170 citations · 547 across the 9 of their papers we have counts for
9 papers
DNA Language Models: An Assessment of Pre-Training for Fine-Tuning Tasks
Romain Karpinsky, Julien Mozziconacci, Mickaël Delcey
Recent breakthroughs in foundation models and Large Language Models (LLMs) have introduced new opportunities for studying and decoding genomic sequences. Several state-of-the-art a…
The 3D genome shapes the regulatory code of developmental genes
Julien Mozziconacci, Mélody Merle, Annick Lesne
We revisit the notion of gene regulatory code in embryonic development in the light of recent findings about genome spatial organisation. By analogy with the genetic code, we posit…
Turing-like patterns in an asymmetric dynamic Ising model
Mélody Merle, Laura Messio, Julien Mozziconacci
To investigate novel aspects of pattern formation in spin systems, we use a mapping between reactive concentrations in a reaction-diffusion system and spin orientations in a dynami…
Kinetic signature of cooperativity in the irreversible collapse of a polymer
Vittore F. Scolari, Guillaume Mercy, Romain Koszul +2
We investigate the kinetics of a polymer collapse due to the formation of irreversible crosslinks between its monomers. Using the contact probability as a scale-dependent or…
The physics of epigenetics
Ruggero Cortini, Maria Barbi, Bertrand R. Caré +4
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only t…
Nucleosome Chiral Transition under Positive Torsional Stress in Single Chromatin Fibers
Aurelien Bancaud, Gaudeline Wagner, Natalia Conde e Silva +10
Using magnetic tweezers to investigate the mechanical response of single chromatin fibers, we show that fibers submitted to large positive torsion transiently trap positive turns,…