Théotime Grohens

I’m a post-doctoral researcher in the Comparative and Integrative Genomics of Organ Development (CIGOGNE) team, at the Laboratory of Biology and Modeling of the Cell at ENS Lyon.

Before that, I did a first postdoc at the Center for Genomic Regulation in Barcelona, in the Weghorn lab, after obtaining my Ph.D. at INSA Lyon in the Inria Beagle team. Even before, I studied at the École Normale Supérieure in Paris, where I obtained an M. Sc. in theoretical computer science and an M. Sc. in ecology and evolution.

You can find my CV here, follow me on Twitter, or look at my code on GitHub and on the Inria GitLab.

You can reach me at theotime (.) grohens (@) ens-lyon (.) fr.

Research interests

My research interests focus on evolutionary biology, and especially mathematical and computational models of evolution.

In the CIGOGNE team, I am currently working on elucidating the molecular mechanisms guiding the evolution of rodent tooth development.

During my postdoc at CRG, I worked on understanding the selection pressures that act upon cancer cells, and in particular on the interaction between cancer and the immune system.

During my PhD, I studied how epistatic interactions between different kinds of mutations help shape evolutionary dynamics, through the lens of the coupling between DNA supercoiling and gene transcription. In order to study this phenomenon under the light of evolution, I developed and used EvoTSC, a simulation aimed at understanding how the transcription-supercoiling coupling can shape bacterial genomes over evolutionary timescales.

Publications

Computational Biology

• Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization.
  Théotime Grohens, Sam Meyer, Guillaume Beslon, Peer Community in: Mathematical & Computational Biology, 2024. (doi, pdf)

• Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation.
  Paul Banse, Juliette Luiselli, David P. Parsons, Théotime Grohens, Marco Foley, Leonardo Trujillo, Jonathan Rouzaud-Cornabas, Carole Knibbe, Guillaume Beslon. Molecular Ecology, 2023. (doi, pdf)

• A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version.
  Théotime Grohens, Sam Meyer, Guillaume Beslon, Artificial Life, 2022. (hal, doi, pdf)

• A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling.
  Théotime Grohens, Sam Meyer, Guillaume Beslon, ALIFE 2021, 2021. (hal, doi, pdf)

Covid-19

• Understanding and monitoring the evolution of the Covid-19 epidemic from medical emergency calls: the example of the Paris area.
  Stéphane Gaubert, Marianne Akian, Xavier Allamigeon, Marin Boyet, Baptiste Colin, Théotime Grohens, Laurent Massoulié, David P. Parsons, Frédéric Adnet, Érick Chanzy, Laurent Goix, Frédéric Lapostolle, Éric Lecarpentier, Christophe Leroy, Thomas Loeb, Jean-Sébastien Marx, Caroline Télion, Laurent Tréluyer, Pierre Carli, Comptes Rendus Mathématique, 2020. (hal, doi, pdf)

Programming Languages

• Symbolic Execution for JavaScript.
  José Fragoso Santos, Petar Maksimovic, Théotime Grohens, Julian Dolby, Philippa Gardner, Principles and Practice of Declarative Programming, 2018. (doi, pdf)

PhD Thesis

• Ride the Supercoiling: Evolution of Supercoiling-Mediated Gene Regulatory Networks through Genomic Inversions.
  Théotime Grohens, 2022. (hal, pdf)

Talks & Posters

• November 2023. ETEE 2023, Gif-sur-Yvette, short talk.
• July 2023. SMBE 2023, Ferrara, poster.
• September 2022. BioSyL, Lyon, short talk.
• November 2021. GDR BIM, Lyon, poster.
• November 2021. CompSysBio winter school, Aussois, short talk and poster.
• July 2021. ALIFE 2021, Prague (virtual), short talk.
• November 2019. GDR AIEM, Toulouse, short talk.

Teaching

During my PhD, I taught computer science at INSA Lyon, in the Biosciences and Computer Science departments, and at IUT Lyon 1.