Publications (see My Citations on Google Scholar, My Profile on Research Gate or my ResearcherID)

  1. *Joint first authors

‘ Joint second authors

** Joint corresponding authors


2021

  1. -M. Di Stefano, J. Paulsen, D. Jost, M. Marti-Renom, 4D Nucleome modeling, Current Opin. Genet. Dev., 67, 25-32 (2021).


2020

  1. -M. Child, J.R. Bateman**, A. Jahangiri, A. Reimer, N.C. Lammers, N. Sabouni, D. Villamarin, G.C. McKenzie-Smith, J.E. Johnson, D. Jost** & H.G. Garcia**, Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila, in submission, bioRxiv 10.1101/2020.08.30.265108 (2020).

  2. -M. Di Stefano**, H.-W. Nutzmann, M.A. Marti-Renom & D. Jost**, Polymer modeling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana, in submission, bioRxiv 10.1101/2020.05.15.098392 (2020).

  3. -M. Tortora, H. Salari & D. Jost, Chromosome dynamics during interphase: a biophysical perspective, Current Opin. Genet. Dev., 61, 37-43 (2020).

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

  5. -S. Sati, B. Bonev’, Q. Szabo’, D. Jost’,... & G. Cavalli, 4D Genome Rewiring during Oncogene-Induced and Replicative Senescence, Molecular Cell, 78, 1-17 (2020).

  6. -C. Decamps, F. Privé, R. Bacher, D. Jost, A. Waguet, HADACA consortium, E.A. Houseman, E. Lurie, P. Lutsik, A. Milosavljevic, M. Scherer, M.G.B. Blum & M. Richard. Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software, BMC Bioinfo., 21, 16 (2020).

  7. -S.K. Ghosh & D. Jost. Genome organization via loop extrusion, insights from polymer physics models, Brief. Func. Genom., 19, 119-127 (2020).


2019

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

  2. -M. Socol*, R. Wang*, D. Jost*, P. Carrivain*, C. Vaillant, E. Le Cam, V. Dahirel, C. Normand, K. Bystricky, J.-M. Victor, O. Gadal & A. Bancaud. A Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes, Nucleic Acids Res, gkz374 (2019).

  3. -C. Vaillant** & D. Jost**. Modeling the functional coupling between 3D chromatin organization and epigenome. Modeling the 3D conformation of genomes (Editors: L. Giorgetti & G. Tiana) (2019).


2018

  1. -S.K. Ghosh & D. Jost. How epigenome drives chromosome folding and dynamics, insights from efficient coarse-grained models of chromosomes, PLoS Comp. Biol., 14, e1006159 (2018).

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

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

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

  5. -D. Jost**, A. Rosa**, C. Vaillant** & R. Everaers**. A polymer physics view on universal and sequence-specific aspects of chromosome folding. Nuclear Architecture and Dynamics (Editors: C. Lavelle & J.-M. Victor), pp 149-170 (2018).


2017

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

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

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


2016

- F. Chuffart, M. Richard, D. Jost, H. Duplus-Bottin, Y. Ohya & G. Yvert. Exploiting single-cell quantitative data to map genetic variants having probabilistic effects, PLoS Genet., 12, e1006213 (2016).

  1. -J.D. Olarte-Plata, N. Haddad, C. Vaillant** & D. Jost**. The folding landscape of epigenome, Phys. Biol., 13, 026001 (2016).


2015

  1. -M. B. Zerihun, C. Vaillant & D. Jost. Effect of replication on epigenetic memory and consequences on gene transcription, Phys. Biol., 12, 026007 (2015).


2014

- R. Sharma, D. Jost, J. Kind, G. Gomez-Saldivar, B. van Steensel, P. Askjaer, C. Vaillant & P. Meister. Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans, Genes Dev., 28, 2591-2596 (2014).

- A. Lavi-Itzkovitz*, N. Peterman*, D. Jost* & E. Levine. Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction, Nucleic Acids Res., 42, 12200-12211 (2014).

- D. Jost, P. Carrivain, G. Cavalli & C. Vaillant. Modeling epigenome folding: formation and dynamics of topologically-associated chromatin domains, Nucleic Acids Res., 42, 9541-9549 (2014).

  1. -D. Jost. Bifurcation in epigenetics: implication to development, proliferation and diseases, Phys. Rev. E, 89, 010701(R) (2014).


2013

- S. Meyer, D. Jost, N. Theodorakopoulos, M. Peyrard, R. Lavery & R. Everaers. Temperature dependence of the DNA double-helix at the nanoscale: structure, elasticity and fluctuations, Biophys. J., 105, 1904-1914 (2013).

- D. Jost. Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA, Bioinformatics, 29, 2479-2481(2013).

  1. -D. Jost, A. Nowojewski & E. Levine. Regulating the many to benefit the few: role of weak small RNA targets, Biophys. J., 104, 1773-1782 (2013).


2011

- D. Jost, A. Nowojewski & E. Levine. sRNA biology is systems biology, BMB Rep. 44, 11-21 (2011).

  1. -D. Jost, A. Zubair & R. Everaers. Bubble statistics and positioning in superhelically stressed DNA, Phys. Rev. E 84, 031912 (2011).


2010

  1. -D. Jost & R. Everaers. Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model, J. Chem. Phys. 132, 095101 (2010).


2009

- D. Jost & R. Everaers. Genome-wide application of DNA melting analysis, J. Phys.: Condens. Matter 21, 034108 (2009).

  1. -D. Jost & R. Everaers. A unified Poland-Scheraga model of oligo- and polynucleotide DNA melting: salt effects and predictive power, Biophys. J. 96, 1056-1067 (2009).


2005

- D. Jost & M.W.C. Dharma-Wardana. Ground-state energy and Wigner crystallization in thick two-dimensional electron systems, Phys. Rev. B 72, 195315 (2005).