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You are here: Home / Teams / Physical Biology of Chromatin - D. Jost / Publications


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

There are 31 references in this bibliography folder.

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

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.

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.

Richard, M, Chuffart, F, Duplus-Bottin, H, Pouyet, F, Spichty, M, Fulcrand, E, Entrevan, M, Barthelaix, A, Springer, M, Jost, D, and Yvert, G (2018).
Assigning function to natural allelic variation via dynamic modeling of gene network induction.
Mol Syst Biol, 14(1):e7803.

Szabo, Q, Jost, D, Chang, J, Cattoni, DI, Papadopoulos, GL, Bonev, B, Sexton, T, Gurgo, J, Jacquier, C, Nollmann, M, Bantignies, F, and Cavalli, G (2018).
TADs are 3D structural units of higher-order chromosome organization in Drosophila.
Sci Adv, 4(2):eaar8082.

Haddad, N, Jost, D, and Vaillant, C (2017).
Perspectives: Using polymer modeling to understand the formation and function of nuclear compartments
Chromosome Research, 25:35-50.

Haddad, N, Vaillant, C, and Jost, D (2017).
IC-Finder: inferring robustly the hierarchical organization of chromatin folding.
Nucleic Acids Res, 45(10):e81.

Jost, D, Vaillant, C, and Meister, P (2017).
Coupling 1D modifications and 3D nuclear organization: data, models and function.
Curr Opin Cell Biol, 44:20-27.

Chuffart, F, Richard, M, Jost, D, Burny, C, Duplus-Bottin, H, Ohya, Y, and Yvert, G (2016).
Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects.
PLoS Genet, 12(8):e1006213.

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