Publications

Publications

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YearTitleJournalAuthorsApplication(s)
2011Comparitive characterization of the PvuRts11 family and application in mapping genomic 5-hydroxymethylcytosineNucl. Acids Res.
2015Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCRScientific Reports
Culture-independent genomic characterisation of Candidatus Chlamydia
Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella
2015Label-free single-cell protein quantification using a drop-based mix-and-read system.Sci. Rep.Abbaspourrad A, Zhang H, Tao Y, Cui N, Asahara H, Zhou Y, Yue D, Koehler SA, Ung LW, Heyman J, Ren Y, Ziblat R, Chong S, Weitz DA.
2014Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNAJ Biol EngAbil Z, Denard CA, Zhao HGolden Gate Assembly, DNA Assembly and Cloning
2014Enhanced gene disruption by programmable nucleases delivered by a minicircle vector.Gene TherA-Bk Dad, S Ramakrishna, M Song, H KimGenome Editing
1992Identification of surrogate rodent hosts for larval Onchocerca lienalis and induction of protective immunity in a model system.J Parasitol.Abraham, D., Eberhard, M.L., Lange, A.M., Yutanawiboonchai, W., Perler, F.B.and Lok, J.B.
2002Development of a Positive Genetic Selection System for Inhibition of Protein Splicing Using Mycobacterial Inteins in Escherichia coli DNA Gyrase Subunit A.J.Mol.Micro.Biotechnol.Adam, E.and Perler, F.B.
2008Cellular Ser/Thr-kinase assays using generic peptide substrates Curr. Chem. Gen. Adams D. G. et al.
1995Extremozymes: expanding the limits of biocatalysis.BiotechnologyAdams, M.W.W., Perler, F.B.and Kelly, R.M.
1996Plant methyltransferases and thier targets in the plant genome. In: Epigenetic Mechanisms of Gene RegulationCold Spring Habor Laboratory PressAdams, R.L.P. Pradhan, S., Johnson, C.A, Lindsay, H., Shek, E.W.L., Jenkins, G.I., Urwin, N.A.R.
2009 The Krüppel-like zinc finger protein Glis3 directly and indirectly activates insulin gene transcription  Nucleic Acids Res. adr, C.E., Hewett, J.W., Breakefield, X.O. and Tannous, B.A.
2016Jmjd2/Kdm4 demethylases are required for expression of Il3ra and survival of acute myeloid leukemia cellsGenes & DevAgger, K. et al.
2016Training the Next Generation of Biomedical Investigators in Glycosciences.J. Clin. Invest.Agre, P., Bertozzi, C., Bissell, M., Campbell, K., Cummings, R., Desai, U., Estes, M., Flotte, T., Fogleman, G.,Gage, F., Ginsburg, D., Gordon, J.I., Hart, G., Hascall, V., Kiessling, L., Kornfeld, S., Lowe, J., Magnani, J., Mahal, L.K., Medzhitov, R., Roberts, R., Sackstein, R., Sarkar, R., Schnaar, R., Schwartz, N., Varki, A., Walt, D., Weissman, I.
2009A new family of receptor tyrosine kinases with a venus flytrap binding domain in insects and other invertebrates activated by aminoacidsPLoS One Ahier A. et al.
2012A terracotta bio-batteryBioresour TechnolAjayi, F.F., Weigele, P.R.
2015Differential connectivity of splicing activators and repressors to the human spliceosomeGenome Biol.Akerman, M., Fregoso, Ol., Das, S., Ruse, C., Jensen, M.A., Pappin, D.J., Zhang, M.Q., Krainer, A.R.
2016Comprehensive Profiling of Glycosphingolipid Glycans Using a Novel Broad Specificity Endoglycoceramidase in a High-Throughput Workflow.Albrecht, S., Vainauskas, S., Stöckmann, H., McManus, C., Taron, C.H. and Rudd, P.M.
2013GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic BiologyPlant PhysiologyAlejandro Sarrion-Perdigones, Marta Vazquez-Vilar, Jorge Palací, Bas Castelijns, Javier Forment, Peio Ziarsolo, José Blanca, Antonio Granell, Diego OrzaezGolden Gate Assembly
2014Polynucleotide 3'-terminal phosphate modifications by RNA and DNA ligasesJournal of Biological ChemistryAlexander M. Zhelkovsky and Larry A. McReynolds
2015Expanding the MDx toolbox for filarial diagnosis and surveillanceTrends Parasitol.Alhassan, A., Li, Z., Poole, C.B. and Carlow, C.K.S.
2014A simple isothermal DNA amplification method to screen black flies for Onchocerca Volvulus infectionPLoS OneAlhassan, A., Makepeace, B.L., LaCourse, E.J., Osei-Atweneboana, M.Y., Carlow, C.K.S.
2016Comparison of a new visual isothermal nucleic acid amplification test with PCR and skin snip analysis for diagnosis of onchocerciasis in humans.Mol Biochem Parasitol.Alhassan, Aa, Osei-Atweneboana, M.Y., Kyeremeh, K.F., Poole, C.B., Li, Z., Tettevi, E., Tanner, N.A. and Carlow, C.K.
1996Thermostable Bst DNA polymerase I lacks a 3' fwdarw 5' proofreading exonuclease activity1.Genetic Analysis Biomolecular Engineering Aliotta, J.M., Pelletier, J.J., Ware, J.L., Moran, L.S., Benner, J.S., and Kong, H.
2013Fully assembled genome sequence for Salmonella enterica subsp. Enterica Serovar Javiana CFSAN001992.  Genome Announcements Allard, M.W. Muruvanda, T., Strain, E., Timme, R., Luo, Y., Wang, C., Keys, C.E., Payne, J., Cooper, T. Luong, K., Song, Y., Chin, C.-S., Korlach, J., Roberts, R.J., Evans, P., Musser, S.M., Brown, E.W.
2015A New Approach to Produce HIV-1 Envelope Trimers: BOTH CLEAVAGE AND PROPER GLYCOSYLATION ARE ESSENTIAL TO GENERATE AUTHENTIC TRIMERS.J Biol ChemAlSalmi W., Mahalingam M., Ananthaswamy N., Hamlin C., Flores D., Gao G., Rao V.B.
2015Developmental exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin alters DNA methyltransferase (dnmt) expression in zebrafish (Danio rerio)Toxicol Appl PharmacolAluru N, Kuo E, Helfrich LW, Karchner SI, Linney EA, Pais JE, Franks DG
1996Comparative analysis of expression of the SalI restriction-modification system in Escherichia coli and StreptomycesMol. Gen. Genet.Alvarez, M.A., Gomez, A., Gomez, P., Brooks, J.E., Rodicio, M.R.
2010Ligand regulation of the quaternary organization of cell surface M3 muscarinic acetylcholine receptors analyzed by fluorescence resonance energy transfer (FRET) imaging and homogenous time-resolved FRET J. Biol. Chem. Alvarez-Curto J. et al.
2015Rational design of 'controller cells' to manipulate protein and phenotype expression.Metab EngAmin Zargar, David N Quan, Milad Emamian, Chen Yu Tsao, Hsuan-Chen Wu, Chelsea R Virgile, William E BentleyHigh-Fidelity PCR
2005Chracterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification.J.Biol.Chem.An.L., Tang, W., Ranalli, T.A., Kim, H-J., Wytiaz, J.and Kong, H.
2013Hedgehog Signaling Regulates MyoD Expression and ActivityJ Biol ChemAnastassia Voronova Erin Coyne, Ashraf Al Madhoun, Joel V. Fair, Neven Bosiljcic, Catherine St-Louis, Grace Li, Sherry Thurig, Valerie A. Wallace, Nadine Wiper-Bergeron, and Ilona S. Skerjanc
2013DNMT1-interacting RNAs block gene-specific DNA methylationNatureAnnalisa Di Ruscio, Alexander K. Ebralidze, Touati Benoukraf, Giovanni Amabile, Loyal A. Goff, Jolyon Terragni, Maria Eugenia Figueroa, Lorena Lobo De Figueiredo Pontes, Meritxell Alberich-Jorda, Konstantin K. Ebralidze, Sriharsa Pradhan, John L. Rinn, Daniel G. Tenen
2013Segregation of Family A G Protein Coupled Receptor Protomers in the Plasma MembraneMolecular PharmacologyAnthony Gavalas, Tien-Hung Lan, Qiuju Liu, Ivan R. Corrêa, Jr., Jonathan A. Javitch, and Nevin A. Lambert
2014Objective: biochemical functionFront GenetAnton BP, Kasif S, Roberts RJ, Steffen M
2013The COMBREX project design methodology and initial resultsPLOS ONE Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L,Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A,Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D,Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.
2004The first amendment and scientific freedom in the era of bioterrorism.J.Biolaw and BusinessAnton, B.P.
2013VectorsBrenner's Encyclopedia of GeneticsAnton, B.P.
2016Complete Genome Sequence of NEB 5-alpha, a Derivative of Escherichia coli K-12 DH5 alpha.Genome Announc. Anton, B.P. and Raleigh, E.A.
2016Complete Genome Sequence of the Engineered Escherichia coli SHuffle Strains and Their Wild-Type Parents Genome Announc.Anton, B.P., Fomenkov, A., Raleigh, E.A. and Berkmen, M.
2016Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi.PLoS OneAnton, B.P., Harhay, G.P., Smith, T.P., Blom, J. and Roberts, R.J.
1997Cloning and characterization of the BglII restriction-modification system reveals a possible evolutionary footprint.GeneAnton, B.P., Heiter, D.F., Benner, J.S., Hess, E.J., Greenough, L., Moran, L.S., Slatko, B.E., and Brooks, J.E.
2015Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12PLoS OneAnton, B.P., Mongodin, E.F., Agrawal, S., Fomenkov, A., Byrd, D.R., Roberts, R.J. and Raleigh, E.A.
2010Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis.Nucl.Acids.Res.Anton, B.P., Russell, S.P., Vertrees, J., Kasif, S., Raleigh, E.A., Limbach, P.A.and Roberts, R.J.
2008RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli.Proc Natl Acad Sci.Anton, B.P., Saleh, L., Benner, J.S., Raleigh, E.A., Kasif, S.and Roberts, R.J.
2004Transposon-mediated linker insertion scanning mutagenesis of the Escherichia coli McrA endonuclease.J.Bacteriol.Anton, B.P.and Raleigh, E.A.
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.
2015Development of a Rapid, Simple Method for Detecting Naegleria fowleri Visually in Water Samples by Loop-Mediated Isothermal Amplification (LAMP).PLoS OneAongart Mahittikorn, Hirotake Mori, Supaluk Popruk, Amonrattana Roobthaisong, Chantira Sutthikornchai, Khuanchai Koompapong, Sukhontha Siri, Yaowalark Sukthana, Duangporn NacapunchaiIsothermal Amplification
2014Tuning the electrical properties of the heart by differential trafficking of KATP ion channel complexesJ Cell SciArakel EC, Brandenburg S, Uchida K, Zhang H, Lin YW, Kohl T, Schrul B, Sulkin MS, Efimov IR, Nichols CG, Lehnart SE, Schwappach BGlycobiology
2016Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments.Ecol Evol. Araneda C, Larraín MA, Hecht B, Narum S.
1987Brugia malayi: recombinant antigens expressed by genomic DNA clones.Exp.Parasitol.Arasu , P., Philipp, M., and Perler, F.
1987Genomic Cloning of Recombinant Antigens Detected by Antiserum Against Infective Larvae of Brugia Malayi.Molecular Paradigms for Eradicating Helminthic ParasitesArasu, P., and Perler, F.B.
1989Human T-cell stimulation, molecular characterization and in situ mRNA localization of a Brugia malayi recombinant antigen.Mol.Biochem.Parasitol.Arasu, P., Nutman, T.B., Steel, C., Mulligan, M.M., Abraham, D., Tuan, R.S., and Perler, F.B.
2010In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme Nucleic Acids Res. Asahara, H. and Chong, S.
2010In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme.Nucl.Acids.Res.Asahara, H.and Chong, S.
2015Targeted Glycoengineering Extends the Protein N-glycosylation Pathway in the Silkworm Silk GlandInsect Biochem Mol BiolAsazuma HM., Sohn BH., Kim Y.S., Kuo CW., Khoo KH., Kucharski CA., Fraser MJ., Jarvis DL.
2008Bioluminescent virion shells; new tools for quantitation of AAV vector dynamics in cells and live animalsGene Ther.Asokan, A., Johnson, J.S., Li, C., Samulski, R.J.
1991Cross-linking of a monoclonal antibody-antigen complex enables detection of parasite antigen in immunoblots and in an expression library.Mol.Biochem.Parasitol.Awobuluyi, M., Mania, C.V., and Carlow, C.K.S.
2008DNA distortion and specificity in a sequence-specific endonuclease.J.Mol.Biol.Babic, A.C., Little, E.J., Manohar, V.M., Bitinaite, J., Horton, N.C.
2008Construction of intein mediated hGMCSF expression vector and its prufication in Pichia pastorisProtein Exp. Purif.Babu, S.K., et. al.
2001Recombinant human DNA (cytosine-5) methyltransferase.III.Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the fragile X CGGCCG sequence.J.Biol.Chem.Bacolla, A., Pradhan, S., Larson, J.E., Roberts, R.J.and Wells, R.D.
1999Human DNA (Cytosine-5) Methyltransferase.II.steady-state kinetics reveal allostericactivation by methylated DNA.J.Biol.Chem.Bacolla, A., Pradhan, S., Roberts, R.J.and Wells, R.D.
2007A highly sensitive assay for monitoring the secretory pathway and ER stress PLoS One Badr, C.E., Hewett, J.W., Breakefield, X.O. and Tannous, B.A.
2007A highly sensitive assay for monitoring the secretory pathway and ER stress.PLoS OneBadr. C.E., Hewett, J.W., Breakefield, X.Q and Tannous, B.A.
1994Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2.J.Mol.Biol.Baldwin, G.S., Kelly, S.M., Price, N.C., Wilson, G.G., Connolly, B.A., Artymiuk, P.J., and Hornby, D.P.
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.
2010Peptides from phage display library modulate gene expression in mesenchymal cells and potentiate osteogenesis in unicortical bone defectsVis. Exp.Balian, G. et al.Phage Display
2008 Caged substrates for protein labeling and immobilizationChembiochem Banala J. et al.
2008Caged substrates for protein labeling and immobilizationChembiochem Banala J. et al.
1999Wolbachia genomes and the many faces of symbiosis.Parasitology Today Bandi, C., Slatko, B.and O'Neill, S.L.
2009Indo-1 Derivatives for local calcium sensingJACS Chemical Biology Bannwarth et. al.
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.
1992The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap.GeneBarany, F., Slatko, B., Danzitz, M., Cowburn, D., Schildkraut, I., and Wilson, G.G.
1999Plasmodium vivax, P.cynomolgi, and P.knowlesi: Identification of Homologue Proteins Associated with the Surface of Merozoites.Exp.Parasitol.Barnwell, J.W., Galinski, M.R., DeSimone, S.G., Perler, F.and Ingravallo, P.
1989Site-directed mutagenesis of the EcoRV methylase for the study of the functional role of the conserved sequences in N6-adenine methylasesJ. Cell BiochemBarshevsky,T. and Benner J.S.
1988Cloning of the HhaI and HinPI restriction-modification systems.GeneBarsomian, J.M., Card, C.O., and Wilson, G.G.
2008Crucial role of aspartic acid at position 265 in the CH2 domain for murine IgG2a and IgG2b Fc-associated effector functions J Immunol. Baudino L, Shinohara Y, Nimmerjahn F, Furukawa J, Nakata M, Martínez-Soria E, Petry F, Ravetch JV, Nishimura S, Izui S.
2016The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase. PLoS OneBauer, R.J., Evans, T.C. Jr. and Lohman, G.J.
2017Rapid Time Scale Analysis of T4 DNA Ligase–DNA Binding.BiochemistryBauer, R.J., Jurkiw, T.J., Evans, T.C. Jr. and Lohman, G.J.
2014Biomimetic Magnetite Formation From Biocombinatorial Approaches to Mineralization EffectsLangmuirBaumgartner J, Carillo MA, Eckes KM, Werner P, Faivre D.Phage Display
2015Terminal Mannose Residues in Seminal Plasma Glycoproteins of Infertile Men Compared to Fertile DonorsInt J Mol SciBeata O., Jarząb A., Kratz E., Zimmer M., Gamian A., Ferens-Sieczkowska M.
2013Digital droplet PCR for rapid quantification of donor DNA in the circulation of transplant recipients as a potential universal biomarker of graft injury.Clin. Chem.Beck J, Bierau S, Balzer S, Andag R, Kanzow P, Schmitz J, Gaedcke J, Moerer O, Slotta JE, Walson P, Kollmar O, Oellerich M, Schütz E.
2015Multivalent site-specific phage modification enhances the binding affinity of receptor ligandsBioconjug ChemBeech, J., Saleh, L., Frentzel, J., Figler, H., Correa, I.R. Jr., Baker, B., Ramspacher, C., Marshall, M., Dasa, S., Linden, J., Noren, C.J. and Kelly, K.A.
1997Homing endonucleases: keeping the house in order.Nucl.Acids Res.Belfort, M., and Roberts, R.J.
2005Cleavage of individual DNA strands by the different subunits of the heterodimeric restriction endonuclease BbvCI.J.Mol.Biol.Bellamy, S.R.W., Milsom, S.E., Scott, D.J., Daniels, L.E., Wilson, G.G.and Halford, S.E.
2013Three-color single molecule imaging shows WASP detachment from Arp2/3 complex triggers actin filament branch formation eLifeBenjamin A Smith, Shae B Padrick, Lynda K Doolittle, Karen Daugherty-Clarke, Ivan R Corrêa Jr, Ming-Qun Xu, Bruce L Goode3, Michael K Rosen, Jeff Gelles
2012Oxidative folding of proteins in Escherichia coliBioPharm InternationalBerkmen, M.
2012Oxidative folding of proteins in Escherichia coliBioProcess InternationalBerkmen, M.
2012Production of disulfide-bonded proteins in Escherichia coliProtein Expression and PurificationBerkmen, M.
Production of disulfide-bonded proteins in Escherichia coliBerkmen, M.
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.
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.
2014Integration of growth and patterning during vascular tissue formation in ArabidopsisScienceBert De Rybel, Milad Adibi, Alice S. Breda, Jos R. Wendrich, Margot E. Smit, Ondej Novk, Nobutoshi Yamaguchi, Saiko Yoshida, Gert Van Isterdael, Joakim Palovaara, Bart Nijsse, Mark V. Boekschoten, Guido Hooiveld, Tom Beeckman, Doris Wagner, Karin Ljung, Christian Fleck, Dolf WeijersHigh-Fidelity PCR
2001Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state.EMBO Reports Besnier, C.E.and Kong, H.
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.
2007New and easy strategy for cloning, expression, purification, and characterization of the 5S subunit of transcarboxylase from Propionibacterium f. shermaniiPrep. Biochem. Biotechnol.Bhat, R. K. and Berger, S.
2013Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancerNucleic Acids ResearchBhattacharyya, S., Yu, Y., Suzuki, M., Campbell, N., Mazdo, J., Vasanthakumar, A., et al.5-hmC Detection & Analysis, Methods of 5-hmC Detection and Analysis
2000A simple in vitro Tn7-based transposition system with low target site selectivity for genome and gene analysis.Nucl.Acids Res.Biery, M.C., Stewart, F.J., Stellwagen, A.E., Raleigh, E.A.and Craig, N.L.