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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 23 references in this bibliography folder.

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.

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.

Ghosh, SK and Jost, D (2019).
Genome organization via loop extrusion, insights from polymer physics models.
Brief Funct Genomics.

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.

Olarte-Plata, JD, Haddad, N, Vaillant, C, and Jost, D (2016).
The folding landscape of the epigenome.
Phys Biol, 13(2):026001.

Zerihun, MB, Vaillant, C, and Jost, D (2015).
Effect of replication on epigenetic memory and consequences on gene transcription.
Phys Biol, 12(2):026007.

Jost, D (2014).
Bifurcation in epigenetics: implications in development, proliferation, and diseases.
Phys Rev E Stat Nonlin Soft Matter Phys, 89(1):010701.

Jost, D, Carrivain, P, Cavalli, G, and Vaillant, C (2014).
Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains.
Nucleic Acids Res, 42(15):9553-61.

Sharma, R, Jost, D, Kind, J, Gomez-Saldivar, G, van Steensel, B, Askjaer, P, Vaillant, C, and Meister, P (2014).
Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans.
Genes Dev, 28(23):2591-6.

Jost, D (2013).
Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA.
Bioinformatics, 29(19):2479-81.

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