Grégoire Siekaniec

My projects

I am a bioinformatician who recently completed a postdoctoral fellowship in the Algorithmic Bioinformatics team at Saarland University, where I developed the second version of ORI, a software tool for bacterial strain identification that I originally created during my PhD (see below). Prior to this, I completed a postdoctoral fellowship focused on processing exome sequencing data from RH+/HER2- metastatic breast cancer patients.
During my PhD, I worked in the field of bacterial genomics, developing rapid approaches for identifying bacterial strains using the Oxford Nanopore MinION platform, with a particular focus on the species Streptococcus thermophilus.
My professional objective is to contribute to the advancement of genomics, transcriptomics, and metagenomics, with a strong and continuing interest in the study of prokaryotic organisms.

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.