Publications

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

There are 64 references in this bibliography folder.

Akilli, N, Puel, P, Stefano, MD, Muzzopappa, F, Fritsch, L, Erdel, F, Jost, D, Cheutin, T, and Cavalli, G (2026).
Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3.
Nucleic Acids Res, 54(17).

Cheutin, T, Akilli, N, Di Stefano, M, Puel, P, Fritsch, L, Jost, D, and Cavalli, G (2026).
PRC1 nanoglobules organize Hox chromatin during Drosophila embryogenesis.
Cell Discov, 12(1).

Dufour, A, Duplus-Bottin, H, Boukéké-Lesplulier, T, Casassa, E, Triqueneaux, G, Tarbouriech, L, Darthenay-Kiennemann, C, Dumont, A, Moali, C, Vittoz, F, Jost, D, and Yvert, G (2026).
Kinetic properties of optogenetic site-specific DNA recombination by LiCre-loxP.
Biol Open, 15(5).

D’Asaro, D, Arbona, J, Vaillant, C, and Jost, D (2026).
Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids
Nucleic Acids Research, 54(15):gkag731.

Giorgetti, L and Jost, D (2026).
Editorial overview: Genome Architecture and Expression
Current opinion in genetics & development, 100:102513.

Paldi, F, Szalay, M, Dufau, S, Di Stefano, M, Reboul, H, Jost, D, Bantignies, F, and Cavalli, G (2026).
Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.
Nat Genet, 58(2):404-417.

Piveteau, V, Dupont, C, Salari, H, Dumont, A, Savocco, J, Jost, D, and Piazza, A (2026).
Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.
EMBO J, 45(9):3124-3155.

Rojat, V, Ciardo, D, Tourancheau, A, Proux, F, Jean, E, Arbona, J, Audit, B, Millot, GA, Bonhomme, F, Arimondo, PB, and others (2026).
Automated mapping of DNA replication fork progression in human cells with ForkML
Nature communications, 17(1):1975.

Bontonou, M, Haget, A, Boulougouri, M, Audit, B, Borgnat, P, and Arbona, J (2025).
A comparative analysis of gene expression profiling by statistical and machine learning approaches.
Bioinform Adv, 5(1):vbae199.

D’Asaro, D, Arbona, J, Piveteau, V, Piazza, A, Vaillant, C, and Jost, D (2025).
Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes
Genome Biology, 26(1):431.

Lage, C, Pustelnik, N, Arbona, J, Audit, B, and Gribonval, R (2025).
Identifying a piecewise affine signal from its nonlinear observation-application to DNA replication analysis
IEEE Transactions on Signal Processing.

Lüthi, BN, Semple, JI, Haemmerli, A, Thapliyal, S, Ghadage, K, Stojanovski, K, D'Asaro, D, Das, M, Gilbert, N, Glauser, DA, Towbin, B, Jost, D, and Meister, P (2025).
Cohesin forms fountains at active enhancers in C. elegans.
Nat Commun, 17(1):681.

Theulot, B, Tourancheau, A, Simonin Chavignier, E, Jean, E, Arbona, J, Audit, B, Hyrien, O, Lacroix, L, and Le Tallec, B (2025).
Telomere-to-telomere DNA replication timing profiling using single-molecule sequencing with Nanotiming.
Nat Commun, 16(1):242.

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.

D’Asaro, D, Tortora, MM, Vaillant, C, Arbona, J, and Jost, D (2024).
DNA replication and polymer chain duplication reshape the genome in space and time
Physical Review X, 14(4):041020.

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.