SuperPhy: A pilot resource for integrated phylogenetic and epidemiological analysis of pathogens

BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014

Volumn , Issue , 2014, Pages 40-48

  Whiteside, Matthew D ^a   Laing, Chad R ^a   Manji, Akiff ^a   Gannon, Victor P J ^a  

^a PUBLIC HEALTH AGENCY OF CANADA   (Canada)

Author keywords

Bacterial Pathogenesis; Bioinformatics; Computational Biology; Epidemiology; Phylogeny; Population Genomics

Indexed keywords

BIOMEDICAL ENGINEERING; DNA SEQUENCES; EPIDEMIOLOGY; ESCHERICHIA COLI; GENE ENCODING; MAXIMUM LIKELIHOOD; MEDICINE; POPULATION STATISTICS; TREES (MATHEMATICS);

ANTIMICROBIAL RESISTANCES; BACTERIAL PATHOGENESIS; BIOLOGICAL INFORMATION; COMPUTATIONAL BIOLOGY; GENOMICS; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISMS; WHOLE GENOME ANALYSIS;

BIOINFORMATICS;

EID: 84902315623     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.5220/0004798800400048     Document Type: Conference Paper

References (29)

1. Altschul, S. F., Madden, T. L., Schffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17):3389-402.
2. Antezana, E., Kuiper, M., and Mironov, V. (2009). Biological knowledge management: The emerging role of the semantic web technologies. Briefings in Bioinformatics, 10(4):392-407.
3. Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2013). GenBank. Nucleic Acids Res., 41(Database issue):36-42.
4. Bostock, M., Ogievetsky, V., and Heer, J. (2011). D3 data-driven documents. Visualization and Computer Graphics, IEEE Transactions on, 17(12):2301-2309.
5. Chen, L., Xiong, Z., Sun, L., Yang, J., and Jin, Q. (2012). VFDB 2012 update: Toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res., 40(Database issue):D641-645.
6. Chen, L., Yang, J., Yu, J., Yao, Z., Sun, L., Shen, Y., and Jin, Q. (2005). VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res., 33(Database issue):D325-328.
7. Fang, H., Oates, M. E., Pethica, R. B., Greenwood, J. M., Sardar, A. J., Rackham, O. J., Donoghue, P. C., Stamatakis, A., de Lima Morais, D. A., and Gough, J. (2013). A daily-updated tree of (sequenced) life as a reference for genome research. Sci Rep, 3:2015.
8. Federhen, S. (2012). The NCBI Taxonomy database. Nucleic Acids Res., 40(Database issue):D136-143.
9. Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M. J., Angiuoli, S. V., Ashburner, M., Axelrod, N., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., Dawyndt, P., De Vos, P., DePamphilis, C., Edwards, R., Faruque, N., Feldman, R., Gilbert, J., Gilna, P., Glockner, F. O., Goldstein, P., Guralnick, R., Haft, D., Hancock, D., Hermjakob, H., Hertz-Fowler, C., Hugenholtz, P., Joint, I., Kagan, L., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann, R., Kolker, E., Kravitz, S., Kyrpides, N., Leebens-Mack, J., Lewis, S. E., Li, K., Lister, A. L., Lord, P.,Maltsev, N.,Markowitz, V.,Martiny, J.,Methe, B.,Mizrachi, I., Moxon, R., Nelson, K., Parkhill, J., Proctor, L.,White, O., Sansone, S. A., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward, N., Whetzel, T., San Gil, I., Wilson, G., andWipat, A. (2008). The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol., 26(5):541-547.
10. Goecks, J., Nekrutenko, A., Taylor, J., and $author. lastName, a. f. (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8):R86.
11. Kahn, S. D. (2011). On the future of genomic data. Science (New York, N.Y.), 331(6018):728-729.
12. Kupferschmidt, K. (2011). Outbreak detectives embrace the genome era. Science, 333(6051):1818-1819.
13. Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., and Salzberg, S. L. (2004). Versatile and open software for comparing large genomes. Genome biology, 5(2):R12.
14. Laing, C., Buchanan, C., Taboada, E. N., Zhang, Y., Kropinski, A., Villegas, A., Thomas, J. E., and Gannon, V. P. J. (2010). Pan-genome sequence analysis using panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics, 11:461.
15. Laing, C., Villegas, A., Taboada, E. N., Kropinski, A., Thomas, J. E., and Gannon, V. P. J. (2011). Identification of salmonella enterica species-and subgroupspecific genomic regions using panseq 2.0. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases.
16. Lanzn, A. and Oinn, T. (2008). The taverna interaction service: enabling manual interaction in workflows. Bioinformatics (Oxford, England), 24(8):1118-1120.
17. Letunic, I. and Bork, P. (2011). Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res., 39(Web Server issue):W475-478.
18. Loman, N. J., Misra, R. V., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J., and Pallen, M. J. (2012). Performance comparison of benchtop highthroughput sequencing platforms. Nature biotechnology, 30(5):434-439.
19. Lukjancenko, O., Wassenaar, T. M., and Ussery, D. W. (2010). Comparison of 61 sequenced escherichia coli genomes. Microbial Ecology, 60(4):708-720.
20. Markowitz, V. M., Chen, I. M., Palaniappan, K., Chu, K., Szeto, E., Pillay, M., Ratner, A., Huang, J., Woyke, T., Huntemann, M., Anderson, I., Billis, K., Varghese, N., Mavromatis, K., Pati, A., Ivanova, N. N., and Kyrpides, N. C. (2013). IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res.
21. McArthur, A. G.,Waglechner, N., Nizam, F., Yan, A., Azad, M. A., Baylay, A. J., Bhullar, K., Canova, M. J., De Pascale, G., Ejim, L., Kalan, L., King, A. M., Koteva, K., Morar, M., Mulvey, M. R., O'Brien, J. S., Pawlowski, A. C., Piddock, L. J., Spanogiannopoulos, P., Sutherland, A. D., Tang, I., Taylor, P. L., Thaker, M., Wang, W., Yan, M., Yu, T., and Wright, G. D. (2013). The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother., 57(7):3348-3357.
22. Mellmann, A., Harmsen, D., Cummings, C. A., Zentz, E. B., Leopold, S. R., Rico, A., Prior, K., Szczepanowski, R., Ji, Y., Zhang, W., McLaughlin, S. F., Henkhaus, J. K., Leopold, B., Bielaszewska, M., Prager, R., Brzoska, P.M.,Moore, R. L., Guenther, S., Rothberg, J. M., and Karch, H. (2011). Prospective genomic characterization of the german enterohemorrhagic escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS ONE, 6(7):e22751.
23. Mungall, C. J., Emmert, D. B., et al. (2007). A chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23(13):i337-i346.
24. Price, M. N., Dehal, P. S., and Arkin, A. P. (2010). FastTree 2 approximately maximum-likelihood trees for large alignments. PLoS ONE, 5(3):e9490.
25. R. Core Team (2013). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
26. Riley, D. R., Angiuoli, S. V., Crabtree, J., Hotopp, J. C. D., and Tettelin, H. (2012). Using sybil for interactive comparative genomics of microbes on the web. Bioinformatics, 28(2):160-166.
27. Scheutz, F., Teel, L. D., Beutin, L., Pirard, D., Buvens, G., Karch, H., Mellmann, A., Caprioli, A., Tozzoli, R., Morabito, S., Strockbine, N. A., Melton-Celsa, A. R., Sanchez, M., Persson, S., and O'Brien, A. D. (2012). Multicenter evaluation of a sequence-based protocol for subtyping shiga toxins and standardizing stx nomenclature. Journal of clinical microbiology, 50(9):2951-2963.
28. Teeling, H. and Glckner, F. O. (2012). Current opportunities and challenges in microbial metagenome analysis-A bioinformatic perspective. Briefings in bioinformatics. Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Le Fevre, F., Longin, C., Mornico, D., Roche, D., Rouy, Z., Salvignol, G., Scarpelli, C., Thil Smith, A. A., Weiman, M., and Medigue, C. (2012). MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Research, 41(D1):D636-D647.
29. Wattam, A. R., Abraham, D., Dalay, O., Disz, T. L., Driscoll, T., Gabbard, J. L., Gillespie, J. J., Gough, R., Hix, D., Kenyon, R., Machi, D., Mao, C., Nordberg, E. K., Olson, R., Overbeek, R., Pusch, G. D., Shukla, M., Schulman, J., Stevens, R. L., Sullivan, D. E., Vonstein, V., Warren, A., Will, R., Wilson, M. J., Yoo, H. S., Zhang, C., Zhang, Y., and Sobral, B. W. (2013). PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res.