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Publications

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

There are 37 references in this bibliography folder.

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.

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.

Rivosecchi, J, Jost, D, Vachez, L, Gautier, FD, Bernard, P, and Vanoosthuyse, V (2021).
RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes.
Life Sci Alliance, 4(6).

Decamps, C, Prive, F, Bacher, R, Jost, D, Waguet, A, Houseman, EA, Lurie, E, Lutsik, P, Milosavljevic, A, Scherer, M, Blum, MGB, and Richard, M (2020).
Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software.
BMC Bioinformatics, 21(1):16.

Ghosh, SK and Jost, D (2020).
Genome organization via loop extrusion, insights from polymer physics models.
Brief Funct Genomics, 19:119-127.

Hennion, M, Arbona, J, Lacroix, L, Cruaud, C, Theulot, B, Tallec, BL, Proux, F, Wu, X, Novikova, E, Engelen, S, Lemainque, A, Audit, B, and Hyrien, O (2020).
FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing.
Genome Biol, 21(1):125.

Richard, M, Decamps, C, Chuffart, F, Brambilla, E, Rousseaux, S, Khochbin, S, and Jost, D (2020).
PenDA, a rank-based method for personalized differential analysis: Application to lung cancer.
PLoS Comput Biol, 16(5):e1007869.

Sati, S, Bonev, B, Szabo, Q, Jost, D, Bensadoun, P, Serra, F, Loubiere, V, Papadopoulos, GL, Rivera-Mulia, J, Fritsch, L, Bouret, P, Castillo, D, Gelpi, JL, Orozco, M, Vaillant, C, Pellestor, F, Bantignies, F, Marti-Renom, MA, Gilbert, DM, Lemaitre, J, and Cavalli, G (2020).
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence.
Mol Cell, 78(3):522-538.e9.

Tortora, MM, Salari, H, and Jost, D (2020).
Chromosome dynamics during interphase: a biophysical perspective.
Curr Opin Genet Dev, 61:37-43.

Pal, K, Forcato, M, Jost, D, Sexton, T, Vaillant, C, Salviato, E, Mazza, EMC, Lugli, E, Cavalli, G, and Ferrari, F (2019).
Global chromatin conformation differences in the Drosophila dosage compensated chromosome X.
Nat Commun, 10(1):5355.

Socol, M, Wang, R, Jost, D, Carrivain, P, Vaillant, C, Le Cam, E, Dahirel, V, Normand, C, Bystricky, K, Victor, J, Gadal, O, and Bancaud, A (2019).
Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes.
Nucleic Acids Res, 47(12):6195-6207.

Vaillant, C and Jost, D (2019).
Modeling the functional coupling between 3D chromatin organization and epigenome
CRC Press, vol. Modeling the 3D conformation of genomes.

Ghosh, SK and Jost, D (2018).
How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes.
PLoS Comput Biol, 14(5):e1006159.

Jost, D and Vaillant, C (2018).
Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance.
Nucleic Acids Res, 46(5):2252-2264.

Jost, D, Rosa, A, Vaillant, C, and Everaers, R (2018).
A polymer physics view on universal and sequence-specific aspects of chromosome folding
Elsevier, vol. Nuclear Architecture and Dynamics.

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