Characterizing scales of genetic recombination and antibiotic resistance in pathogenic bacteria using topological data analysis

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8609 LNAI, Issue , 2014, Pages 540-551

  Emmett, Kevin J ^a   Rabadan, Raul ^b  

^a Department of Physics Columbia University ^*  (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

antibiotic resistance; microbial evolution; topological data analysis

Indexed keywords

ANTIBIOTICS; GENE TRANSFER; HEALTH; INFORMATION SCIENCE; TOPOLOGY;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC RESISTANCE GENES; GENETIC RECOMBINATIONS; LATERAL GENE TRANSFERS; MICROBIAL EVOLUTION; PATHOGENIC BACTERIUM; STAPHYLOCOCCUS AUREUS; TOPOLOGICAL DATA ANALYSIS;

BACTERIA;

EID: 84905222848     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-09891-3_49     Document Type: Conference Paper

References (26)

1. Ayasdi Inc.: Iris, http://www.ayasdi.com
2. Carlsson, G.: Topology and data. Bulletin-American Mathematical Society 46(2), 255 (2009)
3. Chan, J.M., Carlsson, G., Rabadan, R.: Topology of viral evolution. Proceedings of the National Academy of Sciences of the United States of America 110(46), 18566-18571 (2013)
4. Cooper, J.E., Feil, E.J.: The phylogeny of Staphylococcus aureus - which genes make the best intra-species markers? Microbiology 152(5), 1297-1305 (2006)
5. Dagan, T., Martin, W.: The tree of one percent. Genome Biol. 7(10), 118 (2006)
6. de Silva, V., Carlsson, G.: Topological estimation using witness complexes. In: Proceedings of the First Eurographics Conference on Point-Based Graphics, pp. 157-166. Eurographics Association (2004)
7. Edelsbrunner, H., Harer, J.: Computational topology: an introduction. American Mathematical Society (2010)
8. Emmett, K., Rosenbloom, D., Camara, P., Rabadan, R.: Parametric inference using persistence diagrams: A case study in population genetics. In: ICML Workshop on Topological Methods in Machine Learning (2014)
9. Fraser, C., Hanage, W.P., Spratt, B.G.: Recombination and the Nature of Bacterial Speciation. Science 315(5811), 476-480 (2007)
10. Holzinger, A., Dehmer, M., Jurisica, I.: Knowledge Discovery and interactive Data Mining in Bioinformatics-State-of-the-Art, future challenges and research directions. BMC Bioinformatics 15(suppl. 6), 11 (2014)
11. Holzinger, A.: Human-computer interaction and knowledge discovery (HCI-KDD): What is the benefit of bringing those two fields to work together? In: Cuzzocrea, A., Kittl, C., Simos, D.E., Weippl, E., Xu, L. (eds.) CD-ARES 2013. LNCS, vol. 8127, pp. 319-328. Springer, Heidelberg (2013)
12. Jensen, S.O., Lyon, B.R.: Genetics of antimicrobial resistance in Staphylococcus aureus. Future Microbiology 4(5), 565-582 (2009)
13. Jolley, K.A., Maiden, M.C.: BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11(1), 595 (2010)
14. Meyer, F., Overbeek, R., Rodriguez, A.: FIGfams: yet another set of protein families. Nucleic Acids Research 37(20), 6643-6654 (2009)
15. Neu, H.C.: The Crisis in Antibiotic Resistance. Science 257(5073), 1064-1073 (1992)
16. Ochman, H., Lawrence, J.G., Groisman, E.A.: Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784), 299-304 (2000)
17. Penders, J., Stobberingh, E.E., Savelkoul, P.H., Wolffs, P.F.: The human microbiome as a reservoir of antimicrobial resistance. Frontiers in Microbiology 4 (2013)
18. Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N.J., Hentschke, M., Chen, W., Pu, F., Peng, Y., Li, J., Xi, F., Li, S., Li, Y., Zhang, Z., Yang, X., Zhao, M., Wang, P., Guan, Y., Cen, Z., Zhao, X., Christner, M., Kobbe, R., Loos, S., Oh, J., Yang, L., Danchin, A., Gao, G.F., Song, Y., Li, Y., Yang, H., Wang, J., Xu, J., Pallen, M.J., Wang, J., Aepfelbacher, M., Yang, R.: Open-source genomic analysis of shigatoxin - producing E. coli O104:H4. New England Journal of Medicine 365(8), 718-724 (2011)
19. Singh, G., Mémoli, F., Carlsson, G.: Topological methods for the analysis of high dimensional data sets and 3d object recognition. In: Eurographics Symposium on Point-Based Graphics. The Eurographics Association, Prague (2007)
20. Sommer, M.O., Church, G.M., Dantas, G.: The human microbiome harbors a diverse reservoir of antibiotic resistance genes. Virulence 1(4), 299-303 (2010)
21. Tausz, A., Vejdemo-Johansson, M., Adams, H.: Javaplex: A research software package for persistent (co)homology (2011), Software available at http://code.google.com/javaplex
22. The Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature 486(7402), 207-214 (2012)
23. Thomas, C.M., Nielsen, K.M.: Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria. Nature Reviews Microbiology 3(9), 711-721 (2005)
24. 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.C., Yoo, H.S., Zhang, C., Zhang, Y., Sobral, B.W.: PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Research 42(D1), D581-D591 (2013)
25. Woese, C.R., Fox, G.E.: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America 74(11), 5088-5090 (1977)
26. World Health Organization: Antimicrobial Resistance: global report on surveillance 2014 (2014), http://www.who.int/drugresistance/documents/ surveillancereport/en/