Publications

Publications

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YearTitleJournalAuthorsApplication(s)
2017Examining Sources of Error in PCR by Single-Molecule Sequencing.PLoS ONEPotapov Vladamir, Ong Jennifer L
2017Rapid Time Scale Analysis of T4 DNA Ligase–DNA Binding.BiochemistryBauer, R.J., Jurkiw, T.J., Evans, T.C. Jr. and Lohman, G.J.
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.
2017Functional characterisation of cis-regulatory elements governing dynamic Eomes expressionDevelopmentSimon, C.S. et al.
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.
2017Genome AnnounceGenome Announce.Fomenkov, A., Akimov, V.N., Vasilyeva, L.V., Andersen, D.T., Vincze, T., Roberts, R.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.
2017Targeted enrichment and sequencing of recent endosymbiont-host lateral gene transfersSci Rep.Dunning Hotopp, J.C., Slatko, B.E., Foster, J.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.
2017Complete genome sequence and methylome analysis of Acinetobacter calcoaceticus 65Fomenkov, A., Vincze, T., Degtyarev, S.K., Roberts, R.J.
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.
2017A practical guide to the oral microbiome and its relation to health and diseaseKrishnan, K., Chen, T., Paster, B.J.
2017DNA damage is a pervasive cause of sequencing errors, directly confounding variant identificationScienceChen, L., Liu, P., Evans, T.C., Jr., Ettwiller, L.M.
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.
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.
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.
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.
2017Methods for structural and functional analyses of intramembrane prenyltransferases in the UbiA superfamilyMethods EnzymolYang, Y., Ke, N., Liu, S., Li, W.
2017Sequential formation of two branched intermediates during protein splicing of class three inteinsExtrmophilesTori, K. and Perler, F.
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.
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.
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.
2017Evaluating computatonal gene ontology annotationsMethods Mol. Biol.Skunca, N., Roberts, R.J., Steffen, M.
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.
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.
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.
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.
2017Serotyping dengue virus with isothermal amplification and a portable sequencerScientific ReportsYamagishi, J., et al.
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.
2016A DsbA-Deficient Periplasm Enables Functional Display of a Protein with Redox-Sensitive Folding on M13 Phage.BiochemistryChen, M., Samuelson, J.C.
2016A Genetic Map for the Only Self-Fertilizing Vertebrate.G3 (Bethesda)Kanamori A, Sugita Y, Yuasa Y, Suzuki T, Kawamura K, Uno Y, Kamimura K, Matsuda Y, Wilson CA, Amores A, Postlethwait JH, Suga K, Sakakura Y.
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.
2016A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome.BMC GenomicsEttwiller, L., Buswell, J., Yigit, E. and Schildkraut, I
2016Absence of the filarial endosymbiont Wolbachia in seal heartworm (Acanthocheilonema spirocauda) but evidence of ancient lateral gene transfer.J Parasitol.Keroack, C.D., Wurster, J.I., Decker, C.G., Williams, K.M., Slatko, B.E., Foster, J.M. and Williams, S.A.
2016Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments.Ecol Evol. Araneda C, Larraín MA, Hecht B, Narum S.
2016Advanced uracil DNA glycosylase-supplemented real-time reverse transcription loop-mediated isothermal amplification (UDG-rRT-LAMP) method for universal and specific detection of Tembusu virusScientific ReportsTang Y, Chen H, Diao Y
2016AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences.Sci Rep.Grau, J., Reschke, M., Erkes, A., Streubel, J., Morgan, R.D., Wilson, G.G., Koebnik, R. and Boch, J.
2016Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expressionEpigenetics.Ponnaluri, V.K., Ehrlich, K.C., Zhang, G., Lacey, M., Johnston, D., Pradhan, S. and Ehrlich, M.
2016Binding of 14-3-3 reader proteins to phosphorylated DNMT1 facilitates aberrant DNA methylation and gene expression.Nucleic Acids Res.Esteve, P.O., Zhang, G., Ponnaluri, V.K., Deepti, K., Chin, H.G., Dai, N., Saqum, C., Black, K., Correa, I.R. Jr., Bedford, M.T., Cheng, X. and Pradhan, S.
2016Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses.Chemical ReviewsWeigele, P.W. and Raleigh, E. A.
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.
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.
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 and methylome sequences of two SalmonellaGenome AnnouncementsYao, K., Muruvanda, T., Roberts, R.J., Payne, J., Allard, M.W., Hoffmann, M.
2016Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile.Genome Announc.Lim, Y.L., Roberts, R.J., Ee, R., Yin, W.F. and Chan, K.G.
2016Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring.Genome Announc.Fomenkov, A., Vincze, T., Grabovich, M., Anton, B.P., Dubinina, G., Orlova, M., Belousova, E. and Roberts, R.J.
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 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.
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.
2016Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.PLoS One. Tong C, Li H, Wang Y, Li X, Ou J, Wang D, Xu H, Ma C, Lang X, Liu G, Zhang B, Shi J.
2016Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes. BMC Genomics Taylor-Brown, A. et al.
2016De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies.BMC GenomicsMousavi M, Tong C, Liu F, Tao S, Wu J, Li H, Shi J.
2016Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications.Nucleic Acids Res.Hashimoto, H., Zhang, X., Zheng, Y., Wilson, G.G. and Cheng, X.
2016Derivative Engineered To Be Deficient in All Methylcytosine and Methyladenine Restriction Systems.Genome Announc.Jobling, M.G., Raleigh, E.A. and Frank, D.N.
2016<a href="http://biorxiv.org/content/early/2016/04/04/047142" target="_blank">Detecting DNA Methylation using the Oxford Nanopore Technologies MinION sequencer</a>bioRxivSimpson, J.T. et al.
2016Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding.PLoS One. Fan W, Zong J, Luo Z, Chen M, Zhao X, Zhang D, Qi Y, Yuan Z.
2016Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants.Plant Methods. Yang GQ, Chen YM, Wang JP, Guo C, Zhao L, Wang XY, Guo Y, Li L, Li DZ, Guo ZH.
2016DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A: T-rich target.Nucleic Acids Res. Shen, B.W., Heiter, D.F., Lunnen, K.D., Wilson, G.G. and Stoddard, B.L.
2016Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria.ISME J.Seth-Smith, M.B.P. et al.
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.
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.
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.
2016Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing.PLoS One. Yang H, Wei CL, Liu HW, Wu JL, Li ZG, Zhang L, Jian JB, Li YY, Tai YL, Zhang J, Zhang ZZ, Jiang CJ, Xia T, Wan XC.
2016Genetically anchored fluorescent probes for subcellular specific imaging of hydrogen sulfide.AnalystChen, J., Zhao, M., Jiang, X., Sizovs, A., Wang, M.C., Provost, C.R., Huang, J. and Wang, J.
2016Genetics: profiling DNA methylation and beyondNature MethodsMarx V.Epigenetics, Restriction Enzymes for Epigenetics
2016Genomic study of the Ket: a PaleoEskimo-related ethnic group with significant ancient North Eurasian ancestry.Sci Rep.Flegontov, P. et al.
2016Global repositioning of transcription start sites in a plant-fermenting bacterium.Nat CommunBoutard, M., Ettwiller, L., Cerisy, T., Alberti, A., Labadie, K., Salanoubat, M., Schildkraut, I. and Tolonen, A.C.
2016Heme acquisition in the parasitic filarial nematode Brugia malayi.FASEB J.Luck AN, Yuan X, Voronin D, Slatko BE, Hamza I, Foster JM.
2016Heme acquisition in the parasitic filarial nematode Brugia malayi.FASEB J. Luck, A.N., Yuan, X., Voronin, D., Slatko, B.E., Hamza, I. and Foster, J.M.
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.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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.