~ Welcome to my scientific website!


My name is Victor Epain, I am currently an independent scientist (i.e. without affiliation) in computer science, applied in genomics.

Topics: graph algorithms - mathematical programming - genome assembly.

More informations on the About page.

✨ Highlighted pages

Our work on chloroplast structural haplotype scaffolding has been published in Algorithms for Molecular Biology (BMC)!

From a set of short-read contigs and a set of links between the contigs, we aim to assemble several chloroplast structural haplotypes


French thesis poster with a lot of jokes

Title: DNA fragment assembly: graph structures and chloroplast genome scaffolding


To obtain the nucleotide sequence of a DNA molecule, the molecule is fragmented using sequencing technology and the fragments are assembled. These fragments are called reads. They are subject to sequencing errors and must be considered in two orientations: that of their original DNA strand, or the reverse-complementary for the other strand. Assembly is based on pairwise overlaps between oriented reads and consists of three phases: assembling the reads to obtain contigs (sequences longer than the reads), scaffolding the contigs to obtain scaffolds (orders of oriented contigs), and completing the scaffolds (finding the nucleotide sequences separating the oriented contigs in the scaffolds).

In this thesis, we compare graph structures representing succession relations between oriented DNA sequences, useful at different phases of assembly. Then, we address the scaffolding problem dedicated to chloroplast genomes by proposing a new formulation, an exact resolution and an implementation.

📽️ Les retranscriptions de la conférence et de la partie débat/question sont maintenant disponibles sur YouTube !

Photo des intervenant·es et des animateur·ices Photo d'Enka Blanchard et d'Ambre Ayats Photo de Victor Epain et de Bernard Friot

Le résumé de l’atelier, des ressources et d’autres informations sont disponibles sur le site web dédié : https://atelier-ethique-inria2023.gitlab.io/

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