H., Raleigh, E.A., Kumar, S.and Carlow, C.K.S.
2015Evolution of stickleback in 50 years on earthquake-uplifted islands.Proc Natl Acad Sci U S ALescak EA, Bassham SL, Catchen J, Gelmond O, Sherbick ML, von Hippel FA, Cresko WA.
2014Evolution, mechanisms, and applications of intein-mediated protein splicingJ Biol ChemPerler FB, Allewell NM
2015Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents.Mol Ecol.Herrera S, Watanabe H, Shank TM.
2010Evolutionary divergence in the fungal response to fluconazole revealed by soft clusteringGen. Bio. Kuo, D., et al.
1998Evolutionary evidence for recombination among bacteria in nature.E.coli.Horizontal Gene Transfer Milkman, R., Cryderman, D., McKane, M., McWeeny, K.and Raleigh E.A.
2002Evolutionary relationship of Alw261, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequencesMol. Genet. GenomicsBitinaite, J., Mitkaite, G., Dauksaite, V., Jakubauskas, A., Timinskas, A., Vaisvila, R., Lubys, A., Janulaitis, A.
2006Evolving the substrate specificity of O6 alkylguanine DNA alkyltransferase through loop insertion for applications in molecular imagingACS Chem Biol. Heinis C. et al.
2017Examining Sources of Error in PCR by Single-Molecule Sequencing.PLoS ONEPotapov Vladamir, Ong Jennifer L
2011ExonucleasesCurr.Protoc.Mol.Biol.McReynolds, L.A.and Nichols, N.M.
2014Expanded genetic codes in next generation sequencing enable decontamination and mitochondrial enrichmentPLoS OneMcKernan KJ, Spangler J, Zhang L, Tadigotla V, McLaughlin S, Warner J, Zare A, Boles RG
2009Expanding the chemical Biologist's tool kit: chemical labelling strategies and its applications Curr. Med. Chem.  Chattopadhaya S. et al.
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.
2005Explosive Lineage-Specific Expansion of the Orphan Nuclear Receptor HNF4 in Nematodes.J Mol Evol.Robinson-Rechavi, M, Maina, C.V., Gissendanner, C.R., Laudet, V., Sluder, A.
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.
2007Expressed protein ligation using an N-terminal cysteine containing fragment generated in vivo from a pelB fusion proteinProtein Expr. Purif.Hauser, P. S., et al.
2004Expression and function of conserved nuclear receptor genes in Caenorhabditis elegans.Dev.Biol.Gissendanner, C.R., Crossgrove, K., Kraus, K.A., Maina, C.V.and Sluder, A.E.
2007Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants.Protein Expr.Purif.Bao, Y., Higgins, L., Zhang, P., Chan, S-H., Laget, S., Sweeney, S., Lunnen, K.and Xu, S-Y.
2008Expression and purification of BmrI restriction endonucleases and its N-terminal cleavage domain variantsBao, Y., Higgins, Zhang, P., Chan, S.H., Lagaet, S., Sweeney, S., Lunnen, K., Xu, S.Y.
2000Expression and purification of recombinant proteins by fusion to maltose-binding protein.Mol.Biotechnol.Riggs, P.
2016Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymesSci RepXu, S.Y., Klein, P., Degtyarev, S.K.h. and Roberts, R.J.
2008Expression of a cytotoxic cationic antibacterial peptide in Escherichia coli using two fusion partnersProtein Exp. Purif.Chen, Y. Q., et. al.
1994Expression of an Onchocerca volvulus Ov33 homolog in Dirofilaria immitis: potential in immunodiagnosis of heartworm infection.Parasite Immunol.Mejia, S.J., Knenfou, C., Southworth, M.W., Perler, F.B.and Carlow, C.K.
2011Expression of heparin sulfate sulfotransferases in Kluyveromyces lactisand preparation of PAPSGlycobiology Advance AccessZhou, X., et al.
2006Expression of N-terminal Cys-protein fragments using an intein refolding strategyBioorg. Med. Chem.Hackenberger, C. P., et. al.
2011Expression of recombinant cytochromes c in E.coli.Methods Mol.Biol.Londer, Y.Y.
2005Expression of SMAP-29 cathelicidin-like peptide in bacterial cells by intein-mediated systemProtein Expr. Purif.Morassutti, C., et al.
2002Expression of the class 1 outer-membrane protein of Neisseria meningitidis in Escherichia coli and purification using a self-cleavable affinity tagProtein Expr. Purif. Humphries, H. E., Christodoulides, M. and Heckels, J. E.
1994Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition siteProteinsBalendiran, K., Bonventre, J., Knott, R., Jack, W., Benner, J., Schildkraut, I., and Anderson, J.E.
2010Expression, purification, phosphorylation and characterization of recombinant human statherinProtein Expr Purif.Manconi, B., et. al.
2013Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayiBMC GenomicsIonnidis, P., Johnston, K.L., Riley, D.R., Kumar, N., White, J.R., Olarte, K.T., Ott, S., Tallon, L.J., Foster, J.M., Taylor, M.J. and Dunning-Hotopp, J.C.
1995Extremozymes: expanding the limits of biocatalysis.BiotechnologyAdams, M.W.W., Perler, F.B.and Kelly, R.M.