Title: A journey into mathematical modelling for the plasmid binning problem on assembly graphs

Presenter: Dr. Victor Epain

Abstract: Plasmids are short extra-chromosomal molecules found in bacterial cells. They can be exchanged between bacteria via horizontal gene transfer, or integrated into bacterial chromosomes. Therefore, bacteria and their descendants can complete their DNA with antimicrobial resistance genes, enabling them to survive in environments that were previously hostile. Analysing the resistance evolution is of clinical importance in the fight against the emergence of new resistant bacteria. As sequencing data consists of a mixture of reads from bacterial chromosomes and plasmids, the first stage in the analysis process is to identify the plasmid sequences among the chromosomal ones. Then, binning the plasmid sequences enables the reconstruction of each individual plasmid, allowing for differential analysis and the reconstitution of the evolutionary history between plasmids and bacteria. Here, we focus on resolving the plasmid binning problem by defining it as a combinatorial optimisation problem that we address by searching for flows in an assembly graph. We propose illustrating the process of defining and refining an optimization problem, and demonstrating how mathematical programming can be an effective tool for solving it while ensuring the explainability of our solutions.

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