SysGen Seminar – Yao-ban Chan – 11th August, 2017

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Andrew Siebel

T: +61 3 8344 0707

Yao-ban Chan

Centre for Systems Genomics & School of Mathematics & Statistics, UoM

Friday 11th August
Babel Chisholm Theatre, Level 3 Babel Building, The University of Melbourne

Alignment-free detection of lateral genetic transfer and genetic exchange communities

Lateral genetic transfer is an evolutionary phenomenon where organisms can absorb genetic material from a contemporary species and incorporate it into their own genome. It is a major driver of bacterial evolution, in particular the development of antibiotic resistance. In this talk, we propose a new alignment-free method to detect lateral genetic transfers. This method, inspired by the term frequency-inverse document frequency (TF-IDF) method from text mining, treats k-mers (short reads of fixed size) as words in a document. Unlike traditional phylogenetic methods, it is fast and scalable and does not take genes as a unit of transfer. We show extensive results of this method on simulated data, as well as on three real-life bacterial datasets across different evolutionary scales. As we show, the detailed information provided by this method allows us to construct and analyse genetic exchange communities - groups of organisms which share elevated levels of transfers among themselves.

See Yao-ban's profile here.

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