paper-webserver.bib

@article{ronholm2016navigating,
  title={Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing},
  author={Ronholm, J and Nasheri, Neda and Petronella, Nicholas and Pagotto, Franco},
  journal={Clinical Microbiology Reviews},
  volume={29},
  number={4},
  pages={837--857},
  year={2016},
  publisher={Am Soc Microbiol}
}

@article{whiteside2016superphy,
  title={SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli},
  author={Whiteside, Matthew D and Laing, Chad R and Manji, Akiff and Kruczkiewicz, Peter and Taboada, Eduardo N and Gannon, Victor PJ},
  journal={BMC microbiology},
  volume={16},
  number={1},
  pages={65},
  year={2016},
  publisher={BioMed Central}
}

@article{mcarthur2013comprehensive,
  title={The comprehensive antibiotic resistance database},
  author={McArthur, Andrew G and Waglechner, Nicholas and Nizam, Fazmin and Yan, Austin and Azad, Marisa A and Baylay, Alison J and Bhullar, Kirandeep and Canova, Marc J and De Pascale, Gianfranco and Ejim, Linda and others},
  journal={Antimicrobial agents and chemotherapy},
  volume={57},
  number={7},
  pages={3348--3357},
  year={2013},
  publisher={Am Soc Microbiol}
}

@article{laing2010pan,
  title={Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions},
  author={Laing, Chad and Buchanan, Cody and Taboada, Eduardo N and Zhang, Yongxiang and Kropinski, Andrew and Villegas, Andre and Thomas, James E and Gannon, Victor PJ},
  journal={BMC bioinformatics},
  volume={11},
  number={1},
  pages={461},
  year={2010},
  publisher={BioMed Central}
}

@article{doi:10.1093/bioinformatics/btu153,
author = {Seemann, Torsten},
title = {Prokka: rapid prokaryotic genome annotation},
journal = {Bioinformatics},
volume = {30},
number = {14},
pages = {2068-2069},
year = {2014},
doi = {10.1093/bioinformatics/btu153},
URL = { + http://dx.doi.org/10.1093/bioinformatics/btu153},
eprint = {/oup/backfile/content_public/journal/bioinformatics/30/14/10.1093_bioinformatics_btu153/2/btu153.pdf}
}

@article{inouye2014srst2,
  title={SRST2: Rapid genomic surveillance for public health and hospital microbiology labs},
  author={Inouye, Michael and Dashnow, Harriet and Raven, Lesley-Ann and Schultz, Mark B and Pope, Bernard J and Tomita, Takehiro and Zobel, Justin and Holt, Kathryn E},
  journal={Genome medicine},
  volume={6},
  number={11},
  pages={90},
  year={2014},
  publisher={BioMed Central}
}

@article{schatz2015biological,
  title={Biological data sciences in genome research},
  author={Schatz, Michael C},
  journal={Genome research},
  volume={25},
  number={10},
  pages={1417--1422},
  year={2015},
  publisher={Cold Spring Harbor Lab}
}

@article{de2015trends,
  title={Trends in IT innovation to build a next generation bioinformatics solution to manage and analyse biological big data produced by NGS technologies},
  author={de Brevern, Alexandre G and Meyniel, Jean-Philippe and Fairhead, C{\'e}cile and Neuv{\'e}glise, C{\'e}cile and Malpertuy, Alain},
  journal={BioMed research international},
  volume={2015},
  year={2015},
  publisher={Hindawi Publishing Corporation}
}

@article{swaminathan2001pulsenet,
  title={PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States.},
  author={Swaminathan, Bala and Barrett, Timothy J and Hunter, Susan B and Tauxe, Robert V and Force, CDC PulseNet Task},
  journal={Emerging infectious diseases},
  volume={7},
  number={3},
  pages={382},
  year={2001},
  publisher={Centers for Disease Control and Prevention}
}

@article{lytsy2017time,
  title={Time to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology: Comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013--2015},
  author={Lytsy, Birgitta and Engstrand, Lars and Gustafsson, {\AA}ke and Kaden, Rene},
  journal={Infection, Genetics and Evolution},
  year={2017},
  publisher={Elsevier}
}

@article{yuen2015whole,
  title={Whole-genome sequencing of quartet families with autism spectrum disorder},
  author={Yuen, Ryan KC and Thiruvahindrapuram, Bhooma and Merico, Daniele and Walker, Susan and Tammimies, Kristiina and Hoang, Ny and Chrysler, Christina and Nalpathamkalam, Thomas and Pellecchia, Giovanna and Liu, Yi and others},
  journal={Nature medicine},
  volume={21},
  number={2},
  pages={185--191},
  year={2015},
  publisher={Nature Research}
}

@article{wang2014whole,
  title={Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer},
  author={Wang, Kai and Yuen, Siu Tsan and Xu, Jiangchun and Lee, Siu Po and Yan, Helen HN and Shi, Stephanie T and Siu, Hoi Cheong and Deng, Shibing and Chu, Kent Man and Law, Simon and others},
  journal={Nature genetics},
  volume={46},
  number={6},
  pages={573--582},
  year={2014},
  publisher={Nature Research}
}

@article{willig2015whole,
  title={Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings},
  author={Willig, Laurel K and Petrikin, Josh E and Smith, Laurie D and Saunders, Carol J and Thiffault, Isabelle and Miller, Neil A and Soden, Sarah E and Cakici, Julie A and Herd, Suzanne M and Twist, Greyson and others},
  journal={The Lancet Respiratory Medicine},
  volume={3},
  number={5},
  pages={377--387},
  year={2015},
  publisher={Elsevier}
}


@article{dewey2014clinical,
  title={Clinical interpretation and implications of whole-genome sequencing},
  author={Dewey, Frederick E and Grove, Megan E and Pan, Cuiping and Goldstein, Benjamin A and Bernstein, Jonathan A and Chaib, Hassan and Merker, Jason D and Goldfeder, Rachel L and Enns, Gregory M and David, Sean P and others},
  journal={Jama},
  volume={311},
  number={10},
  pages={1035--1045},
  year={2014},
  publisher={American Medical Association}
}

@article{thomsen2016bacterial,
  title={A bacterial analysis platform: an integrated system for analysing bacterial whole genome sequencing data for clinical diagnostics and surveillance},
  author={Thomsen, Martin Christen Fr{\o}lund and Ahrenfeldt, Johanne and Cisneros, Jose Luis Bellod and Jurtz, Vanessa and Larsen, Mette Voldby and Hasman, Henrik and Aarestrup, Frank M{\o}ller and Lund, Ole},
  journal={PloS one},
  volume={11},
  number={6},
  pages={e0157718},
  year={2016},
  publisher={Public Library of Science}
}

@article{goecks2010galaxy,
  title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
  author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James},
  journal={Genome biology},
  volume={11},
  number={8},
  pages={R86},
  year={2010},
  publisher={BioMed Central}
}

@article{naccache2014cloud,
  title={A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples},
  author={Naccache, Samia N and Federman, Scot and Veeraraghavan, Narayanan and Zaharia, Matei and Lee, Deanna and Samayoa, Erik and Bouquet, Jerome and Greninger, Alexander L and Luk, Ka-Cheung and Enge, Barryett and others},
  journal={Genome research},
  volume={24},
  number={7},
  pages={1180--1192},
  year={2014},
  publisher={Cold Spring Harbor Lab}
}

@article{berners2001semantic,
  title={The semantic web},
  author={Berners-Lee, Tim and Hendler, James and Lassila, Ora and others},
  journal={Scientific american},
  volume={284},
  number={5},
  pages={28--37},
  year={2001},
  publisher={New York, NY, USA:}
}

@inproceedings{horrocks2005semantic,
  title={Semantic web architecture: Stack or two towers?},
  author={Horrocks, Ian and Parsia, Bijan and Patel-Schneider, Peter and Hendler, James},
  booktitle={International Workshop on Principles and Practice of Semantic Web Reasoning},
  pages={37--41},
  year={2005},
  organization={Springer}
}

@article{bolleman2016faldo,
  title={FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation},
  author={Bolleman, Jerven T and Mungall, Christopher J and Strozzi, Francesco and Baran, Joachim and Dumontier, Michel and Bonnal, Raoul JP and Buels, Robert and Hoehndorf, Robert and Fujisawa, Takatomo and Katayama, Toshiaki and others},
  journal={Journal of biomedical semantics},
  volume={7},
  number={1},
  pages={39},
  year={2016},
  publisher={BioMed Central}
}

@article{griffiths2017context,
  title={Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance},
  author={Griffiths, Emma and Dooley, Damion and Graham, Morag and Van Domselaar, Gary and Brinkman, Fiona SL and Hsiao, William WL},
  journal={Frontiers in Microbiology},
  volume={8},
  year={2017},
  pages={1068},
  publisher={Frontiers Media SA}
}

@article{whiteside2017phylotyper,
  title={Phylotyper: in silico predictor of gene subtypes},
  author={Whiteside, Matthew D and Laing, Chad R and Gannon, Victor PJ},
  journal={Bioinformatics},
  year={2017}
}

@article{kleinheinz2014applying,
  title={Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences},
  author={Kleinheinz, Kortine Annina and Joensen, Katrine Grimstrup and Larsen, Mette Voldby},
  journal={Bacteriophage},
  volume={4},
  number={2},
  pages={e27943},
  year={2014},
  publisher={Taylor \& Francis}
}

@article{wattam2016improvements,
  title={Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center},
  author={Wattam, Alice R and Davis, James J and Assaf, Rida and Boisvert, S{\'e}bastien and Brettin, Thomas and Bun, Christopher and Conrad, Neal and Dietrich, Emily M and Disz, Terry and Gabbard, Joseph L and others},
  journal={Nucleic acids research},
  volume={45},
  number={D1},
  pages={D535--D542},
  year={2016},
  publisher={Oxford University Press}
}

@article{vaz2014typon,
  title={TypOn: the microbial typing ontology},
  author={Vaz, C{\'a}tia and Francisco, Alexandre P and Silva, Mickael and Jolley, Keith A and Bray, James E and Pouseele, Hannes and Rothganger, Joerg and Ramirez, M{\'a}rio and Carri{\c{c}}o, Jo{\~a}o A},
  journal={Journal of biomedical semantics},
  volume={5},
  number={1},
  pages={43},
  year={2014},
  publisher={BioMed Central}
}

@inproceedings{felter2015updated,
  title={An updated performance comparison of virtual machines and linux containers},
  author={Felter, Wes and Ferreira, Alexandre and Rajamony, Ram and Rubio, Juan},
  booktitle={Performance Analysis of Systems and Software (ISPASS), 2015 IEEE International Symposium On},
  pages={171--172},
  year={2015},
  organization={IEEE}
}

@article{gupta2014arg,
  title={ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes},
  author={Gupta, Sushim Kumar and Padmanabhan, Babu Roshan and Diene, Seydina M and Lopez-Rojas, Rafael and Kempf, Marie and Landraud, Luce and Rolain, Jean-Marc},
  journal={Antimicrobial agents and chemotherapy},
  volume={58},
  number={1},
  pages={212--220},
  year={2014},
  publisher={Am Soc Microbiol}
}

@article{hunt2017ariba,
  title={ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads},
  author={Hunt, Martin and Mather, Alison E and S{\'a}nchez-Bus{\'o}, Leonor and Page, Andrew J and Parkhill, Julian and Keane, Jacqueline A and Harris, Simon R},
  journal={Microbial genomics},
  volume={3},
  number={10},
  year={2017},
  publisher={Microbiology Society}
}

@article{lambert2015genesippr,
  title={GeneSippr: a rapid whole-genome approach for the identification and characterization of foodborne pathogens such as priority Shiga toxigenic Escherichia coli},
  author={Lambert, Dominic and Carrillo, Catherine D and Koziol, Adam G and Manninger, Paul and Blais, Burton W},
  journal={PLoS One},
  volume={10},
  number={4},
  pages={e0122928},
  year={2015},
  publisher={Public Library of Science}
}

@article{joensen2015rapid,
  title={Rapid and easy in silico serotyping of Escherichia coli using whole genome sequencing (WGS) data},
  author={Joensen, Katrine G and Tetzschner, Anna MM and Iguchi, Atsushi and Aarestrup, Frank M and Scheutz, Flemming},
  journal={Journal of clinical microbiology},
  pages={JCM--00008},
  year={2015},
  publisher={Am Soc Microbiol}
}

@article{ingle2016silico,
  title={In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O: H serotype combinations within and between pathogenic lineages},
  author={Ingle, Danielle J and Valcanis, Mary and Kuzevski, Alex and Tauschek, Marija and Inouye, Michael and Stinear, Tim and Levine, Myron M and Robins-Browne, Roy M and Holt, Kathryn E},
  journal={Microbial genomics},
  volume={2},
  number={7},
  year={2016},
  publisher={Microbiology Society}
}

@article{carrillo2016comparative,
  title={Comparative evaluation of genomic and laboratory approaches for determination of Shiga toxin subtypes in Escherichia coli},
  author={Carrillo, Catherine D and Koziol, Adam G and Mathews, Amit and Goji, Noriko and Lambert, Dominic and Huszczynski, George and Gauthier, Martine and Amoako, Kingsley and Blais, Burton W},
  journal={Journal of food protection},
  volume={79},
  number={12},
  pages={2078--2085},
  year={2016},
  publisher={International Association for Food Protection}
}