{"id":898,"date":"2017-10-03T13:43:56","date_gmt":"2017-10-03T11:43:56","guid":{"rendered":"http:\/\/iict-space.heig-vd.ch\/cpn\/?p=898"},"modified":"2017-10-03T13:43:56","modified_gmt":"2017-10-03T11:43:56","slug":"the-13th-bc2-the-basel-computational-biology-conference","status":"publish","type":"post","link":"http:\/\/iict-space.heig-vd.ch\/cpn\/the-13th-bc2-the-basel-computational-biology-conference\/","title":{"rendered":"The 13th [BC]2 – the Basel Computational Biology Conference"},"content":{"rendered":"

Diogo Leite presented a Poster at the Basel Computational Biology Conference<\/h1>\n

Computational models able to predict phage-bacteria relationships through genomics data analysis<\/span><\/b><\/span><\/span><\/span><\/h3>\n

Diogo Manuel Carvalho Leite 1,2<\/sup>, Xavier Brochet 1,2<\/sup>, Gr\u00e9gory Resch 3<\/sup>, Yok-Ai Que 4<\/sup>, and Carlos Pe\u00f1a-Reyes 1,2<\/sup>
\n1<\/sup> School of Business and Engineering Vaud (HEIG-VD), University of Applied Sciences of Western Switzerland (HES-SO), Yverdon-Les-Bains, Switzerland {diogo.leite,xavier.brochet,carlos.pena}@heig-vd.ch
\n2<\/sup> SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
\n3<\/sup> Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
\n4<\/sup> Department of Intensive Care Medicine, Bern University Hospital (Inselspital), Bern, Switzerland <\/span><\/p>\n

Abstract<\/strong><\/p>\n

\nThe emergence and rapid dissemination of antibiotic resistance worldwide hinders medical progress and threatens with a return to the pre-antibiotic era. This therapy uses viruses that specifically infect and kill bacteria during their life cycle to reduce\/eliminate bacterial load. However, as phages are highly strain-specific, the challenge is finding suitable matches to a bacterium among a fully-characterized phage library. Currently, scientists perform phage selection by means of infection tests that may take several days of lab work. We address such a challenge by combining genomic feature extraction and machine-learning predictive modelling.<\/p>\n

\nTo address this, we created a dataset containing more than 1000 known phage-bacteria interactions with their genomes based on public data from Genbank and phagesdb.org databases. From these genomes we extracted features, which include the distribution of protein-protein interaction scores, proteins’ amino acids frequency and chemical composition, to build a quantitative dataset to train our predictive machine learning models.<\/p>\n

\nOur approach attains, in average, performance values of around 90% in terms of f-measure, accuracy, specificity, and sensitivity. In addition, they are obtained in much less time than the corresponding in-vitro experiments. This promising results encourage us to further investigate new features to extract as well as additional predictive models (e.g., weighted ensemble-learning voting system). We will also enlarge our phage-bacteria interaction database so as to increase the predictive value and the possibility of prediction at the bacterial strain level.<\/p>\n<\/div>\n

Computational models able to predict phage-bacteria relationships through genomics data analysis<\/a><\/p>\n

<\/div>\n","protected":false},"excerpt":{"rendered":"

Diogo Leite presented a Poster at the Basel Computational Biology Conference Computational models able to predict phage-bacteria relationships through genomics data analysis Diogo Manuel Carvalho Leite 1,2, Xavier Brochet 1,2, Gr\u00e9gory Resch 3, Yok-Ai Que 4, and Carlos Pe\u00f1a-Reyes 1,2 Continue reading The 13th [BC]2 – the Basel Computational Biology Conference<\/span>→<\/span><\/a><\/p>\n","protected":false},"author":13,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[15],"tags":[],"_links":{"self":[{"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/posts\/898"}],"collection":[{"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/comments?post=898"}],"version-history":[{"count":4,"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/posts\/898\/revisions"}],"predecessor-version":[{"id":952,"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/posts\/898\/revisions\/952"}],"wp:attachment":[{"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/media?parent=898"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/categories?post=898"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/iict-space.heig-vd.ch\/cpn\/wp-json\/wp\/v2\/tags?post=898"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}