Publications

Publications

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YearTitleJournalAuthorsApplication(s)
2017Examining Sources of Error in PCR by Single-Molecule Sequencing.PLoS ONEPotapov Vladamir, Ong Jennifer L
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.
2016Efficient In Situ Detection of mRNAs using the Chlorella virus DNA ligase for Padlock Probe LigationRNASchneider, N and Meier, M.
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.
2016Folate-/FAD-dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures.Genes Cells Yamagami, R., Tomikawa, C., Shigi, N., Kazayama, A., Asai, S.I., Takuma, H., Hirata, A., Fourmy, D., Asahara, H., Watanabe, K., Yoshizawa, S. and Hori, H.
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.
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
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 sequencesPublicationScience Blaxter, M., Danchin, A., Savakis, B., Fukami-Kobayashi, K., Kurokawa, K., Sugano, S., Roberts, R.J., Salzberg, S.L. and Wu, C.I.
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.
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
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 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.
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.
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 Res Pingoud, 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.
2016Using glycosidases to remove, trim, or modify glycans on therapeutic proteinsPublication.BioProcess 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.
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
2015A database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids ResearchRoberts, R.J., Vincze, T., Posfai, J., Macelis, D.
2015A high-throughput assay for the comprehensive profiling of DNA ligase fidelityNucleic Acids ResLohman GJ, Bauer RJ, Nichols NM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Evans TC Jr.
2015A lipid switch unlocks Parkinson's disease-associated ATP13A2Proc Natl Acad Sci U S AHolemans T., Sørensen DM., Veen S., Martin S., Hermans D., Kemmer GC., Haute C., Baekelandt V., Pomorski TG., Agostinis P., Wuytack F., Palmgren M., Eggermont J., Vangheluwe P.
2015A metagenomics and case-control study to identify viruses associated with bovine respiratory disease.J VirolTerry Fei Fan Ng, Nikola O Kondov, Xutao Deng, Alison Van Eenennaam, Holly L Neibergs, Eric DelwartcDNA Synthesis
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.
2015A Proline-Rich Domain in the Genotype 4 Hepatitis E Virus ORF3 PLoS OneWang H., Fangxiao J., Liang H., Gu H.