Grégoire Siekaniec

My projects

I am a bioinformatician currently working on the assembly of European Jaera genomes (a small marine isopod) using PacBio and Illumina sequencing data in the ABiMS platform of the Roscoff Biological Station. Previously, I completed a postdoctoral fellowship in the Algorithmic Bioinformatics group at Saarland University, where I worked on the second version of ORI, a software tool for bacterial strain identification that I originally developed during my PhD (see below). Before that, I completed a postdoctoral fellowship focused on the analysis of exome sequencing data from HR+/HER2− metastatic breast cancer patients at the Institut de Cancérologie de l’Ouest (ICO). During my PhD, conducted within the Genscale team at Inria Rennes and the Microbio team at STLO (INRAE), I worked in the field of bacterial genomics. My research focused on developing rapid methods for bacterial strain identification using the Oxford Nanopore MinION sequencing platform, with particular emphasis on the species Streptococcus thermophilus. My professional goal is to contribute to advances in genomics, transcriptomics, and metagenomics across a broad range of research areas.

For more details on my scientific and professional background you can download my resume:

Scientific paper

Siekaniec, G. et al.. Identification of Isolated or Mixed Strains from Long Reads: A Challenge met on Streptococcus thermophilus Using a MinION Sequencer. Microbial Genomics 7, 11 (2021). https://doi.org/10.1099/mgen.0.000654

Roux, E. et al. The genomic basis of the Streptococcus thermophilus health-promoting properties. BMC Genomics 23, 210 (2022). https://doi.org/10.1186/s12864-022-08459-y

My thesis manuscript entitled "Identification of strains of a bacterial species from long reads" is available here

Informatics

ORI (Oxford nanopore Read Identification) can be found here: https://github.com/gsiekaniec/ORI

Other projects can be found on my github : https://github.com/gsiekaniec

Teaching

2018-2019:

• TP Python - License L1 Biologie: 24h
• TP/TD Python - Master M1 BioInformatique: 19h
• TP/TD Python - Master M1 Santé publique: 21h

Popularization of sciences

Participation at the 2019 edition of Sciences en Cour[t]s with Nicolas Guillaudeux

Sciences en Cour[t]s is a very short film festival for popular science. We win the public price for our film called "Me, my dog and the others: in search of lost transcripts". This video explains in a simplified way a part of Nicolas's thesis.

Organisation of the 2020 edition of Sciences en Cour[t]s

In addition to the 2019 participation, I take care, with Nicolas Guillaudeux and Raphael Truffet, of the organization of the 2020 Sciences en cour[t]s festival. I notably made the poster for the 2020 year edition below.

Little extra 1: sport skills

Climbing (since 2022)

Running (sometimes)

Longboard (beginner)

Little extra 2: animals

I have a little cat called Taffy.

I also take part in the education of a White Swiss Shepherd dog called Snow.