Publications

This folder holds the following references to publications, sorted by year and author.

There are 50 references in this bibliography folder.

Dumont, A, Mendiboure, N, Savocco, J, Anani, L, Moreau, P, Thierry, A, Modolo, L, Jost, D, and Piazza, A (2024).
Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae.
Mol Cell, 84(17):3237-3253.e6.

Lage, C, Pustelnik, N, Arbona, JM, and Audit, B (2024).
Space-Scale Hybrid Continuous-Discrete Sliding Frank-Wolfe Method
IEEE Signal Processing Letters, 31:830-834.

Salari, H, Fourel, G, and Jost, D (2024).
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.
Nat Commun, 15(1):5393.

Xompero, A, Bontonou, M, Arbona, J, Benetos, E, and Cavallaro, A (2024).
Explaining Models Relating Objects and Privacy
In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops, pp. 8194-8198.

Abdulla, AZ, Salari, H, Tortora, MMC, Vaillant, C, and Jost, D (2023).
4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling.
Curr Opin Genet Dev, 79:102033.

Abdulla, AZ, Tortora, MMC, Vaillant, C, and Jost, D (2023).
Topological Constraints and Finite-Size Effects in Quantitative Polymer Models of Chromatin Organization
Macromolecules, 56(21):8697-8709.

Arbona, J, Kabalane, H, Barbier, J, Goldar, A, Hyrien, O, and Audit, B (2023).
Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.
PLoS Comput Biol, 19(5):e1011138.

Bonnet, KA, Hulo, N, Mourad, R, Ewing, A, Croce, O, Naville, M, Vassetzky, N, Gilson, E, Picard, D, and Fourel, G (2023).
ProA and ProB repeat sequences shape genome organization, and enhancers open domains
bioRxiv.

Chahar, S, Ben Zouari, Y, Salari, H, Kobi, D, Maroquenne, M, Erb, C, Molitor, AM, Mossler, A, Karasu, N, Jost, D, and Sexton, T (2023).
Transcription induces context-dependent remodeling of chromatin architecture during differentiation.
PLoS Biol, 21(12):e3002424.

Orsi, GA, Tortora, MMC, Horard, B, Baas, D, Kleman, J, Bucevičius, J, Lukinavičius, G, Jost, D, and Loppin, B (2023).
Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis.
Nat Commun, 14(1):4187.

Tortora, MM and Jost, D (2023).
Orientational Wetting and Topological Transitions in Confined Solutions of Semiflexible Polymers
Macromolecules, 56(4):1339–1351.

Tortora, MMC, Brennan, LD, Karpen, G, and Jost, D (2023).
HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation.
Proc Natl Acad Sci U S A, 120(33):e2211855120.

Abdulla, AZ, Vaillant, C, and Jost, D (2022).
Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory.
Nucleic Acids Res, 50(16):9083-9104.

Belokopytova, P, Viesná, E, Chiliński, M, Qi, Y, Salari, H, Di Stefano, M, Esposito, A, Conte, A, Chiariello, AM, Teif, VB, Plewczynski, D, Zhang, B, Jost, D, and Fishman, V (2022).
3DGenBench: a web-server to benchmark computational models for 3D Genomics.
Nucleic Acids Res.

Gitchev, T, Zala, G, Meister, P, and Jost, D (2022).
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion.
Bioinformatics, 38(24):5454-5456.

Hennion, M, Theulot, B, Arbona, J, Audit, B, and Hyrien, O (2022).
FORK-seq: Single-Molecule Profiling of DNA Replication.
Methods Mol Biol, 2477:107-128.

Jost, D (2022).
Polymer Modeling of 3D Epigenome Folding: Application to Drosophila.
Methods Mol Biol, 2301:293-305.

Newar, K, Abdulla, AZ, Salari, H, Fanchon, E, and Jost, D (2022).
Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells.
PLoS Comput Biol, 18(9):e1010450.

Parmentier, R, Racine, L, Moussy, A, Chantalat, S, Sudharshan, R, Papili Gao, N, Stockholm, D, Corre, G, Fourel, G, Deleuze, J, Gunawan, R, and Paldi, A (2022).
Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells.
PLoS Biol, 20(10):e3001849.

Salari, H, Di Stefano, M, and Jost, D (2022).
Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin.
Genome Res, 32(1):28-43.

Theulot, B, Lacroix, L, Arbona, J, Millot, GA, Jean, E, Cruaud, C, Pellet, J, Proux, F, Hennion, M, Engelen, S, Lemainque, A, Audit, B, Hyrien, O, and Le Tallec, B (2022).
Genome-wide mapping of individual replication fork velocities using nanopore sequencing.
Nat Commun, 13(1):3295.

Child, MB6, Bateman, JR, Jahangiri, A, Reimer, A, Lammers, NC, Sabouni, N, Villamarin, D, McKenzie-Smith, GC, Johnson, JE, Jost, D, and Garcia, HG (2021).
Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila.
Elife, 10.

Ciardo, D, Haccard, O, Narassimprakash, H, Arbona, J, Hyrien, O, Audit, B, Marheineke, K, and Goldar, A (2021).
Organization of DNA Replication Origin Firing in Xenopus Egg Extracts: The Role of Intra-S Checkpoint.
Genes (Basel), 12(8).

Di Stefano, M, Nützmann, H, Marti-Renom, MA, and Jost, D (2021).
Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana.
Nucleic Acids Res, 49(4):1840-1858.

Di Stefano, M, Paulsen, J, Jost, D, and Marti-Renom, MA (2021).
4D nucleome modeling.
Curr Opin Genet Dev, 67:25-32.