@article{RN143, author = {LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey}, title = {Deep learning}, journal = {Nature}, volume = {521}, number = {7553}, pages = {436-444}, ISSN = {0028-0836}, DOI = {10.1038/nature14539}, url = {http://dx.doi.org/10.1038/nature14539}, year = {2015}, type = {Journal Article} } @article{RN35, author = {Badran, A. H. and Guzov, V. M. and Huai, Q. and Kemp, M. M. and Vishwanath, P. and Kain, W. and Nance, A. M. and Evdokimov, A. and Moshiri, F. and Turner, K. H. and Wang, P. and Malvar, T. and Liu, D. R.}, title = {Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance}, journal = {Nature}, volume = {533}, number = {7601}, pages = {58-63}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature17938}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27120167 http://www.nature.com/nature/journal/v533/n7601/pdf/nature17938.pdf}, year = {2016}, type = {Journal Article} } @article{RN95, author = {Jain, Miten and Olsen, Hugh E. and Paten, Benedict and Akeson, Mark}, title = {The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community}, journal = {Genome Biology}, volume = {17}, number = {1}, pages = {239}, ISSN = {1474-760X}, DOI = {10.1186/s13059-016-1103-0}, url = {http://dx.doi.org/10.1186/s13059-016-1103-0 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124260/pdf/13059_2016_Article_1103.pdf}, year = {2016}, type = {Journal Article} } @article{RN141, author = {Norris, A. L. and Workman, R. E. and Fan, Y. and Eshleman, J. R. and Timp, W.}, title = {Nanopore sequencing detects structural variants in cancer}, journal = {Cancer Biol Ther}, volume = {17}, DOI = {10.1080/15384047.2016.1139236}, url = {http://dx.doi.org/10.1080/15384047.2016.1139236}, year = {2016}, type = {Journal Article} } @article{RN136, author = {Wescoe, Z. L. and Schreiber, J. and Akeson, M.}, title = {Nanopores discriminate among five C5-cytosine variants in DNA}, journal = {J Am Chem Soc}, volume = {136}, DOI = {10.1021/ja508527b}, url = {http://dx.doi.org/10.1021/ja508527b}, year = {2014}, type = {Journal Article} } @article{RN134, author = {Wei, S. and Williams, Z.}, title = {Rapid short-read sequencing and aneuploidy detection using MinION nanopore technology}, journal = {Genetics}, volume = {202}, DOI = {10.1534/genetics.115.182311}, url = {http://dx.doi.org/10.1534/genetics.115.182311}, year = {2016}, type = {Journal Article} } @article{RN133, author = {Watson, M. and Thomson, M. and Risse, J. and Talbot, R. and Santoyo-Lopez, J. and Gharbi, K.}, title = {poRe: an R package for the visualization and analysis of nanopore sequencing data}, journal = {Bioinformatics}, volume = {31}, DOI = {10.1093/bioinformatics/btu590}, url = {http://dx.doi.org/10.1093/bioinformatics/btu590}, year = {2015}, type = {Journal Article} } @article{RN132, author = {Ward, A. C. and Kim, W.}, title = {MinIONTM: new, long read, portable nucleic acid sequencing device}, journal = {J Bacteriol Virol}, volume = {45}, DOI = {10.4167/jbv.2015.45.4.285}, url = {http://dx.doi.org/10.4167/jbv.2015.45.4.285}, year = {2015}, type = {Journal Article} } @article{RN135, author = {Schreiber, J. and Wescoe, Z. L. and Abu-Shumays, R. and Vivian, J. T. and Baatar, B. and Karplus, K.}, title = {Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, DOI = {10.1073/pnas.1310615110}, url = {http://dx.doi.org/10.1073/pnas.1310615110}, year = {2013}, type = {Journal Article} } @article{RN139, author = {Loose, M. and Malla, S. and Stout, M.}, title = {Real time selective sequencing using nanopore technology}, journal = {Nat Methods}, volume = {13}, DOI = {10.1038/nmeth.3930}, url = {http://dx.doi.org/10.1038/nmeth.3930}, year = {2016}, type = {Journal Article} } @misc{RN138, type = {Generic} } @misc{RN137, type = {Generic} } @article{RN130, author = {Wang, J. and Moore, N. E. and Deng, Y. -. M. and Eccles, D. A. and Hall, R. J.}, title = {MinION nanopore sequencing of an influenza genome}, journal = {Front Microbiol}, volume = {6}, year = {2015}, type = {Journal Article} } @article{RN129, author = {Risse, J. and Thomson, M. and Patrick, S. and Blakely, G. and Koutsovoulos, G. and Blaxter, M.}, title = {A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data}, journal = {Gigascience}, volume = {4}, DOI = {10.1186/s13742-015-0101-6}, url = {http://dx.doi.org/10.1186/s13742-015-0101-6}, year = {2015}, type = {Journal Article} } @article{RN128, author = {Ramgren, A. C. and Newhall, H. S. and James, K. E.}, title = {DNA barcoding and metabarcoding with the Oxford Nanopore MinION}, journal = {Genome}, volume = {58}, year = {2015}, type = {Journal Article} } @article{RN127, author = {Quick, J. and Quinlan, A. R. and Loman, N. J.}, title = {A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer}, journal = {Gigascience}, volume = {3}, DOI = {10.1186/2047-217x-3-22}, url = {http://dx.doi.org/10.1186/2047-217X-3-22}, year = {2014}, type = {Journal Article} } @article{RN126, author = {Quick, J. and Loman, N. J. and Duraffour, S. and Simpson, J. T. and Severi, E. and Cowley, L.}, title = {Real-time, portable genome sequencing for ebola surveillance}, journal = {Nature}, volume = {530}, DOI = {10.1038/nature16996}, url = {http://dx.doi.org/10.1038/nature16996}, year = {2016}, type = {Journal Article} } @article{RN124, author = {Quick, J. and Ashton, P. and Calus, S. and Chatt, C. and Gossain, S. and Hawker, J.}, title = {Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella}, journal = {Genome Biol}, volume = {16}, DOI = {10.1186/s13059-015-0677-2}, url = {http://dx.doi.org/10.1186/s13059-015-0677-2}, year = {2015}, type = {Journal Article} } @article{RN123, author = {Pallen, M. J.}, title = {Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections}, journal = {Parasitology}, volume = {141}, DOI = {10.1017/s0031182014000134}, url = {http://dx.doi.org/10.1017/S0031182014000134}, year = {2014}, type = {Journal Article} } @article{RN122, author = {Miller, R. R. and Montoya, V. and Gardy, J. L. and Patrick, D. M. and Tang, P.}, title = {Metagenomics for pathogen detection in public health}, journal = {Genome Med}, volume = {5}, DOI = {10.1186/gm485}, url = {http://dx.doi.org/10.1186/gm485}, year = {2013}, type = {Journal Article} } @article{RN121, author = {Miles, G. and Hoisington-Lopez, J. and Duncavage, E.}, title = {Nanopore sequencing of a DNA library prepared from formalin-fixed paraffin-embedded tissue}, journal = {Lab Invest}, volume = {95}, year = {2015}, type = {Journal Article} } @misc{RN131, type = {Generic} } @misc{RN125, type = {Generic} } @article{RN108, author = {Sović, I. and Šikić, M. and Wilm, A. and Fenlon, S. N. and Chen, S. and Nagarajan, N.}, title = {Fast and sensitive mapping of nanopore sequencing reads with GraphMap}, journal = {Nat Commun}, volume = {7}, DOI = {10.1038/ncomms11307}, url = {http://dx.doi.org/10.1038/ncomms11307}, year = {2016}, type = {Journal Article} } @article{RN106, author = {Quick, J. and Quinlan, A. and Loman, N.}, title = {A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer}, journal = {GigaScience}, volume = {3}, DOI = {10.1186/2047-217x-3-22}, url = {http://dx.doi.org/10.1186/2047-217X-3-22}, year = {2014}, type = {Journal Article} } @article{RN120, author = {Mikheyev, A. S. and Tin, M. M. Y.}, title = {A first look at the Oxford Nanopore MinION sequencer}, journal = {Mol Ecol Resour}, volume = {14}, DOI = {10.1111/1755-0998.12324}, url = {http://dx.doi.org/10.1111/1755-0998.12324}, year = {2014}, type = {Journal Article} } @article{RN119, author = {Madoui, M. -. A. and Engelen, S. and Cruaud, C. and Belser, C. and Bertrand, L. and Alberti, A.}, title = {Genome assembly using Nanopore-guided long and error-free DNA reads}, journal = {BMC Genomics}, volume = {16}, DOI = {10.1186/s12864-015-1519-z}, url = {http://dx.doi.org/10.1186/s12864-015-1519-z}, year = {2015}, type = {Journal Article} } @article{RN118, author = {Loman, N. J. and Quinlan, A. R.}, title = {Poretools: a toolkit for analyzing nanopore sequence data}, journal = {Bioinformatics}, volume = {30}, DOI = {10.1093/bioinformatics/btu555}, url = {http://dx.doi.org/10.1093/bioinformatics/btu555}, year = {2014}, type = {Journal Article} } @article{RN117, author = {Loman, N. J. and Pallen, M. J.}, title = {Twenty years of bacterial genome sequencing}, journal = {Nat Rev Microbiol}, volume = {13}, DOI = {10.1038/nrmicro3565}, url = {http://dx.doi.org/10.1038/nrmicro3565}, year = {2015}, type = {Journal Article} } @article{RN116, author = {Leggett, R. M. and Heavens, D. and Caccamo, M. and Clark, M. D. and Davey, R. P.}, title = {NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles}, journal = {Bioinformatics}, volume = {32}, year = {2016}, type = {Journal Article} } @article{RN107, author = {Kilianski, A. and Haas, J. L. and Corriveau, E. J. and Liem, A. T. and Willis, K. L. and Kadavy, D. R.}, title = {Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer}, journal = {Gigascience}, volume = {4}, DOI = {10.1186/s13742-015-0051-z}, url = {http://dx.doi.org/10.1186/s13742-015-0051-z}, year = {2015}, type = {Journal Article} } @article{RN114, author = {Karlsson, E. and Lärkeryd, A. and Sjödin, A. and Forsman, M. and Stenberg, P.}, title = {Scaffolding of a bacterial genome using MinION nanopore sequencing}, journal = {Sci Rep}, volume = {5}, DOI = {10.1038/srep11996}, url = {http://dx.doi.org/10.1038/srep11996}, year = {2015}, type = {Journal Article} } @article{RN113, author = {Judge, K. and Harris, S. R. and Reuter, S. and Parkhill, J. and Peacock, S. J.}, title = {Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes}, journal = {J Antimicrob Chemother}, volume = {70}, DOI = {10.1093/jac/dkv206}, url = {http://dx.doi.org/10.1093/jac/dkv206}, year = {2015}, type = {Journal Article} } @article{RN105, author = {Jain, M. and Fiddes, I. T. and Miga, K. H. and Olsen, H. E. and Paten, B. and Akeson, M.}, title = {Improved data analysis for the MinION nanopore sequencer}, journal = {Nat Methods}, volume = {12}, DOI = {10.1038/nmeth.3290}, url = {http://dx.doi.org/10.1038/nmeth.3290}, year = {2015}, type = {Journal Article} } @article{RN111, author = {Hargreaves, A. D. and Mulley, J. F.}, title = {Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing}, journal = {Peer J}, volume = {3}, DOI = {10.7717/peerj.1441}, url = {http://dx.doi.org/10.7717/peerj.1441}, year = {2015}, type = {Journal Article} } @article{RN110, author = {Greninger, A. L. and Naccache, S. N. and Federman, S. and Yu, G. and Mbala, P. and Bres, V.}, title = {Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis}, journal = {Genome Med}, volume = {7}, DOI = {10.1186/s13073-015-0220-9}, url = {http://dx.doi.org/10.1186/s13073-015-0220-9}, year = {2015}, type = {Journal Article} } @article{RN109, author = {Goodwin, S. and Gurtowski, J. and Ethe-Sayers, S. and Deshpande, P. and Schatz, M. C. and McCombie, W. R.}, title = {Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome}, journal = {Genome Res}, volume = {25}, DOI = {10.1101/gr.191395.115}, url = {http://dx.doi.org/10.1101/gr.191395.115}, year = {2015}, type = {Journal Article} } @article{RN112, author = {Cao, M. D. and Ganesamoorthy, D. and Elliott, A. and Zhang, H. and Cooper, M. A. and Coin, L. J. M.}, title = {Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION™ sequencing}, journal = {GigaScience}, volume = {5}, DOI = {10.1186/s13742-016-0137-2}, url = {http://dx.doi.org/10.1186/s13742-016-0137-2}, year = {2016}, type = {Journal Article} } @misc{RN115, type = {Generic} } @article{RN104, author = {Bolisetty, M. T. and Rajadinakaran, G. and Graveley, B. R.}, title = {Determining exon connectivity in complex mRNAs by nanopore sequencing}, journal = {Genome Biol}, volume = {16}, DOI = {10.1186/s13059-015-0777-z}, url = {http://dx.doi.org/10.1186/s13059-015-0777-z}, year = {2015}, type = {Journal Article} } @article{RN101, author = {Manrao, E. A. and Derrington, I. M. and Laszlo, A. H. and Langford, K. W. and Hopper, M. K. and Nathaniel, G.}, title = {Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase}, journal = {Nat Biotechnol}, volume = {30}, DOI = {10.1038/nbt.2171}, url = {http://dx.doi.org/10.1038/nbt.2171}, year = {2012}, type = {Journal Article} } @article{RN102, author = {Ashton, P. M. and Nair, S. and Dallman, T. and Rubino, S. and Rabsch, W. and Mwaigwisya, S.}, title = {MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island}, journal = {Nat Biotechnol}, volume = {33}, DOI = {10.1038/nbt.3103}, url = {http://dx.doi.org/10.1038/nbt.3103}, year = {2015}, type = {Journal Article} } @article{RN99, author = {Cherf, G. M. and Lieberman, K. R. and Hytham, R. and Lam, C. E. and Kevin, K. and Mark, A.}, title = {Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision}, journal = {Nat Biotechnol}, volume = {30}, DOI = {10.1038/nbt.2147}, url = {http://dx.doi.org/10.1038/nbt.2147}, year = {2012}, type = {Journal Article} } @article{RN100, author = {Ayub, M. and Bayley, H.}, title = {Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore}, journal = {Nano Lett}, volume = {12}, DOI = {10.1021/nl3027873}, url = {http://dx.doi.org/10.1021/nl3027873}, year = {2012}, type = {Journal Article} } @article{RN98, author = {Kasianowicz, J. J. and Brandin, E. and Branton, D. and Deamer, D. W.}, title = {Characterization of individual polynucleotide molecules using a membrane channel}, journal = {Proc Natl Acad Sci U S A}, volume = {93}, DOI = {10.1073/pnas.93.24.13770}, url = {http://dx.doi.org/10.1073/pnas.93.24.13770}, year = {1996}, type = {Journal Article} } @article{RN97, author = {Deamer, D. and Akeson, M. and Branton, D.}, title = {Three decades of nanopore sequencing}, journal = {Nat Biotechnol}, volume = {34}, DOI = {10.1038/nbt.3423}, url = {http://dx.doi.org/10.1038/nbt.3423}, year = {2016}, type = {Journal Article} } @article{RN96, author = {Branton, D. and Daniel, B. and Deamer, D. W. and Andre, M. and Hagan, B. and Benner, S. A.}, title = {The potential and challenges of nanopore sequencing}, journal = {Nat Biotechnol}, volume = {26}, DOI = {10.1038/nbt.1495}, url = {http://dx.doi.org/10.1038/nbt.1495}, year = {2008}, type = {Journal Article} } @article{RN93, author = {Ondov, B. D. and Treangen, T. J. and Melsted, P. and Mallonee, A. B. and Bergman, N. H. and Koren, S.}, title = {Mash: fast genome and metagenome distance estimation using MinHash}, journal = {Genome Biol}, volume = {17}, DOI = {10.1186/s13059-016-0997-x}, url = {http://dx.doi.org/10.1186/s13059-016-0997-x}, year = {2016}, type = {Journal Article} } @misc{RN94, url = {https://github.com/minoTour/minoTour}, type = {Generic} } @article{RN91, author = {Chen, Y. -. T. and Iseli, C. and Venditti, C. A. and Old, L. J. and Simpson, A. J. G. and Jongeneel, C. V.}, title = {Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome}, journal = {Genes Chromosomes Cancer}, volume = {45}, DOI = {10.1002/gcc.20298}, url = {http://dx.doi.org/10.1002/gcc.20298}, year = {2006}, type = {Journal Article} } @article{RN92, author = {Berlin, K. and Koren, S. and Chin, C. -. S. and Drake, J. P. and Landolin, J. M. and Phillippy, A. M.}, title = {Assembling large genomes with single-molecule sequencing and locality-sensitive hashing}, journal = {Nat Biotechnol}, volume = {33}, DOI = {10.1038/nbt.3238}, url = {http://dx.doi.org/10.1038/nbt.3238}, year = {2015}, type = {Journal Article} } @article{RN89, author = {Nivala, J. and Marks, D. B. and Akeson, M.}, title = {Unfoldase-mediated protein translocation through an α-hemolysin nanopore}, journal = {Nat Biotechnol}, volume = {31}, DOI = {10.1038/nbt.2503}, url = {http://dx.doi.org/10.1038/nbt.2503}, year = {2013}, type = {Journal Article} } @article{RN90, author = {Hood, L. E. and Omenn, G. S. and Moritz, R. L. and Aebersold, R. and Yamamoto, K. R. and Amos, M.}, title = {New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences}, journal = {Proteomics}, volume = {12}, DOI = {10.1002/pmic.201270086}, url = {http://dx.doi.org/10.1002/pmic.201270086}, year = {2012}, type = {Journal Article} } @article{RN88, author = {Horgan, R. P. and Kenny, L. C.}, title = {‘Omic’ technologies: genomics, transcriptomics, proteomics and metabolomics}, journal = {Obstetrician Gynaecologist}, volume = {13}, DOI = {10.1576/toag.13.3.189.27672}, url = {http://dx.doi.org/10.1576/toag.13.3.189.27672}, year = {2011}, type = {Journal Article} } @misc{RN87, url = {https://vimeo.com/168851338}, type = {Generic} } @article{RN85, author = {Smith, A. M. and Abu-Shumays, R. and Akeson, M. and Bernick, D. L.}, title = {Capture, unfolding, and detection of individual tRNA molecules using a nanopore device}, journal = {Front Bioeng Biotechnol}, volume = {3}, DOI = {10.3389/fbioe.2015.00091}, url = {http://dx.doi.org/10.3389/fbioe.2015.00091}, year = {2015}, type = {Journal Article} } @article{RN86, author = {Henley, R. Y. and Ashcroft, B. A. and Farrell, I. and Cooperman, B. S. and Lindsay, S. M. and Wanunu, M.}, title = {Electrophoretic deformation of individual transfer RNA molecules reveals their identity}, journal = {Nano Lett}, volume = {16}, DOI = {10.1021/acs.nanolett.5b03331}, url = {http://dx.doi.org/10.1021/acs.nanolett.5b03331}, year = {2016}, type = {Journal Article} } @article{RN79, author = {Zaaijer, S.}, title = {Columbia University Ubiquitous Genomics 2015 Class, Erlich Y}, journal = {Elife}, volume = {5}, DOI = {10.7554/eLife.14258}, url = {http://dx.doi.org/10.7554/eLife.14258}, year = {2016}, type = {Journal Article} } @article{RN75, author = {Szalay, T. and Golovchenko, J. A.}, title = {De novo sequencing and variant calling with nanopores using PoreSeq}, journal = {Nat Biotechnol}, volume = {33}, DOI = {10.1038/nbt.3360}, url = {http://dx.doi.org/10.1038/nbt.3360}, year = {2015}, type = {Journal Article} } @article{RN72, author = {Loman, N. J. and Quick, J. and Simpson, J. T.}, title = {A complete bacterial genome assembled de novo using only nanopore sequencing data}, journal = {Nat Methods}, volume = {12}, DOI = {10.1038/nmeth.3444}, url = {http://dx.doi.org/10.1038/nmeth.3444}, year = {2015}, type = {Journal Article} } @article{RN76, author = {Li, C. and Chng, K. R. and Boey, J. H. E. and Ng, H. Q. A. and Wilm, A. and Nagarajan, N.}, title = {INC-Seq: accurate single molecule reads using nanopore sequencing}, journal = {GigaScience}, volume = {5}, DOI = {10.1186/s13742-016-0140-7}, url = {http://dx.doi.org/10.1186/s13742-016-0140-7}, year = {2016}, type = {Journal Article} } @article{RN74, author = {Lee, C. and Grasso, C. and Sharlow, M. F.}, title = {Multiple sequence alignment using partial order graphs}, journal = {Bioinformatics}, volume = {18}, DOI = {10.1093/bioinformatics/18.3.452}, url = {http://dx.doi.org/10.1093/bioinformatics/18.3.452}, year = {2002}, type = {Journal Article} } @article{RN77, author = {Hoenen, T. and Groseth, A. and Rosenke, K. and Fischer, R. J. and Hoenen, A. and Judson, S. D.}, title = {Nanopore sequencing as a rapidly deployable ebola outbreak tool}, journal = {Emerg Infect Dis}, volume = {22}, DOI = {10.3201/eid2202.151796}, url = {http://dx.doi.org/10.3201/eid2202.151796}, year = {2016}, type = {Journal Article} } @article{RN70, author = {Frith, M. C. and Hamada, M. and Horton, P.}, title = {Parameters for accurate genome alignment}, journal = {BMC Bioinformatics}, volume = {11}, DOI = {10.1186/1471-2105-11-80}, url = {http://dx.doi.org/10.1186/1471-2105-11-80}, year = {2010}, type = {Journal Article} } @article{RN73, author = {Eid, J. and Fehr, A. and Gray, J. and Luong, K. and Lyle, J. and Otto, G.}, title = {Real-time DNA sequencing from single polymerase molecules}, journal = {Science}, volume = {323}, DOI = {10.1126/science.1162986}, url = {http://dx.doi.org/10.1126/science.1162986}, year = {2009}, type = {Journal Article} } @article{RN81, author = {Chen, S. and Li, S. and Xie, W. and Li, X. and Zhang, C. and Jiang, H.}, title = {Performance comparison between rapid sequencing platforms for ultra-low coverage sequencing strategy}, journal = {PLoS One}, volume = {9}, DOI = {10.1371/journal.pone.0092192}, url = {http://dx.doi.org/10.1371/journal.pone.0092192}, year = {2014}, type = {Journal Article} } @misc{RN84, type = {Generic} } @misc{RN83, url = {http://www.nasa.gov/mission_pages/station/research/news/biomolecule_sequencer}, type = {Generic} } @misc{RN82, url = {http://www.technologyreview.com/s/601669/now-theyre-sequencing-dna-in-outer-space/}, type = {Generic} } @misc{RN80, url = {http://www.bio-itworld.com/2015/12/9/citizen-sequencers-taking-oxford-nanopores-minion-classroom-beyond.html}, type = {Generic} } @misc{RN78, url = {http://apps.who.int/ebola/current-situation/ebola-situation-report-11-november-2015}, type = {Generic} } @misc{RN71, type = {Generic} } @misc{RN69, type = {Generic} } @article{RN34, author = {Dovrat, D. and Aharoni, A.}, title = {Bioengineering: Evolved to overcome Bt-toxin resistance}, journal = {Nature}, volume = {533}, number = {7601}, pages = {39-40}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature17893}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27120166}, year = {2016}, type = {Journal Article} } @article{RN32, author = {Carlson, J. C. and Badran, A. H. and Guggiana-Nilo, D. A. and Liu, D. R.}, title = {Negative selection and stringency modulation in phage-assisted continuous evolution}, journal = {Nat Chem Biol}, volume = {10}, number = {3}, pages = {216-22}, ISSN = {1552-4469 (Electronic) 1552-4450 (Linking)}, DOI = {10.1038/nchembio.1453}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24487694}, year = {2014}, type = {Journal Article} } @article{RN68, author = {Bassalo, M. C. and Liu, R. and Gill, R. T.}, title = {Directed evolution and synthetic biology applications to microbial systems}, journal = {Curr Opin Biotechnol}, volume = {39}, pages = {126-33}, ISSN = {1879-0429 (Electronic) 0958-1669 (Linking)}, DOI = {10.1016/j.copbio.2016.03.016}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27054950}, year = {2016}, type = {Journal Article} } @book{RN33, author = {Alberts, Bruce}, title = {Molecular biology of the cell}, publisher = {Garland Science, Taylor and Francis Group}, address = {New York, NY}, edition = {Sixth edition.}, pages = {1 volume (various pagings)}, ISBN = {9780815344322 (hardcover) 0815344325 (hardcover) 9780815344643 (paperback) 0815344643 (paperback) 9780815345244 (looseleaf) 0815345240 (looseleaf)}, year = {2015}, type = {Book} } @article{RN67, author = {Willbanks, A. and Leary, M. and Greenshields, M. and Tyminski, C. and Heerboth, S. and Lapinska, K. and Haskins, K. and Sarkar, S.}, title = {The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences}, journal = {Genet Epigenet}, volume = {8}, pages = {25-36}, ISSN = {1179-237X (Linking)}, DOI = {10.4137/GEG.S31863}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27512339}, year = {2016}, type = {Journal Article} } @article{RN64, author = {Toth-Fejel, S. and Muller, P. and Ham, B. and Esvelt, K. and Dumas, N. and Calhoun, K. and Pommier, R.}, title = {DNA fingerprints provide a patient-specific breast cancer marker}, journal = {Ann Surg Oncol}, volume = {11}, number = {6}, pages = {560-7}, ISSN = {1068-9265 (Print) 1068-9265 (Linking)}, DOI = {10.1245/ASO.2004.03.049}, url = {https://www.ncbi.nlm.nih.gov/pubmed/15150063}, year = {2004}, type = {Journal Article} } @article{RN61, author = {Mali, P. and Yang, L. and Esvelt, K. M. and Aach, J. and Guell, M. and DiCarlo, J. E. and Norville, J. E. and Church, G. M.}, title = {RNA-guided human genome engineering via Cas9}, journal = {Science}, volume = {339}, number = {6121}, pages = {823-6}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.1232033}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23287722}, year = {2013}, type = {Journal Article} } @article{RN65, author = {Friedland, A. E. and Tzur, Y. B. and Esvelt, K. M. and Colaiacovo, M. P. and Church, G. M. and Calarco, J. A.}, title = {Heritable genome editing in C. elegans via a CRISPR-Cas9 system}, journal = {Nat Methods}, volume = {10}, number = {8}, pages = {741-3}, ISSN = {1548-7105 (Electronic) 1548-7091 (Linking)}, DOI = {10.1038/nmeth.2532}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23817069}, year = {2013}, type = {Journal Article} } @article{RN58, author = {Friedland, A. E. and Tzur, Y. B. and Esvelt, K. M. and Colaiacovo, M. P. and Church, G. M. and Calarco, J. A.}, title = {Heritable genome editing in C. elegans via a CRISPR-Cas9 system}, journal = {Nat Methods}, volume = {10}, number = {8}, pages = {741-3}, ISSN = {1548-7105 (Electronic) 1548-7091 (Linking)}, DOI = {10.1038/nmeth.2532}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23817069}, year = {2013}, type = {Journal Article} } @article{RN60, author = {Esvelt, K. M. and Wang, H. H.}, title = {Genome-scale engineering for systems and synthetic biology}, journal = {Mol Syst Biol}, volume = {9}, pages = {641}, ISSN = {1744-4292 (Electronic) 1744-4292 (Linking)}, DOI = {10.1038/msb.2012.66}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23340847}, year = {2013}, type = {Journal Article} } @article{RN66, author = {Esvelt, K. M. and Carlson, J. C. and Liu, D. R.}, title = {A system for the continuous directed evolution of biomolecules}, journal = {Nature}, volume = {472}, number = {7344}, pages = {499-503}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature09929}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21478873}, year = {2011}, type = {Journal Article} } @article{RN63, author = {Esvelt, K. M. and Carlson, J. C. and Liu, D. R.}, title = {A system for the continuous directed evolution of biomolecules}, journal = {Nature}, volume = {472}, number = {7344}, pages = {499-503}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature09929}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21478873}, year = {2011}, type = {Journal Article} } @article{RN59, author = {Dickinson, B. C. and Leconte, A. M. and Allen, B. and Esvelt, K. M. and Liu, D. R.}, title = {Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, number = {22}, pages = {9007-12}, ISSN = {1091-6490 (Electronic) 0027-8424 (Linking)}, DOI = {10.1073/pnas.1220670110}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23674678}, year = {2013}, type = {Journal Article} } @article{RN57, author = {Mali, P. and Aach, J. and Stranges, P. B. and Esvelt, K. M. and Moosburner, M. and Kosuri, S. and Yang, L. and Church, G. M.}, title = {CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering}, journal = {Nat Biotechnol}, volume = {31}, number = {9}, pages = {833-8}, ISSN = {1546-1696 (Electronic) 1087-0156 (Linking)}, DOI = {10.1038/nbt.2675}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23907171}, year = {2013}, type = {Journal Article} } @article{RN54, author = {Yaung, S. J. and Esvelt, K. M. and Church, G. M.}, title = {CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4}, journal = {PLoS One}, volume = {9}, number = {6}, pages = {e98811}, ISSN = {1932-6203 (Electronic) 1932-6203 (Linking)}, DOI = {10.1371/journal.pone.0098811}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24886988}, year = {2014}, type = {Journal Article} } @article{RN53, author = {Oye, K. A. and Esvelt, K. and Appleton, E. and Catteruccia, F. and Church, G. and Kuiken, T. and Lightfoot, S. B. and McNamara, J. and Smidler, A. and Collins, J. P.}, title = {Biotechnology. Regulating gene drives}, journal = {Science}, volume = {345}, number = {6197}, pages = {626-8}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.1254287}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25035410}, year = {2014}, type = {Journal Article} } @article{RN55, author = {Mali, P. and Esvelt, K. M. and Church, G. M.}, title = {Cas9 as a versatile tool for engineering biology}, journal = {Nat Methods}, volume = {10}, number = {10}, pages = {957-63}, ISSN = {1548-7105 (Electronic) 1548-7091 (Linking)}, DOI = {10.1038/nmeth.2649}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24076990}, year = {2013}, type = {Journal Article} } @article{RN56, author = {Esvelt, K. M. and Mali, P. and Braff, J. L. and Moosburner, M. and Yaung, S. J. and Church, G. M.}, title = {Orthogonal Cas9 proteins for RNA-guided gene regulation and editing}, journal = {Nat Methods}, volume = {10}, number = {11}, pages = {1116-21}, ISSN = {1548-7105 (Electronic) 1548-7091 (Linking)}, DOI = {10.1038/nmeth.2681}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24076762}, year = {2013}, type = {Journal Article} } @article{RN52, author = {Esvelt, K. M. and Smidler, A. L. and Catteruccia, F. and Church, G. M.}, title = {Concerning RNA-guided gene drives for the alteration of wild populations}, journal = {Elife}, volume = {3}, ISSN = {2050-084X (Electronic) 2050-084X (Linking)}, DOI = {10.7554/eLife.03401}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25035423}, year = {2014}, type = {Journal Article} } @article{RN51, author = {Oye, K. A. and Esvelt, K. M.}, title = {Gene drives raise dual-use concerns--response}, journal = {Science}, volume = {345}, number = {6200}, pages = {1010-1}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.345.6200.1010-c}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25170143}, year = {2014}, type = {Journal Article} } @article{RN50, author = {Yaung, S. J. and Esvelt, K. M. and Church, G. M.}, title = {Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68}, journal = {Genome Announc}, volume = {3}, number = {1}, DOI = {10.1128/genomeA.01122-14}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25555735}, year = {2015}, type = {Journal Article} } @article{RN49, author = {Akbari, O. S. and Bellen, H. J. and Bier, E. and Bullock, S. L. and Burt, A. and Church, G. M. and Cook, K. R. and Duchek, P. and Edwards, O. R. and Esvelt, K. M. and Gantz, V. M. and Golic, K. G. and Gratz, S. J. and Harrison, M. M. and Hayes, K. R. and James, A. A. and Kaufman, T. C. and Knoblich, J. and Malik, H. S. and Matthews, K. A. and O'Connor-Giles, K. M. and Parks, A. L. and Perrimon, N. and Port, F. and Russell, S. and Ueda, R. and Wildonger, J.}, title = {BIOSAFETY. Safeguarding gene drive experiments in the laboratory}, journal = {Science}, volume = {349}, number = {6251}, pages = {927-9}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.aac7932}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26229113}, year = {2015}, type = {Journal Article} } @article{RN48, author = {Lipsitch, M. and Esvelt, K. and Inglesby, T.}, title = {Calls for caution in genome engineering should be a model for similar dialogue on pandemic pathogen research}, journal = {Ann Intern Med}, volume = {163}, number = {10}, pages = {790-1}, ISSN = {1539-3704 (Electronic) 0003-4819 (Linking)}, DOI = {10.7326/M15-1048}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26344802}, year = {2015}, type = {Journal Article} } @article{RN47, author = {DiCarlo, J. E. and Chavez, A. and Dietz, S. L. and Esvelt, K. M. and Church, G. M.}, title = {Safeguarding CRISPR-Cas9 gene drives in yeast}, journal = {Nat Biotechnol}, volume = {33}, number = {12}, pages = {1250-1255}, ISSN = {1546-1696 (Electronic) 1087-0156 (Linking)}, DOI = {10.1038/nbt.3412}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26571100}, year = {2015}, type = {Journal Article} } @article{RN46, author = {Braff, J. L. and Yaung, S. J. and Esvelt, K. M. and Church, G. M.}, title = {Characterizing Cas9 Protospacer-Adjacent Motifs with High-Throughput Sequencing of Library Depletion Experiments}, journal = {Cold Spring Harb Protoc}, volume = {2016}, number = {5}, pages = {pdb prot090183}, ISSN = {1559-6095 (Electronic) 1559-6095 (Linking)}, DOI = {10.1101/pdb.prot090183}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27140916}, year = {2016}, type = {Journal Article} } @article{RN45, author = {Braff, J. L. and Yaung, S. J. and Esvelt, K. M. and Church, G. M.}, title = {Characterization of Cas9-Guide RNA Orthologs}, journal = {Cold Spring Harb Protoc}, volume = {2016}, number = {5}, pages = {pdb top086793}, ISSN = {1559-6095 (Electronic) 1559-6095 (Linking)}, DOI = {10.1101/pdb.top086793}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27140923}, year = {2016}, type = {Journal Article} } @article{RN44, author = {Esvelt Klos, K. and Gordon, T. and Bregitzer, P. and Hayes, P. and Chen, X. M. and Del Blanco, I. A. and Fisk, S. and Bonman, J. M.}, title = {Barley Stripe Rust Resistance QTL: Development and Validation of SNP Markers for Resistance to Puccinia striiformis f. sp. hordei}, journal = {Phytopathology}, volume = {106}, number = {11}, pages = {1344-1351}, ISSN = {0031-949X (Print) 0031-949X (Linking)}, DOI = {10.1094/PHYTO-09-15-0225-R}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27213558}, year = {2016}, type = {Journal Article} } @article{RN43, author = {Esvelt, K.}, title = {Gene editing can drive science to openness}, journal = {Nature}, volume = {534}, number = {7606}, pages = {153}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/534153a}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27279174}, year = {2016}, type = {Journal Article} } @article{RN41, author = {Winkler, L. R. and Michael Bonman, J. and Chao, S. and Admassu Yimer, B. and Bockelman, H. and Esvelt Klos, K.}, title = {Population Structure and Genotype-Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars}, journal = {Front Plant Sci}, volume = {7}, pages = {1077}, ISSN = {1664-462X (Linking)}, DOI = {10.3389/fpls.2016.01077}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27524988}, year = {2016}, type = {Journal Article} } @article{RN39, author = {Rashid, A. and Baldwin, T. and Gines, M. and Bregitzer, P. and Esvelt Klos, K.}, title = {A High-Throughput RNA Extraction for Sprouted Single-Seed Barley (Hordeum vulgare L.) Rich in Polysaccharides}, journal = {Plants (Basel)}, volume = {6}, number = {1}, ISSN = {2223-7747 (Linking)}, DOI = {10.3390/plants6010001}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28025509}, year = {2016}, type = {Journal Article} } @article{RN40, author = {Esvelt Klos, K. and Huang, Y. F. and Bekele, W. A. and Obert, D. E. and Babiker, E. and Beattie, A. D. and Bjornstad, A. and Bonman, J. M. and Carson, M. L. and Chao, S. and Gnanesh, B. N. and Griffiths, I. and Harrison, S. A. and Howarth, C. J. and Hu, G. and Ibrahim, A. and Islamovic, E. and Jackson, E. W. and Jannink, J. L. and Kolb, F. L. and McMullen, M. S. and Mitchell Fetch, J. and Murphy, J. P. and Ohm, H. W. and Rines, H. W. and Rossnagel, B. G. and Schlueter, J. A. and Sorrells, M. E. and Wight, C. P. and Yan, W. and Tinker, N. A.}, title = {Population Genomics Related to Adaptation in Elite Oat Germplasm}, journal = {Plant Genome}, volume = {9}, number = {2}, ISSN = {1940-3372 (Electronic) 1940-3372 (Linking)}, DOI = {10.3835/plantgenome2015.10.0103}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27898836}, year = {2016}, type = {Journal Article} } @article{RN42, author = {Esvelt, K.}, title = {Turning point: Kevin Esvelt}, journal = {Nature}, volume = {536}, number = {7614}, pages = {117}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27508287}, year = {2016}, type = {Journal Article} } @article{RN38, author = {Esvelt, K. M.}, title = {Precaution: Open gene drive research}, journal = {Science}, volume = {355}, number = {6325}, pages = {589-590}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.aal5325}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28183944}, year = {2017}, type = {Journal Article} } @article{RN37, author = {Esvelt, K. M.}, title = {Unnatural Responsibilities}, journal = {Sci Am}, volume = {316}, number = {4}, pages = {50-51}, ISSN = {0036-8733 (Print) 0036-8733 (Linking)}, DOI = {10.1038/scientificamerican0417-50}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28296855}, year = {2017}, type = {Journal Article} } @article{RN36, author = {Dickinson, B. C. and Leconte, A. M. and Allen, B. and Esvelt, K. M. and Liu, D. R.}, title = {Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, number = {22}, pages = {9007-12}, ISSN = {1091-6490 (Electronic) 0027-8424 (Linking)}, DOI = {10.1073/pnas.1220670110}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23674678}, year = {2013}, type = {Journal Article} } @article{RN31, author = {Badran, A. H. and Guzov, V. M. and Huai, Q. and Kemp, M. M. and Vishwanath, P. and Kain, W. and Nance, A. M. and Evdokimov, A. and Moshiri, F. and Turner, K. H. and Wang, P. and Malvar, T. and Liu, D. R.}, title = {Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance}, journal = {Nature}, volume = {533}, number = {7601}, pages = {58-63}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature17938}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27120167}, year = {2016}, type = {Journal Article} } @misc{RN29, ISBN = {9783662466896 3662466899 9783662466889 3662466880}, type = {Generic} } @article{RN23, author = {Harms, M. J. and Thornton, J. W.}, title = {Analyzing protein structure and function using ancestral gene reconstruction}, journal = {Curr Opin Struct Biol}, volume = {20}, number = {3}, pages = {360-6}, ISSN = {1879-033X (Electronic) 0959-440X (Linking)}, DOI = {10.1016/j.sbi.2010.03.005}, url = {https://www.ncbi.nlm.nih.gov/pubmed/20413295 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916957/pdf/nihms216280.pdf}, year = {2010}, type = {Journal Article} } @article{RN21, author = {Gumulya, Yosephine and Gillam, Elizabeth M. J.}, title = {Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the ‘retro’ approach to protein engineering}, journal = {Biochemical Journal}, volume = {474}, number = {1}, pages = {1-19}, DOI = {10.1042/bcj20160507}, year = {2017}, type = {Journal Article} } @article{RN19, author = {Gumulya, Yosephine and Gillam, Elizabeth M. J.}, title = {Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the ‘retro’ approach to protein engineering}, journal = {Biochemical Journal}, volume = {474}, number = {1}, pages = {1-19}, DOI = {10.1042/bcj20160507}, year = {2017}, type = {Journal Article} } @article{RN28, type = {Journal Article} } @article{RN25, author = {Ben-Yoav, H. and Melamed, S. and Freeman, A. and Shacham-Diamand, Y. and Belkin, S.}, title = {Whole-cell biochips for bio-sensing: integration of live cells and inanimate surfaces}, journal = {Crit Rev Biotechnol}, volume = {31}, number = {4}, pages = {337-53}, ISSN = {1549-7801 (Electronic) 0738-8551 (Linking)}, DOI = {10.3109/07388551.2010.532767}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21190513}, year = {2011}, type = {Journal Article} } @article{RN22, author = {Whitfield, J. H. and Zhang, W. H. and Herde, M. K. and Clifton, B. E. and Radziejewski, J. and Janovjak, H. and Henneberger, C. and Jackson, C. J.}, title = {Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction}, journal = {Protein Sci}, volume = {24}, number = {9}, pages = {1412-22}, ISSN = {1469-896X (Electronic) 0961-8368 (Linking)}, DOI = {10.1002/pro.2721}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26061224}, year = {2015}, type = {Journal Article} } @article{RN26, author = {Park, K. and Jung, J. and Son, J. and Kim, S. H. and Chung, B. H.}, title = {Anchoring foreign substances on live cell surfaces using Sortase A specific binding peptide}, journal = {Chem Commun (Camb)}, volume = {49}, number = {83}, pages = {9585-7}, ISSN = {1364-548X (Electronic) 1359-7345 (Linking)}, DOI = {10.1039/c3cc44753g}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24018381}, year = {2013}, type = {Journal Article} } @article{RN27, author = {Lee, M. K. and Rai, P. and Williams, J. and Twieg, R. J. and Moerner, W. E.}, title = {Small-molecule labeling of live cell surfaces for three-dimensional super-resolution microscopy}, journal = {J Am Chem Soc}, volume = {136}, number = {40}, pages = {14003-6}, ISSN = {1520-5126 (Electronic) 0002-7863 (Linking)}, DOI = {10.1021/ja508028h}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25222297}, year = {2014}, type = {Journal Article} } @article{RN24, author = {Wheeler, L. C. and Lim, S. A. and Marqusee, S. and Harms, M. J.}, title = {The thermostability and specificity of ancient proteins}, journal = {Curr Opin Struct Biol}, volume = {38}, pages = {37-43}, ISSN = {1879-033X (Electronic) 0959-440X (Linking)}, DOI = {10.1016/j.sbi.2016.05.015}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27288744}, year = {2016}, type = {Journal Article} } @article{RN18, author = {Votteler, J. and Ogohara, C. and Yi, S. and Hsia, Y. and Nattermann, U. and Belnap, D. M. and King, N. P. and Sundquist, W. I.}, title = {Designed proteins induce the formation of nanocage-containing extracellular vesicles}, journal = {Nature}, volume = {540}, number = {7632}, pages = {292-295}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature20607}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27919066}, year = {2016}, type = {Journal Article} } @article{RN17, author = {Mrazek, Jan and Toso, Daniel and Ryazantsev, Sergey and Zhang, Xing and Zhou, Z. Hong and Fernandez, Beatriz Campo and Kickhoefer, Valerie A. and Rome, Leonard H.}, title = {Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles}, journal = {ACS Nano}, volume = {8}, number = {11}, pages = {11552-11559}, ISSN = {1936-0851 1936-086X}, DOI = {10.1021/nn504778h}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245718/}, year = {2014}, type = {Journal Article} } @article{RN20, author = {Bonnet, Jerome and Yin, Peter and Ortiz, Monica E. and Subsoontorn, Pakpoom and Endy, Drew}, title = {Amplifying Genetic Logic Gates}, journal = {Science}, volume = {340}, number = {6132}, pages = {599-603}, DOI = {10.1126/science.1232758}, year = {2013}, type = {Journal Article} } @article{kazumori1981electron, title={Electron microscopic studies of bacteriophage $\varphi$ X174 intact and ‘eclipsing’particles, and the genome by the staining and shadowing method}, author={Kazumori, Yazaki}, journal={Journal of virological methods}, volume={2}, number={3}, pages={159--167}, year={1981}, publisher={Elsevier} } @article{lee2012virus, title={Virus-based piezoelectric energy generation}, author={Lee, Byung Yang and Zhang, Jinxing and Zueger, Chris and Chung, Woo-Jae and Yoo, So Young and Wang, Eddie and Meyer, Joel and Ramesh, Ramamoorthy and Lee, Seung-Wuk}, journal={Nature nanotechnology}, volume={7}, number={6}, pages={351--356}, year={2012}, publisher={Nature Research} } @misc{astmstandard, title={Standard test method for resistance of materials used in protective clothing to penetration by blood-borne pathogens using Phi-X 174 bacteriophage penetration as a test system 1671}, author={ASTM, F}, publisher={1997} } @article{lin1972role, title={Role of bacteriophage M13 gene 2 in viral DNA replication}, author={Lin, Norm S-C and Pratt, David}, journal={Journal of molecular biology}, volume={72}, number={1}, pages={37--49}, year={1972}, publisher={Elsevier} } @article{Neubauer2001, doi = {10.1002/bit.1068}, url = {https://doi.org/10.1002/bit.1068}, year = {2001}, month = {jun}, publisher = {John Wiley & Sons, Inc. ({OUP})}, volume = {73}, number = {5}, pages = {347--357}, author = {H. Y. Lin, B. Mathiszik, B. Xu, S.-O. Enfors, P. Neubauer}, title = {Determination of the maximum specific uptake capacities for glucose and oxygen in glucose-limited fed-batch cultivations of Escherichia coli}, journal = {Biotechnology and Bioengineering} } @article{Milo2009, doi = {10.1093/nar/gkp889}, url = {https://doi.org/10.1093/nar/gkp889}, year = {2009}, month = {oct}, publisher = {Oxford University Press ({OUP})}, volume = {38}, number = {suppl{\_}1}, pages = {D750--D753}, author = {Ron Milo and Paul Jorgensen and Uri Moran and Griffin Weber and Michael Springer}, title = {Bionumbers - the database of key numbers in molecular and cell biology - ID 109837}, journal = {Nucleic Acids Research} } @article{RN158, author = {Pu, Jinyue and Zinkus-Boltz, Julia and Dickinson, Bryan C.}, title = {Evolution of a split RNA polymerase as a versatile biosensor platform}, journal = {Nat Chem Biol}, volume = {13}, number = {4}, pages = {432-438}, ISSN = {1552-4450}, DOI = {10.1038/nchembio.2299 http://www.nature.com/nchembio/journal/v13/n4/abs/nchembio.2299.html#supplementary-information}, url = {http://dx.doi.org/10.1038/nchembio.2299}, year = {2017}, type = {Journal Article} } @article{RN159, author = {Badran, Ahmed H. and Liu, David R.}, title = {Development of potent in vivo mutagenesis plasmids with broad mutational spectra}, volume = {6}, pages = {8425}, DOI = {10.1038/ncomms9425 https://www.nature.com/articles/ncomms9425#supplementary-information}, url = {http://dx.doi.org/10.1038/ncomms9425}, year = {2015}, type = {Journal Article} } @article{trinci1969, author = "TRINCI, A. P. J.", title = "A Kinetic Study of the Growth of Aspergillus nidulans and Other Fungi", journal = "Microbiology", year = "1969", volume = "57", number = "1", pages = "11-24", url = "http://mic.microbiologyresearch.org/content/journal/micro/10.1099/00221287-57-1-11" }