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We believe that basic research and the cultivation of scientific knowledge is critical for us to stay connected with our customers and to drive scientific breakthroughs. At NEB, over 30 labs participate in research projects, which are aided by post-doctoral fellows and students in Masters and Ph.D. programs. NEB researchers have authored or co-authored over 1,000 publications (as of 1/17) many of which are in peer-reviewed journals. Further, NEB products have been used successfully in numerous publications by scientists throughout the world.

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Year Title Journal Authors Application(s)
2017 The advantages of SMRT™ sequencing.  Genome Biology Roberts, R.J., Carneiro, M.O., Schatz, M.C.
2017 ​Colorimetric tests for diagnosis of filarial infection and vector surveillance using non-instrumented nucleic acid loop-mediated isothermal amplification (NINA-LAMP). PLoS One Poole, 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.
2017 Examining Sources of Error in PCR by Single-Molecule Sequencing. PLoS ONE Potapov Vladamir, Ong Jennifer L
2017 Rapid Time Scale Analysis of T4 DNA Ligase–DNA Binding. Biochemistry Bauer, R.J., Jurkiw, T.J., Evans, T.C. Jr. and Lohman, G.J.
2017 Methods for structural and functional analyses of intramembrane prenyltransferases in the UbiA superfamily Methods Enzymol Yang, Y., Ke, N., Liu, S., Li, W.
2017 Mechanism and timing of Mcm2-7 ring closure during DNA replication origin licensing Nat. Struct. Mol. Biol. Ticau, S., Friedman, L.J., Champasa, K., Correa, I.R., Jr., Gelles, J., Bell, S.P.
2017 Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host rematode RNA by Cappable-seqTM PLoS One Luck, A.N., Slatko, B.E., Foster, J.M.
2017 NicE-seq: High resolution open chromatin profiling Genome Biology Ponnaluri, V.K.C., Zhang, G., Estève, P.-O., Spracklin, G., Sian, S., Xu, S.-Y., Benoukraf, T., Pradhan, S.
2017 Genome Announce Genome Announce. Fomenkov, A., Akimov, V.N., Vasilyeva, L.V., Andersen, D.T., Vincze, T., Roberts, R.J.
2017 High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding PNAS Evan A. Boyle, Johan O.L. Andreasson, Lauren M. Chircus, Samuel H. Sternberg, Michelle J. Wu, Chantal K. Guegler, Jennifer A. Doudna, and William J. Greenleaf
2017 Macrocycle peptides delineate locked-open inhibition mechanism for micoorganism phosphoglycerate mutases Nat. 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.
2017 Highly specific imaging of mRNA in single cells by target RNA-initiated rolling circle amplification Chem Sci Deng, Ruijie., Zhang, Kaixiang., Sun, Yupeng., Ren, Xiaojun., Li, Jinghong.
2017 The GAN exonuclease, or the flap endonuclease Fen1 and RNase HII are necessary for viability of Thermococcus kodakarensis J. Bacteriol Burkhart, B.W., Cubonova, L., Heider, M.R., Kelman, Z., Reeve, J.N., Santangelo, T.J.
2017 Whole genome amplification provides suitable control DNA for use in DNA barcoding applications Biop. Bourque, D.A., Naaum, A.M., Distel, D.L., Hanner, R.H.
2017 Targeted enrichment and sequencing of recent endosymbiont-host lateral gene transfers Sci Rep. Dunning Hotopp, J.C., Slatko, B.E., Foster, J.M.
2017 Various Mutations compensate for a deleterious lacZα insert in the replication enhancer of M13 bacteriophage PLoS One Zygiel, 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.
2017 Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and their Contribution to Rec-A-Independent Horizontal Transfer J. Bacteriol Kingston, A.W., Ponkratz, C. and Raleigh, E.A.
2017 Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA Nucleic Acids Res. Tamulaitiene, G., Jovaisaite, V., Tamulaitis, G., Songailiene, I., Manakova, E., Zaremba, M., Grazulis, S., Xu, S.Y., Siksnys, V.
2017 Serotyping dengue virus with isothermal amplification and a portable sequencer Scientific Reports Yamagishi, J., et al.
2017 Sequential formation of two branched intermediates during protein splicing of class three inteins Extrmophiles Tori, K. and Perler, F.
2017 Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression Epigenetics Ponnaluri, V.K., Ehrlich, K.C., Zhang, G., Lacey, M., Johnston, D., Pradhan, S., Ehrlich, M.
2017 A refined DNA methylation detection method using MspJI coupled quantitative PCR Analytical Biochemistry Petell, C.J., Loiseau, G., Gandy, R., Pradhan, S., Gowher, H.
2017 Complete genome sequence and methylome analysis of Acinetobacter calcoaceticus 65 Fomenkov, A., Vincze, T., Degtyarev, S.K., Roberts, R.J.
2017 Complete genome and methylome sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB collection Genome Announce Yao, K., Roberts, R.J., Allard, M.W., Hoffmann, M.
2017 A practical guide to the oral microbiome and its relation to health and disease Krishnan, K., Chen, T., Paster, B.J.
2017 EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determination PLoS One Fomenkov, A., Sun, Z., Dila, D.K., Anton, B.P., Roberts, R.J., Raleigh, E.A.
2017 Dynamics of 5-carboxylcytosine during hepatic differentiation: potential general role for active demethylation by DNA repair in lineage specification Lewis, 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.
2017 Functional characterisation of cis-regulatory elements governing dynamic Eomes expression Development Simon, C.S. et al.
2017 Evaluating computatonal gene ontology annotations Methods Mol. Biol. Skunca, N., Roberts, R.J., Steffen, M.
2017 DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification Science Chen, L., Liu, P., Evans, T.C., Jr., Ettwiller, L.M.
2017 Defining the RNaseH2 enzyme-initiated ribonucleotide excision repair pathway in Archaea J. Biol Chem. Heider, M.R., Burkhart, B.W., Santangelo, T.J., Gardner, A.F.
2017 DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus Nucl. 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.
2017 DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target Nucl. Acids Res. Shen, B.W., Heiter, D.F., Lunnen, K.D., Wilson, G.G., Stoddard, B.L.
2017 De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii BMC Genomics Deptula, P., Laine, P.K., Roberts, R.J., Smolander, O.-P., Vihinen, H., Piironen, V., Paulin, L., Jokitalo, E., Savijoki, K., Auvinen, P., Varmanen, P.
2017 Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia Johnston, C.D., Skeete, C.A., Fomenkov, A., Roberts, R.J., Rittling, S.R.
2016 Visualization of Periplasmic and Cytoplasmic Proteins with a Self-Labeling Protein Tag. J Bacteriol Ke, N., Landgraf, D., Paulsson, J. and Berkmen, M.
2016 Using glycosidases to remove, trim, or modify glycans on therapeutic proteins BioProcess International Guthrie, E.P., Magneilli, P.E.
2016 The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase. PLoS One Bauer, R.J., Evans, T.C. Jr. and Lohman, G.J.
2016 Sensitive 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 Dis Britton, 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.
2016 The 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.
2016 Sensitive and specific miRNA detection method using SplintR LigasePublication. Nucleic Acids Res. Jin, J., Vaud, S., Zhelkovsky, A.M., Posfai, J. and McReynolds, L.A.
2016 Structure 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.
2016 Phenotypic and molecular analysis of the effect of 20-hydroxyecdysone on the human filarial parasite Brugia malayi. Int J Parasitol Mhashilkar, 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.
2016 A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome. BMC Genomics Ettwiller, L., Buswell, J., Yigit, E. and Schildkraut, I
2016 A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders. Sci Rep Cui, 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.
2016 Absence 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.
2016 Comprehensive 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.
2016 Complete 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.
2016 Genetics: profiling DNA methylation and beyond Nature Methods Marx V. Epigenetics,Restriction Enzymes for Epigenetics
2016 Genetically anchored fluorescent probes for subcellular specific imaging of hydrogen sulfide. Analyst Chen, J., Zhao, M., Jiang, X., Sizovs, A., Wang, M.C., Provost, C.R., Huang, J. and Wang, J.
2016 Complete 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.
2016 Characterization of innate immunity genes in the parasitic nematode Brugia malayi Symbiosis Libro, S., Slatko, B.E. and Foster, J.M.
2016 AnnoTALE: 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.
2016 Complete 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.
2016 Complete 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.
2016 Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts. Genome Biol. Evol. Qi, W. et al.
2016 Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencing Sex. Transm. Infect Graham, R.M.A. et al.
2016 The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease Sci Rep. Hieken, T.J. et al.
2016 omplete Genome Sequence and Methylome Analysis of Bacillus globigii ATCC 49760. Genome Announc. Morgan, R.D.
2016 Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy induced neutropenia. Sci Rep. Gyarmati, P. et al.
2016 Genomic study of the Ket: a PaleoEskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci Rep. Flegontov, P. et al.
2016 Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses. Chemical Reviews Weigele, P.W. and Raleigh, E. A.
2016 Identification 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.
2016 mRNA capping: biological functions and applications. Nucleic Acids Res Ramanathan, A., Robb, G.B. and Chan, S.H.
2016 Detecting DNA Methylation using the Oxford Nanopore Technologies MinION sequencer bioRxiv Simpson, J.T. et al.
2016 Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria. ISME J. Seth-Smith, M.B.P. et al.
2016 Type II restriction endonucleases - a historical perspective and more. Nucleic Acids Res Pingoud, A., Wilson, G.G. and Wende, W.
2016 Jmjd2/Kdm4 demethylases are required for expression of Il3ra and survival of acute myeloid leukemia cells Genes & Dev Agger, K. et al.
2016 Reminder to deposit DNA sequences Science Blaxter, M., Danchin, A., Savakis, B., Fukami-Kobayashi, K., Kurokawa, K., Sugano, S., Roberts, R.J., Salzberg, S.L. and Wu, C.I.
2016 Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes Sci Rep Xu, S.Y., Klein, P., Degtyarev, S.K.h. and Roberts, R.J.
2016 Advanced uracil DNA glycosylase-supplemented real-time reverse transcription loop-mediated isothermal amplification (UDG-rRT-LAMP) method for universal and specific detection of Tembusu virus Scientific Reports Tang Y, Chen H, Diao Y
2016 Folate-/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.
2016 Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling Genome Biology Flygare, S. et al.
2016 A DsbA-Deficient Periplasm Enables Functional Display of a Protein with Redox-Sensitive Folding on M13 Phage. Biochemistry Chen, M., Samuelson, J.C.
2016 Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes G3 Fu YB, Peterson G. W., Dong Y Restriction Enzyme Digestion,Restriction Enzyme Digestion
2016 Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi. PLoS One Anton, B.P., Harhay, G.P., Smith, T.P., Blom, J. and Roberts, R.J.
2016 Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes. BMC Genomics Taylor-Brown, A. et al.
2016 Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads. Sci Rep. Jiang, G.F. et al.
2016 Comparison 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.
2016 Derivative Engineered To Be Deficient in All Methylcytosine and Methyladenine Restriction Systems. Genome Announc. Jobling, M.G., Raleigh, E.A. and Frank, D.N.
2016 Use of the Shuffle Strains in Production of Proteins. Curr Protoc Protein Sci. Ren, G., Ke, N. and Berkmen, M.
2016 Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction Nature Biotechnology Mooijman D, Dey S S, Boisset JC, Crosetto N, van Oudenaarden A Epigenetics
2016 Simple Isothermal Strategy for Multiplexed, Rapid, Sensitive, and Accurate miRNA Detection ACS Sens Wee E J H, Trau M,
2016 WGS 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 Salmonella. J Antimicrob Chemother. Nair, S. et al.
2016 High-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.
2016 Erratum 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.
2016 Heme acquisition in the parasitic filarial nematode Brugia malayi. FASEB J. Luck AN, Yuan X, Voronin D, Slatko BE, Hamza I, Foster JM.
2016 Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Medicine Doan, T. et al.
2016 Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components Cell Pardee 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
2016 Quantitative profiling of glycans and glycopeptides: an informatics' perspective Curr Opin Struct Biol. Walsh, I., Zhao, S., Campbell, M., Taron, C.H. and Rudd, P.M.
2016 Perpetuating 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.
2016 Phytochromes function as thermosensors in Arabidopsis. Science Jung, J-H. et al.
2016 Profiling 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.
2016 Novel 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.
2016 Reconstitution 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.
2016 Redox 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.
2016 Novel 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.
2016 Complete genome and methylome sequences of two Salmonella Genome Announcements Yao, K., Muruvanda, T., Roberts, R.J., Payne, J., Allard, M.W., Hoffmann, M.
2016 Denys-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.
2016 Metabolic Incorporation of Azide Functionality into Cellular RNA. Chembiochem Nainar, S., Beasley, S., Fazio, M., Kubota, M., Dai, N., Correa, I.R. Jr. and Spitale, R.C.