Sylvain Pulicani

Sylvain Pulicani

PhD in Bioinformatics

About me

Biologist by formation, I made a PhD thesis on the modelling of chromosomal rearrangements using the chromatin structure. This allowed me to learn of lot of computer science and modelling material.

Now, I’m looking forward to apply that knowledge on biological questions. Opportunities welcome!

Interests

  • Data Analysis
  • Evolution & Phylogeny
  • Learning new stuff!

Education

  • PhD in Bioinformatics, 2018

    University of Montpellier

  • MDs in Genomics, 2015

    Aix-Marseille University

  • BSc in Cellular Biology, 2013

    Aix-Marseille University

Skills

Statistics

  • Validation of experimental results against models.
  • Combined use of regressions and representation methods to extract relationships.
  • Use of the bootstrap method.
  • Modelling of biological experiments.

Bioinformatics

  • Performing of NGS analysis, including setting up pipelines.
  • Use of multiple biological databases and genome browsers.
  • Setting up of specific biological database.
  • Analysis of sequences, including multiple alignment and motif finding.
  • Inference of phylogenetic histories.
  • Good knowledge of biological networks.

Programming

  • Use of standard algorithms and data structures.
  • Day-to-day use of Python for scientific tasks, using numpy, scipy, matplotlib.
  • Day-to-day use of Bash for scripts automation, using hastables and GNU parallel.
  • Good knownledge of Perl, Java, C, Rust and R.

Computing

  • Day-to-day use of Linux, for desktop ( Ubuntu and Manjaro) as well as for server ( CentOS and Debian).
  • Use of computing clusters (SGE like).
  • Good knowledge of databases systems, both relational ( SQLite and MySQL) and NoSQL (graph database with Neo4J or dgraph, and document database CouchDB).

Communication

  • Scientific writing and talks.
  • Popularisation
  • Teaching

Experiences

 
 
 
 
 

Bioinformatician

Cellectis

Apr 2021 – Present Paris, FRANCE
Analysis of internally generated biological data - Integration of public datasets - Design of analysis pipelines - Bibliography.
 
 
 
 
 

Computer Engineer

IT-med

Oct 2020 – Mar 2021 Marseille, FRANCE
Set up of an ERP system (installation, configuration and additional developments).
 
 
 
 
 

Computer Engineer

IT-med

Mar 2020 – May 2020 Marseille, FRANCE
Set up of an computational environment supervision for a customer.
 
 
 
 
 

Computer Engineer

IT-med

Aug 2019 – Nov 2019 Marseille, FRANCE
Set up of an computational environment supervision for a customer.
 
 
 
 
 

Computer Engineer

IT-med

Apr 2019 – Jun 2019 Marseille, FRANCE
Development of a real-time supervision application for a data warehouse (monitoring of I/O, latency, etc.).
 
 
 
 
 

PhD Thesis

LIRMM UMR 5506 and IGH UMR 9002

Oct 2015 – Nov 2018 Montpellier, FRANCE
Linking Large Scale Chromosomal Rearrangement with Chromatin Structure in the Drosophila.
 
 
 
 
 

Master’s Thesis Work Experience

Inmed – INSERM U901

Jan 2015 – Jul 2015 Marseille, FRANCE
Study of the link between Necdin and MageL2 genes.
 
 
 
 
 

Master’s Thesis Work Experience

Inmed – INSERM U901

Mar 2014 – Jun 2014 Marseille, FRANCE
Study of conserved patterns in the N-terminal part of MAGEL2.

Teachings

Programming for Bioinformatics - Master

Introduction to Python programming and application to scientific computing.

Introduction to the Scientific Culture - MathC2+

As part of the MathC2+ project, I set up a bioinformatics workshop to help high schools students discovering the scientific methodology.

Algorithms 101 - First year

Introduction to algorithmic and programming.

Projects

Fastax

Make phylogenetic trees and lineages from the NCBI Taxonomy database

PhyloHiC

Make a phylogeny using the chromatin structure information extracted from Hi-C experiments.

Talks

Linking Large Scale Chromosomal Rearrangements with Chromatin Structure in Drosophila

I presented my works at the annual scientific meeting of my doctoral school.

Comprendre l'ADN

I used the DNA research field to present real life effects and issues to high school students.

Linking Large Scale Chromosomal Rearrangements with Chromatin Structure in Drosophila

I presented my works at the EpiGenMed annual scientific meeting.

Rearrangement Scenarios Guided by Chromatin Structure

I presented the work we published at that conference.

L'évolution : un phénomene, plusieurs théories

I introduced high school students to the scientific reasoning using the study of the evolution as an example.

Publications

Accounting for Ambiguity in Ancestral Sequence Reconstruction

Motivation
The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve …

Linking Large Scale Genome Rearrangement to Chromatin Structure in Drosophila

Different species have different genome organization. Whether it be the karyotype or gene order, these differences are seen even with …

Rearrangement Scenarios Guided by Chromatin Structure

Genome architecture can be drastically modified through a succession of large-scale rearrangements. In the quest to infer these …