Education

  • 2019 Bioinformatic PhD- CRBM (CNRS), Montpellier - France
    Bioinformatic methods development for the study of proteins non-globular regions and their conservation over evolution.
    Thesis funded over 3 years by state funding and extended for 1 year thanks to the association “la ligue contre le cancer”. Thesis memoir is not yet publicly available.

  • 2015 Software engineering diploma- ENSIBS (Université de Bretagne Sud), Vannes - France
    Focus on software engineering, software architecture, software quality assessment.

  • 2014 Study aboard semester- Software engineering, UQAC (Université du Québec à Chicoutimi), Chicoutimi - Quebec, Canada
    Focus on software architecture and data mining.

  • 2012 Diplome universitaire de technologie d’analyste programmeur. - IUT de l’Université de Bretagne Sud, Vannes
    Focus on programming, algorithm and software engineering.

Generic technical skills

  • Main programming languages :
    – Ruby for everyday scripting (thanks to its high expressivity) and in a lesser extent for standalone application development with JRuby (that allow to pseudo-compile ruby code in java byte code)
    – Java for standalone application development, the high verbosity and strong structuration of the language make it a perfect tool for long-lasting applications
    – SQL for relational databases query (MySQL)
  • Other programming languages :
    – Bash, good notions : short script writing and modification mainly for jobs management on calcul cluster
    – Python, good notions : short script writing and modification
    – Perl, notions, modifications de scripts existants
    – R/Julia, good notions, short scripts writing for statistical treatment and plotting
  • Tools for software development:
    – UML/OCL, for software modelling
    – Git, for source management, versioning and collaborative work
  • Operating system – GNU/Linux on calcul cluster, server or desktop (Debian and Debian based distributions mainly) – Windows … sometimes, to help colleagues
  • Other tools
    – Calcul on cluster (with both Slurm and SGE scheduler)
    – Machine learning with weka (both through the graphical interface and as a Java/JRuby API)
    – LaTex (and classical Microsoft Office suite) for redaction

  • Protein sequences annotation For previous studies I wrote a large protein sequence annotation pipeline, I got a strong experience in the annotation of various kinds of protein regions using state-of-the-art-predictors : disordered regions, amyloidogenic regions, domains (Pfam Cath), transmembrane regions, signal peptide, short eukaryotic linear motifs

  • Relational database design for OMICS data For previous studies I organised a vast amount of data (~1.000.000 proteins fully annotated) as a relational database to make it “readable” for other treatments (web interface, statistical analysis, machine learning …)

  • Protein mutations mapping on structure prediction of mutation (truncation and point mutation) effects on an already determined protein structure

Teaching

  • Teaching of the graphical interface theory at Montpellier IUT (> 30 H per group, ~ 25 students per group, 2 groups) : how to collect, reshape and organise users need, how to produce a user interface that fit the needs and how to produce an evolutive interface. And more theoretically what is a “good quality” interface.

Publications

  • Villain E, Nikekhin AA, Kajava AV.
    Porins and Amyloids are Coded by Similar Sequence Motifs.
    Proteomics. 2019 Mar;19(6):1800075.

  • Roche DB, Villain E, Kajava AV.
    Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms.
    Protein Science. 2017 Sep;26(9):1864-9.

  • Arsic N., Gadea G., Slatter T. , Villain E. , Fournet A., Kazantseva M., Allemand F., Sibille N., Seveno M., Urbach S., Bourdon J-C., Bernado P., Kajava A.V., Braithwaite. A., Roux P.
    ∆133p53β isoform pro-invasive activity is regulated through an aggregation-dependent mechanism.
    Nature Communication, under revision.

  • Villain E., Fort P. and Kajava A.V.
    Aspartate-phobia of thermophiles as a reaction to deleterious chemical transformations.
    Submitted.

Conferences

  • 2019 Microbiology department external seminar, Paris Sud XI Orsay University :
    Relationship between protein’s disordered regions and organism thermal adaptation
    Villain E.

  • 2016 Journées ouvertes de biologie, informatique et mathématiques, avec la présentation :
    Large-scale analysis of amyloidogenic proteins in a dataset of 93 evolutionary diverse proteomes
    Villain E., Richard F., Fort P. and Kajava A.V.

Posters

  • 2020 Pipeline for large-scale analysis of amyloidogenic regions in proteomes.
    Falgarone T., Villain E., Leclercq J., Richard F. and Kajava A.V.

  • 2019 Winter workshop du COST action “Non-globular protein network” :
    Amyloidogenic regions selection over evolution, a proteome wide study.
    Villain E., Richard F., Fort P. and Kajava A.V.

Miscellaneous

  • Writing of 3 theses extra year funding applications (2 successful)
  • 3 Interns supervised : 2 master II (6-month internship) and a master I (3-month internship)