Who am I?

I am currently a postdoc researcher in computational biology in the AlgoLab research group at the University of Milano-Bicocca.

I did my PhD study in the Inria Rennes lab’ (FR), at the GenScale team.

My works are about genome assembly and scaffolding. For this purpose, I implement graph algorithms and graph structures, and I formalise these problems thanks to mathematical programming.

I am member 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)