Who am I?

I am currently a postdoc researcher in computational biology at the Mathematic department of Simon Fraser University (Canada).

I did my PhD study in the Inria Rennes lab’ (FR), at the GenScale team. After one year of research at home (i.e. unemployed, research activity validated by the French national university commission of informatics - CNU27), I joined the AlgoLab research group at the University of Milano-Bicocca for a one year postdoc contract.

My research activities are about graph algorithms and mixed-integer linear programming applied to genomics: scaffolding, haplotyping and plasmid binning.

I am the secretary of the non-profit organization Alia for academic freedom and the associate treasurer of the Nicomaque association for the popularisation of doctoral science. I also play the piano (you can find here some improvisations!)

📨 Professional e-mail address <first_name><last_name><at>disroot.org

✨ NEW ✨ Check my activity report for assistant professor french qualification for CNU 27

👤 Work colleagues

👤 PhD Inria main supervisor Rumen Andonov

👤 PhD INRAe main supervisor Jean-François Gibrat

👤 PhD second supervisor Dominique Lavenier

🔗 On the Internet

ORCID https://orcid.org/0000-0003-0049-0954

CV HAL victor-epain

Mastodon @vepain@sciences.re (to be preferred)

BlueSky @victorepain.cpesr.fr

GitLab @vepain

GitHub vepain

🎹 Piano @ProfesseurChep

You can find my CV below partitioned into several categories.

🎓 Education

2020 - 2023 | Computer science PhD applied to genomics, Inria centre at Rennes

• DNA fragment assembly: graph structures and chloroplast genome scaffolding – Comparative analysis, combinatorial optimisation problem formulation and implementation

2018 – 2020 | Bioinformatics Master’s degree

• University of Rennes
• Master’s degree, with the highest honour

2017 – 2018 | 3rd year bachelor’s degree in computer science

• University of Rennes – ISTIC
• Bachelor’s degree with honours

2015 – 2017 | Preparation for national competitive entrance exams to leading French “grandes écoles”, specialising in mathematics and PHYSICS

• Lycée Dupuy de Lôme, LORIENT

👥 Research project and collaborations

2021 - 2022 | PhD mobility at Heinrich Heine University Düsseldorf, Germany

• ALBI team, welcomed by Gunnar Klau - collaboration with Sven Schrinner
• 2 months

2020 | Master’s degree internship in bioinformatics - Inria centre at Rennes

• Integer linear programming strategy for long reads de novo genome assembly GenScale team, leaders: Dominique Lavenier, Pierre Peterlongo
• 6 months

2019 | Master’s degree internship in bioinformatics Los Alamos National Laboratory (LANL), NM and Inria centre at Rennes, FR

• Overlap graph partitioning for de novo long read assembly
• 3 months research visit financed by the grant HipcoGen (High-Performance Combinatorial Optimization for Computational Genomics), associated team Inria-LANL
  • (1 month) LANL, Information Science Group CCS-3, leader: Hristo Djidjev
  • (2 months) Inria centre at Rennes, GenScale team, leader: Dominique Lavenier

2018 | Bachelor’s degree end internship, bioinformatic team Inria centre at Rennes

• Real chloroplast data and metadata extraction
• GenScale team, leader: Dominique Lavenier
• 2 months

📰 Publications

Legend :

• IJ international journal with peer reviewing
• NC national conference with peer reviewing
• AC conference abstract
• PP preprint

IJ Epain, V., Andonov, R. Global exact optimisations for chloroplast structural haplotype scaffolding. Algorithms Mol Biol 19, 5 (2024). https://doi.org/10.1186/s13015-023-00243-1

NC V. Epain, R. Andonov, D. Lavenier. Optimal Scaffolding for Chloroplasts’ Inverted Repeats. JOBIM2022, Jul 2022, Rennes, France. ⟨hal-03625229⟩

PP V. Epain. Overlap Graph for Assembling and Scaffolding Algorithms: Paradigm Review and Implementation Proposals. 2022. ⟨hal-03815190v3⟩ [preprint]

AC R. Andonov, V. Epain, D. Lavenier. Optimal de novo assemblies for chloroplast genomes based on inverted repeats patterns. BiATA 2021 - 4th International conference Bioinformatics: from Algorithms to Applications, Jul 2021, St. Petersbourg, Russia. pp.1-2. ⟨hal-03534195⟩

🗣️ Talks

2023 | ROADEF2023 - national conference

• Linear Integer Programming Approaches for Chloroplast Genome Scaffolding

2022 | ROADEF2022 - national conference

• Linear integer programming approach for chloroplast genome scaffolding

2022 | JOBIM2022 - Francophone conference

• Optimal Scaffolding for Chloroplasts’ Inverted Repeats

2022 | DSB2022 - international workshop

• The reverse complement symmetry advantage of DNA fragments relationships for their storage in a directed graph

2021 | BiATA2021 - international conference

• Optimal de novo assemblies for chloroplast genomes based on inverted repeats patterns

2021 | SeqBIM2021 Lyon - national workshop

• The advantage of DNA reads overlaps’ reverse complement symmetry for their storage in an oriented graph

2020 | ROADEF2020 - national conference

• Assemblage de Novo de Longues Lectures Par Programmation Linéaire

🏫 Teaching

2021 | Co-supervisor of Pauline Hamon-Giraud

• First master’s degree student in bioinformatic, University of Rennes
• 3 months

2021 | Algorithmic Methods for Graph

• Third year Bachelor (INFO & MIAGE)
• Exercises lectures: 40h

2021 | Operational Research

• First year Master (MIAGE)
• Practical tutorial: 12h

2021 | Algorithmic for Bioinformatic

• Second year Master (Bioinformatic)
• Lecture: 2h
• Exercises lectures: 4h
• Practical tutorial: 6h

2020 | Algorithmic Methods for Graph

• Third year Bachelor (INFO & MIAGE)
• Exercises lectures: 40h

2020 | Operational Research

• First year Master (MIAGE)
• Practical tutorial: 12h

  Statements and organisations of the practical tutorials have been rewritten to use PuLP Python package. The new versions are currently being taught for M1 MIAGE/INFO and M2 Bioinformatic Operational Research classes.

🥼 Services

2023 | Data Knowledge Management IRISA/Inria Department

• Organisation of monthly department seminar
• Organisation of departments days (1.5 days)
  • Round table about how we can participate in the laboratory’s and university’s activities (teaching, council etc.)
  • Round table about scientific publication system

2023 | ROADEF2023 - national conference

• Co-chairman for bioinformatic session (Recherche Opérationnelle en Bio-Informatique)

2023 | Treasurer in Nicomaque PhD association

2023 | Organisation of internship oral training for the first and second Master’s degrees students

2022 | Data Knowledge Management IRISA/Inria Department

• Organisation of monthly department seminar
• Organisation of departments days (1.5 days)

2022 | ROADEF2022 - national conference

• Co-chairman for bioinformatic session (Recherche Opérationnelle en Bio-Informatique)

2022 | JOBIM2022 Francophone conference

• Referent organiser for social activity

2022 | Organisation of internship oral training for the first and second Master’s degrees students

2021 | Supervisor of Pauline Hamon-Giraud (first Master degree student in bioinformatic)

2021 | Organisation of internship oral training for the second Master’s degrees students

💬 Science popularisation

2023 | Organisation of a conference on ethics in academia

• The recorded event (FR)
• Recognised as scientific integrity and ethics training by Bretagne’s PhD college

2022 | Organisation of PhD popularisation film festival Sciences en Cour[t]s

• The recorded event (FR)
• Collaboration with Espace des Sciences for the Fête de la Science

2021 | Team member in Sciences en Cour[t]s PhD popularisation film festival

• Making a 5min animated film: Cocktail de bio-informatique (FR)

🖥️ Skills

Programming languages and affiliated

C / C++ / Rust (in progress)

• revsymg: fragment graph package

Python3 (advanced)

• khloraascaf: chloroplast genome scaffolder
• revsymg: fragment graph package

BASH (advanced) | AMPL (advanced) | Java

$\LaTeX$ (advanced) | Markdown | Git

Languages

• French (native speaker)
• English (good working knowledge)
• Spanish (notions)