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Physique statistique du repliement et de la dénaturation des acides nucléiques

Daniel Jost
Biophysique [physics.bio-ph]. Ecole normale supérieure de lyon - ENS LYON, 2010. Français. ⟨NNT : ⟩
Theses tel-00544804v1
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3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion

Todor Gitchev , Gabriel Zala , Peter Meister , Daniel Jost
Bioinformatics, In press
Journal articles hal-03797993v1
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Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory

Amith Abdulla , Cédric Vaillant , Daniel Jost
Nucleic Acids Research, 2022, 50 (16), pp.9083-9104. ⟨10.1093/nar/gkac702⟩
Journal articles hal-03797965v1

Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance

Daniel Jost , Cédric Vaillant
Nucleic Acids Research, 2018, 46 (5), pp.2252-2264
Journal articles hal-01976597v1

Temperature Dependence of the DNA Double Helix at the Nanoscale: Structure, Elasticity, and Fluctuations

Sam Meyer , Daniel Jost , Nikos Theodorakopoulos , Michel Peyrard , Richard Lavery et al.
Biophysical Journal, 2013, 105 (8), pp.1904-1914
Journal articles hal-01976546v1

Bifurcation in epigenetics: Implications in development, proliferation, and diseases

Daniel Jost
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, 2014, 89 (1)
Journal articles hal-01976531v1
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Global chromatin conformation differences in the Drosophila dosage compensated chromosome X

Koustav Pal , Mattia Forcato , Daniel Jost , Thomas Sexton , Cédric Vaillant et al.
Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-13350-8⟩
Journal articles hal-02386022v1

Modeling the Functional Coupling between 3D Chromatin Organization and Epigenome

Cédric Vaillant , Daniel Jost
Modeling the 3D conformation of genomes, 1, CRC Press, pp.21-56, 2019, 9781315144009
Book sections hal-02273692v1

Effect of replication on epigenetic memory and consequences on gene transcription

Mehari Zerihun , Cédric Vaillant , Daniel Jost
Physical Biology, 2015, 12 (2), pp.026007
Journal articles hal-01976588v1
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Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

Marco Di Stefano , Hans-Wilhelm Nutzmann , Marc A Marti-Renom , Daniel Jost
2020
Preprints, Working Papers, ... hal-03012893v1

Modeling the functional coupling between 3D chromatin organization and epigenome

Cédric Vaillant , Daniel Jost
Modeling the 3D conformation of genomes, 2019
Book sections hal-02386050v1

Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction

Anat Lavi-Itzkovitz , Neil Peterman , Daniel Jost , Erel Levine
Nucleic Acids Research, 2014, 42 (19), pp.12200-12211
Journal articles hal-01976585v1

Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects

Florent Chuffart , Magali Richard , Daniel Jost , Claire Burny , Hélène Duplus-Bottin et al.
PLoS Genetics, 2016, 12 (8), pp.e1006213
Journal articles hal-01976590v1

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes

Surya Ghosh , Daniel Jost
PLoS Computational Biology, 2018, 14 (5), pp.e1006159
Journal articles hal-01976607v1
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Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila

Myron Child , Jack R Bateman , Amir Jahangiri , Armando Reimer , Nicholas Lammers et al.
2020
Preprints, Working Papers, ... hal-03012922v1

A Unified Poland-Scheraga Model of Oligo- and Polynucleotide DNA Melting: Salt Effects and Predictive Power

Daniel Jost , Ralf Everaers
Biophysical Journal, 2009, 96 (3), pp.1056-1067
Journal articles hal-01976506v1

Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA

Daniel Jost
Bioinformatics, 2013, 29 (19), pp.2479-2481
Journal articles hal-01976602v1

Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans

Rahul Sharma , Daniel Jost , Jop Kind , Georgina Gómez-Saldivar , Bas van Steensel et al.
Genes and Development, 2014, 28 (23), pp.2591-2596. ⟨10.1101/gad.248864.114⟩
Journal articles hal-01976528v1

The folding landscape of the epigenome

Juan Olarte-Plata , Noelle Haddad , Cédric Vaillant , Daniel Jost
Physical Biology, 2016, 13 (2), pp.026001
Journal articles hal-01976579v1

Small RNA biology is systems biology

Daniel Jost , Andrzej Nowojewski , Erel Levine
BMB Reports, 2011, 44 (1), pp.11-21
Journal articles hal-01976509v1

IC-Finder: inferring robustly the hierarchical organization of chromatin folding

Noelle Haddad , Cédric Vaillant , Daniel Jost
Nucleic Acids Research, 2017, 45 (10), pp.gkx036. ⟨10.1093/nar/gkx036⟩
Journal articles hal-01976542v1

Genome wide application of DNA melting analysis

Daniel Jost , Ralf Everaers
Journal of Physics: Condensed Matter, 2009, 21 (3), pp.034108
Journal articles hal-01976559v1
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Genome organization via loop extrusion, insights from polymer physics models

Surya Ghosh , Daniel Jost
Briefings in Functional Genomics and Proteomics, 2020, 19 (2), pp.119-127. ⟨10.1093/bfgp/elz023⟩
Journal articles hal-03012763v1
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Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells

Kapil Newar , Amith Zafal Abdulla , Hossein Salari , Eric Fanchon , Daniel Jost et al.
PLoS Computational Biology, 2022, 18, ⟨10.1371/journal.pcbi.1010450⟩
Journal articles hal-03431877v1
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Temporal trends in the use of targeted temperature management after cardiac arrest and association with outcome: insights from the Paris Sudden Death Expertise Centre

Jean-Baptiste Lascarrou , Florence Dumas , Wulfran Bougouin , Richard Chocron , Frankie Beganton et al.
Critical Care, 2019, 23 (1), pp.391. ⟨10.1186/s13054-019-2677-1⟩
Journal articles inserm-02464708v1
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Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

Clémentine Decamps , Florian Privé , Raphael Bacher , Daniel Jost , Arthur Waguet et al.
BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-019-3307-2⟩
Journal articles hal-03012777v1
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TADs are 3D structural units of higher-order chromosome organization in Drosophila

Quentin Szabo , Daniel Jost , Jia-Ming Chang , Diego Cattoni , Giorgio Papadopoulos et al.
Science Advances , 2018, 4 (2), pp.eaar8082. ⟨10.1126/sciadv.aar8082⟩
Journal articles hal-01726709v1
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Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila

Myron Barber Child , Jack R Bateman , Amir Jahangiri , Armando Reimer , Nicholas C Lammers et al.
eLife, 2021, 10, ⟨10.7554/eLife.64412⟩
Journal articles hal-03431632v1
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Assigning function to natural allelic variation via dynamic modeling of gene network induction

Magali Richard , Florent Chuffart , Hélène Duplus‐bottin , Fanny Pouyet , Martin Spichty et al.
Molecular Systems Biology, 2018, 14 (1), pp.e7803. ⟨10.15252/msb.20177803⟩
Journal articles hal-01976613v1
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PenDA, a rank-based method for personalized differential analysis: Application to lung cancer

Magali Richard , Clémentine Decamps , Florent Chuffart , Elisabeth Brambilla , Sophie Rousseaux et al.
PLoS Computational Biology, 2020, 16 (5), pp.e1007869. ⟨10.1371/journal.pcbi.1007869⟩
Journal articles inserm-02868566v1