Mots-Clés
modélisation
simulation
transcription
chromatine
surenroulement de l'ADN
topologie
regulation
biologie computationnelle
Description
**We are looking for highly motivated students for a M2 internship followed by a 3-year PhD contract (already funded). Students from biomaths, biophysics, bioinformatics programs with strong interest in fundamental biological questions. **
Skills required: Excellent skills in mathematics, numerical computation, and knowledge of Python programming (NumPy, Pandas) are required. Knowledge in biology and experience in handling biological data (especially omics data) are strongly recommended. Complementary experimental (wet lab) and physics skills are encouraged.
Context: The internship will take place in a microbiology institute with close computational-experimental collaboration and a more specific dedication to plant pathogenic bacteria.
The candidate will integrate a project dedicated to deciphering the complex relationship between the chromosome conformation (physical structure) and gene expression (biological function). The bacterial nucleoid is shaped by DNA-binding architectural proteins and DNA supercoiling, and their dynamics underpins the regulation of gene expression.
Ongoing projects involve the computational analysis of high-throughput “omics” data (RNA-Seq, ChIP-Seq) to analyze the role of specific architectural proteins (Lrp, H-NS, Fis) and variations of DNA supercoiling (by antibiotics inhibiting topoisomerases), and biophysical simulations of transcription and DNA supercoiling.
Objectives: Depending on the candidate’s background, skills and preferences, the internship can be oriented towards (1) computational analysis of high-throughput data, to uncover new relations between protein binding, DNA topology and gene expression, or (2) computational modeling of transcription and DNA supercoiling, to uncover how the genome architecture underpins gene regulatory networks. An experimental part can be added to the project, depending on the candidate’s skills and motivations.
[1] Pineau et al. (2025), NAR 53, https://doi.org/10.1093/nar/gkaf452
[2] Forquet et al. (2022), NAR 50, 7287-7297, https://doi.org/10.1093/nar/gkac579
[3] El Houdaigui et al. (2019), NAR 46, 5648-5657, https://doi.org/10.1093/nar/gkz300
[4] Martis et al. (2019), CSBJ 17, 1047-1055, https://doi.org/10.1016/j.csbj.2019.07.013