Publications

Publications

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YearTitleJournalAuthorsApplication(s)
2017NicE-seq: High resolution open chromatin profilingGenome BiologyPonnaluri, V.K.C., Zhang, G., Estève, P.-O., Spracklin, G., Sian, S., Xu, S.-Y., Benoukraf, T., Pradhan, S.
2017N-glycosylation affects the stability and barrier function of the MUC16 mucinJ. Biol Chem.Taniguchi, T., Woodward, A.M., Magnelli, P., McColgan, N.M., Lehoux, S., Jacobo, S.M.P., Mauris, J., Argueso, P.
2017Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host rematode RNA by Cappable-seqTMPLoS OneLuck, A.N., Slatko, B.E., Foster, J.M.
2017Rapid Time Scale Analysis of T4 DNA Ligase–DNA Binding.BiochemistryBauer, R.J., Jurkiw, T.J., Evans, T.C. Jr. and Lohman, G.J.
2017Methods for structural and functional analyses of intramembrane prenyltransferases in the UbiA superfamilyMethods EnzymolYang, Y., Ke, N., Liu, S., Li, W.
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.
2017Mechanism and timing of Mcm2-7 ring closure during DNA replication origin licensingNat. Struct. Mol. Biol.Ticau, S., Friedman, L.J., Champasa, K., Correa, I.R., Jr., Gelles, J., Bell, S.P.
2017Macrocycle peptides delineate locked-open inhibition mechanism for micoorganism phosphoglycerate mutasesNat. Commun.Yu, H., Dranchak, P., Li, Zhiru, MacArthur, R., Munson, M.S., Mehzabeen, N., Baird, N.J., Battalie, K.P., Ross, D., Lovell, Sc., Carlow, C.K.S., Suga, H., Inglese, J.
2017Using high-throughput barcode sequencing to efficiently map connectomesNucleic Acids ResearchPeikon, I.D., Kebschull, J.M., Vagin, V.V., Ravens, D.I, Sun, Y.-C., Brouzes, E., Correa, I.R., Bressan, D., Zador, A.M.
2017The GAN exonuclease, or the flap endonuclease Fen1 and RNase HII are necessary for viability of Thermococcus kodakarensisJ. BacteriolBurkhart, B.W., Cubonova, L., Heider, M.R., Kelman, Z., Reeve, J.N., Santangelo, T.J.
2017Whole genome amplification provides suitable control DNA for use in DNA barcoding applicationsBiop.Bourque, D.A., Naaum, A.M., Distel, D.L., Hanner, R.H.
2017Various Mutations compensate for a deleterious lacZα insert in the replication enhancer of M13 bacteriophagePLoS OneZygiel, E.M., Noren, K.A., Adamkiewicz, M.A., Aprile, R.J., Bowditch, H.K., Carroll, C.L., Cerezo, M.A.S., Dagher, A.M., Hebert, C.R., Hebert, L.E., Mahame, G.M., Milne, S.C., Silvestri, K.M., Sutherland, S.E., Sylvia, A.M., Taveira, C.N., VanValkenburgh, D.J., Noren, C.J., Hall, M.F.
2017Targeted enrichment and sequencing of recent endosymbiont-host lateral gene transfersSci Rep.Dunning Hotopp, J.C., Slatko, B.E., Foster, J.M.
2017Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and their Contribution to Rec-A-Independent Horizontal TransferJ. BacteriolKingston, A.W., Ponkratz, C. and Raleigh, E.A.
2017Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNANucleic Acids Res.Tamulaitiene, G., Jovaisaite, V., Tamulaitis, G., Songailiene, I., Manakova, E., Zaremba, M., Grazulis, S., Xu, S.Y., Siksnys, V.
2017Serotyping dengue virus with isothermal amplification and a portable sequencerScientific ReportsYamagishi, J., et al.
2017Sequential formation of two branched intermediates during protein splicing of class three inteinsExtrmophilesTori, K. and Perler, F.
2017Complete genome and methylome analysis of psychrotrophic bacterial isolates from Lake Untersee in AntarcticaGenome Announce.Fomenkov, A., Akimov, V.N., Vasilyeva, L.V., Andersen, D.T., Vincze, T., Roberts, R.J.
2017Complete genome sequence and methylome analysis of Acinetobacter calcoaceticus 65Fomenkov, A., Vincze, T., Degtyarev, S.K., Roberts, R.J.
2017Complete genome and methylome sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB collectionGenome AnnounceYao, K., Roberts, R.J., Allard, M.W., Hoffmann, M.
2017Defining the RNaseH2 enzyme-initiated ribonucleotide excision repair pathway in ArchaeaJ. Biol Chem.Heider, M.R., Burkhart, B.W., Santangelo, T.J., Gardner, A.F.
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.
2017​Colorimetric tests for diagnosis of filarial infection and vector surveillance using non-instrumented nucleic acid loop-mediated isothermal amplification (NINA-LAMP).PLoS OnePoole, C.B., Li, Z., Alhassan, A., Guelig, D., Diesburg, S., Tanner, N.A., Zhang, Y., Evans, T.C. Jr., LaBarre, P., Wanji, S., Burton R.A. and Carlow, C.K.
2017A practical guide to the oral microbiome and its relation to health and diseaseKrishnan, K., Chen, T., Paster, B.J.
2017Caenorhabditis elegans CES-1 snail represses Pig-1 MELK expression to control asymmetric cell divisionGeneticsWei, H., Yan, B., Gagneur, J., Conradt, B.
2017Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expressionEpigeneticsPonnaluri, V.K., Ehrlich, K.C., Zhang, G., Lacey, M., Johnston, D., Pradhan, S., Ehrlich, M.
2017Examining Sources of Error in PCR by Single-Molecule Sequencing.PLoS ONEPotapov Vladamir, Ong Jennifer L
2017Evaluating computatonal gene ontology annotationsMethods Mol. Biol.Skunca, N., Roberts, R.J., Steffen, M.
2017Functional characterisation of cis-regulatory elements governing dynamic Eomes expressionDevelopmentSimon, C.S. et al.
2017EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determinationPLoS OneFomenkov, A., Sun, Z., Dila, D.K., Anton, B.P., Roberts, R.J., Raleigh, E.A.
2017DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich targetNucl. Acids Res.Shen, B.W., Heiter, D.F., Lunnen, K.D., Wilson, G.G., Stoddard, B.L.
2017DNA damage is a pervasive cause of sequencing errors, directly confounding variant identificationScienceChen, L., Liu, P., Evans, T.C., Jr., Ettwiller, L.M.
2017Dynamics of 5-carboxylcytosine during hepatic differentiation: potential general role for active demethylation by DNA repair in lineage specificationLewis, L.C., Lo, P.C., Foster, J.M., Dai, N., Correa, I.R., Jr., Durczak, P.M., Duncan, G., Ramsawhook, A., Aithal, G.P., Denning, C., Hannan, N.R., Ruzov, A.
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.
2017Fidelity of RNA templated end-joining by chlorella virus DNA ligase and a novel iLock assay with improved direct RNA detection accuracy Nucleic Acids ResearchKrzywkowski, T. Nilsson M.
2016Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preferenceNucleic Acids Res.Roy, A.C., Wilson, G.G. and Edgell, D.R.
2016Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference.Nucleic Acids Res.Roy, A.C., Wilson, G.G. and Edgell, D.R.
2016Phenotypic and molecular analysis of the effect of 20 hydroxyecdysone on the human filarial parasite Brugia malayiInt J ParasitolMhashilkar, A.S., Adapa, S.R., Jiang, R.H., Williams, S.A., Zaky, W., Slatko, B.E., Luck, A.N., Moorhead, A.R. and Unnasch, T.R.
2016Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov.Front Microbiol Ee, R., Lim, Y.L., Yin, W.F., See-Too, W.S., Roberts, R.J. and Chan, K.G.
2016omplete Genome Sequence and Methylome Analysis of Bacillus globigii ATCC 49760.Genome Announc.Morgan, R.D.
2016One-pot system for synthesis, assembly, and display of functional single-span membrane proteins on oil-water interfacesProc. Natl Acad Sci USAYunker, P.J., Asahara, H., Hung, K.C., Landry, C., Arriaga, L.R., Akartuna, I., Heyman, J., Chong, S., Weitz, D.A.
2016Phenotypic and molecular analysis of the effect of 20-hydroxyecdysone on the human filarial parasite Brugia malayi.Int J ParasitolMhashilkar, A.S., Adapa, S.R., Jiang, R.H., Williams, S.A., Zaky, W., Slatko, B.E., Luck, A.N., Moorhead, A.R. and Unnasch, T.R.
2016Quantitative profiling of glycans and glycopeptides: an informatics' perspectiveCurr Opin Struct Biol.Walsh, I., Zhao, S., Campbell, M., Taron, C.H. and Rudd, P.M.
2016RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region.Mol Ecol. Qiu S, Bergero R, Guirao-Rico S, Campos JL, Cezard T, Gharbi K, Charlesworth D.
2016RAD mapping reveals an evolving polymorphic and fuzzy boundary of a plant pseudoautosomal regionMol Ecol. Qiu S, Bergero R, Guirao-Rico S, Campos JL, Cezard T, Gharbi K, Charlesworth D.
2016Phytochromes function as thermosensors in Arabidopsis.ScienceJung, J-H. et al.
2016Plasmid-based one-pot saturation mutagenesisNature MethodsWrenbeck E.E., Klesmith J.R., Stapleton J.A., Adeniran A., Tyo K.E., & Whitehead T.A
2016Profiling of core fucosylated N-glycans using a novel bacterial lectin that specifically recognizes α1,6 fucosylated chitobiose. Sci Rep.Vainauskas, S., Duke, R.M., McFarland, J., McClung, C., Ruse, C. and Taron, C.H.
2016Novel m4C modification in type I restriction-modification systems.Nucleic Acids Res. Morgan, R.D., Luyten, Y.A., Johnson, S.A., Clough, E.M., Clark, T.A. and Roberts, R.J.
2016Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA.Nucleic acids researchCarson, S., Wilson, J., Aksimentiev, A., Weigele, P. R., & Wanunu, M.
2016Identification of Ecdysone Hormone Receptor Agonists as a Therapeutic Approach for Treating Filarial Infections.PLoS Negl Trop Dis.Mhashilkar, A.S., Vankayala, S.L., Liu, C., Kearns, F., Mehrotra, P., Tzertzinis, G., Palli, S.R., Woodcock, H.L. and Unnaschm, T.R.
2016Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.Genome MedicineDoan, T. et al.
2016High-temperature single-molecule kinetic analysis of thermophilic archaeal MCM helicasesNucleic Acids Res.Schermerhorn, K.M., Tanner, N., Kelman, Z. and Gardner, A.F.
2016High-efficiency generation of induced pluripotent mesenchymal stem cells from human dermal fibroblasts using recombinant proteins.Stem Cell Res Ther.Chen, F., Zhang, G., Yu, L., Feng, Y., Li, X., Zhang, Z., Wang, Y., Sun, D. and Pradhan, S.
2016Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts.Genome Biol. Evol.Qi, W. et al.
2016Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats?Ecol Evol.Kautt AF, Machado-Schiaffino G, Torres-Dowdall J, Meyer A.
2016Metabolic Incorporation of Azide Functionality into Cellular RNA.ChembiochemNainar, S., Beasley, S., Fazio, M., Kubota, M., Dai, N., Correa, I.R. Jr. and Spitale, R.C.
2016Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy induced neutropenia.Sci Rep.Gyarmati, P. et al.
2016mRNA capping: biological functions and applications. Nucleic Acids ResRamanathan, A., Robb, G.B. and Chan, S.H.
2016Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes G3Fu YB, Peterson G. W., Dong YRestriction Enzyme Digestion, Restriction Enzyme Digestion
2016Jmjd2/Kdm4 demethylases are required for expression of Il3ra and survival of acute myeloid leukemia cellsGenes & DevAgger, K. et al.
2016Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing.BMC Genomics. Brown JK, Taggart JB, Bekaert M, Wehner S, Palaiokostas C, Setiawan AN, Symonds JE, Penman DJ.
2016The Epigenomic Landscape of Prokaryotes.PLoS Genet.Blow, M.J., Clark, T.A., Daum, C.G., Deutschbauer, A.M., Fomenkov, A., Fries, R., Froula, J., Kang, D.D., Malmstrom, R.R., Morgan, R.D., Posfai, J., Singh, K., Visel, A., Wetmore, K., Zhao, Z., Rubin, E.M., Korlach, J., Pennacchio, L.A. and Roberts, R.J.
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.
2016The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant DiseaseSci Rep.Hieken, T.J. et al.
2016Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities.PLoS Biol.Callahan, S.J., Luyten, Y.A., Gupta, Y.K., Wilson, G.G., Roberts, R.J., Morgan, R.D. and Aggarwal, A.K.
2016Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profilingGenome BiologyFlygare, S. et al.
2016The endoplasmic reticulum: structure, function and response to cellular signalingCell Mol Life Sci.Schwarz, D.S., Blower, M.D.
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.
2016Using glycosidases to remove, trim, or modify glycans on therapeutic proteinsBioProcess InternationalGuthrie, E.P., Magneilli, P.E.
2016Visualization of Periplasmic and Cytoplasmic Proteins with a Self-Labeling Protein Tag.J BacteriolKe, N., Landgraf, D., Paulsson, J. and Berkmen, M.
2016WGS for surveillance of antimicrobial resistance: a pilot study to detect the prevalence and mechanism of resistance to azithromycin in a UK population of non-typhoidal <em>Salmonella</em>.J Antimicrob Chemother. Nair, S. et al.
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.
2016Type II restriction endonucleases - a historical perspective and more.Nucleic Acids ResPingoud, A., Wilson, G.G. and Wende, W.
2016Use of the Shuffle Strains in Production of Proteins.Curr Protoc Protein Sci.Ren, G., Ke, N. and Berkmen, M.
2016Structural basis for human PRDM9 action at recombination hot spotsGenes DevPatel, A., Horton, J.R., Wilson, G.G., Zhang, X. and Cheng, X.
2016Reconstitution of Protein Translation of Mycobacterium Reveals Functional Conservation and Divergence with the Gram-Negative Bacterium Escherichia coli.PLoS One.Srivastava, A., Asahara, H., Zhang, M., Zhang, W., Liu, H., Cui, S., Jin, Q. and Chong, S.
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.
2016Reminder to deposit DNA sequencesScienceBlaxter, M., Danchin, A., Savakis, B., Fukami-Kobayashi, K., Kurokawa, K., Sugano, S., Roberts, R.J., Salzberg, S.L. and Wu, C.I.
2016RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae).Mol Phylogenet Evol. Hou Y, Nowak MD, Mirré V, Bjorå CS, Brochmann C, Popp M.
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.
2016Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular ComponentsCellPardee P, Green A A, Takahashi M K, Braff D, Lambert G, Lee J W, Ferrante T, Ma D, Donghia N, Fan M, Daringer N M, Bosch I, Dudley D M, O’Connor D H, Gehrke H, Collins J J
2016Selective depletion of abundant RNAs to enable transcriptome analysis of low-input and highly degraded human RNA.Curr. Protoc. Mol. Biol.Munafó, D.B., Langhorst, B.W., Chater, C.L., Sumner, C.J., Rodriguez, D.N., Russello, S., Gardner, A.F., Slatko, B.E., Stewart, F.J., Sinicropi, D., Morlan, J., Qu, K., Dimalanta, E.T., Davis, T.B.
2016Simple and Highly Sensitive Molecular Diagnosis of Zika Virus by Lateral Flow Assays.Anal Chem.Lee D, Shin Y, Chung S, Hwang KS, Yoon DS, Lee JH
2016Simple Isothermal Strategy for Multiplexed, Rapid, Sensitive, and Accurate miRNA DetectionACS SensWee E J H, Trau M,
2016Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstructionNature BiotechnologyMooijman D, Dey S S, Boisset JC, Crosetto N, van Oudenaarden AEpigenetics
2016Sensitive and specific miRNA detection method using SplintR LigasePublication.Nucleic Acids Res.Jin, J., Vaud, S., Zhelkovsky, A.M., Posfai, J. and McReynolds, L.A.
2016Sensitive Detection of Plasmodium vivax Using a High-Throughput, Colourimetric Loop Mediated Isothermal Amplification (HtLAMP) Platform: A Potential Novel Tool for Malaria Elimination.PLoS Negl Trop DisBritton, S., Cheng, Q., Grigg, M.J., Poole, C.B., Pasay, C., William, T., Fornace, K., Anstey, N.M., Sutherland, C.J., Drakeley, C. and McCarthy, J.S.
2016Sequential formation of two branched intermediates during protein splicing of class three inteinsExtremophilesTori, K. and Perler, F.
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.
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.
2016Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads.Sci Rep.Jiang, G.F. et al.
2016Characterization of innate immunity genes in the parasitic nematode Brugia malayiSymbiosisLibro, S., Slatko, B.E. and Foster, J.M.
2016Characterizing Two Inter-specific Bin Maps for the Exploration of the QTLs/Genes that Confer Three Soybean Evolutionary Traits.Front Plant Sci. Wang W, Liu M, Wang Y, Li X, Cheng S, Shu L, Yu Z, Kong J, Zhao T, Gai J.
2016COMBREX-DB: An experiment centered database of protein function: knowledge, predictions and knowledge gaps. Nucl. Acids Res.Chang, Y.-C., Hu, Z., Rachlin, J., Anton, B.P., Kasif, S., Roberts, R.J. and Steffen, 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.
2016Complete genome sequence of Brevibacterium linens SMQ-1335.Genome AnnouncementsDe Melo, A., Labrie, S., Dumaresq, J., Roberts, R., Tremblay, D. and Moineau, S.
2016Complete Genome Sequence of Escherichia coli ER1821R, a Laboratory K-12 Derivative Engineered To Be Deficient in All Methylcytosine and Methyladenine Restriction SystemsGenome Announc.Jobling, M.G., Raleigh, E.A. and Frank, D.N.
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 and methylome sequences of two SalmonellaGenome AnnouncementsYao, K., Muruvanda, T., Roberts, R.J., Payne, J., Allard, M.W., Hoffmann, M.