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CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus.

 Ivan Junier , Ryan K Dale , Chunhui Hou , François Képès , Ann Dean
Nucleic Acids Research, 2012, 40 (16), pp.7718-7727. ⟨10.1093/nar/gks536⟩
Article dans une revue hal-00732516v1

Experimental free-energy measurements of kinetic molecular states using fluctuation theorems

 Anna Alemany , Alessandro Mossa , Ivan Junier , Felix Ritort
Nature Physics, 2012, 8 (9), pp.688 - 694. ⟨10.1038/NPHYS2375⟩
Article dans une revue hal-01635957v1
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Spatial and topological organization of DNA chains induced by gene co-localization

 Ivan Junier , Olivier C. Martin , François Képès
PLoS Computational Biology, 2010, 6 (2), pp.1000678. ⟨10.1371/journal.pcbi.1000678⟩
Article dans une revue hal-00484355v1
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Parallel stepwise stochastic simulation: Harnessing GPUs to Explore Possible Futures States of a Chromosome Folding Model Thanks to the Possible Futures Algorithm (PFA)

 Jonathan Passerat-Palmbach , Jonathan Caux , Yannick Le Pennec , Romain Reuillon , Ivan Junier , et al.
SIGSIM-PADS’13 - ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS), May 2013, Montreal, Canada. pp.169 - 177, ⟨10.1145/2486092.2486114⟩
Communication dans un congrès hal-01098546v1
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Computational tools for the multiscale analysis of Hi-C data in bacterial chromosomes

 Nelle Varoquaux , Virginia S Lioy , Frédéric Boccard , Ivan Junier
Hi-C Data Analysis, 2301, Springer US, pp.197-207, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1390-0_10⟩
Chapitre d'ouvrage hal-03375884v1

Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation

 Ivan Junier , Olivier Rivoire
PLoS ONE, 2016, 11 (5), ⟨10.1371/journal.pone.0155740⟩
Article dans une revue hal-01653838v1

The layout of a bacterial genome

 François Képès , Brian C. Jester , Thibaut Lepage , Nafiseh Rafiei , Bianca Rosu , et al.
FEBS Letters, 2012, 586 (15), pp.2043 - 2048. ⟨10.1016/j.febslet.2012.03.051⟩
Article dans une revue hal-01635955v1

Tailoring symmetry groups using external alternate fields

 Ivan Junier , Jorge Kurchan
EPL - Europhysics Letters, 2003, 63 (5), pp.674--680
Article dans une revue hal-00160769v1

CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus

 Ivan Junier , Ryan K. Dale , Chunhui Hou , François Képès , Ann Dean
Nucleic Acids Research, 2012, 40 (16), pp.7718 - 7727. ⟨10.1093/nar/gks536⟩
Article dans une revue hal-01635956v1
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Spatial Information and Boolean Genetic Regulatory Networks.

 Matthieu Manceny , Marc Aiguier , Pascale Le Gall , Joan Hérisson , Ivan Junier , et al.
Bioinformatics and Computational Biology (BICoB), Apr 2008, New Orleans, United States. pp.270-281, ⟨10.1007/978-3-642-00727-9_26⟩
Communication dans un congrès hal-00812184v1
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A polymer model of bacterial supercoiled DNA including structural transitions of the double helix

 Thibaut Lepage , Ivan Junier
Physica A: Statistical Mechanics and its Applications, 2019, 527, pp.121196. ⟨10.1016/j.physa.2019.121196⟩
Article dans une revue hal-02283136v1
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Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells

 Julie Dauverd -Girault , Charlène Planchenault , Marine Pons , Caroline Schiavon , Patricia Siguier , et al.
Journal of Molecular Biology, 2020, 432 (3), pp.745-761. ⟨10.1016/j.jmb.2019.11.027⟩
Article dans une revue hal-02392007v1

Stable community cores in complex networks

 Massoud Seifi , Jean-Loup Guillaume , Ivan Junier , Jean-Baptiste Rouquier , Svilen Iskrov
3rd Workshop on Complex Networks (CompleNet 2012), Mar 2012, Melbourne, Florida, United States. pp.87-98, ⟨10.1007/978-3-642-30287-9_10⟩
Communication dans un congrès istex hal-01273060v1
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Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome

 Marc Joyeux , Ivan Junier
Biophysical Journal, 2020, 119 (6), pp.1215-1225. ⟨10.1016/j.bpj.2020.08.004⟩
Article dans une revue hal-03017254v1

Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium

 Ivan Junier , E. besray Unal , Eva Yus , Verónica Lloréns-Rico , Luis Serrano
Cell Systems, 2016, 2 (6), pp.391 - 401. ⟨10.1016/j.cels.2016.04.015⟩
Article dans une revue hal-01653839v1
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Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

 Thibaut Lepage , Ivan Junier
The Bacterial Nucleoid, 2017
Chapitre d'ouvrage hal-01655027v1

Genomic Organization of Evolutionarily Correlated Genes in Bacteria: Limits and Strategies

 Ivan Junier , Joan Hérisson , François Képès
Journal of Molecular Biology, 2012, 419 (5), pp.369 - 386. ⟨10.1016/j.jmb.2012.03.009⟩
Article dans une revue istex hal-01635954v1

Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling

 Jean-Charles Walter , Thibaut Lepage , Jerome Dorignac , Frederic Geniet , Andrea Parmeggiani , et al.
2020
Pré-publication, Document de travail hal-02990631v1

Universal and idiosyncratic characteristic lengths in bacterial genomes

 Ivan Junier , Paul Frémont , Olivier Rivoire
Physical Biology, 2018, 15 (3), pp.035001. ⟨10.1088/1478-3975/aab4ac⟩
Article dans une revue hal-01972786v1

From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments

 Marco Cosentino Lagomarsino , Olivier Espéli , Ivan Junier
FEBS Letters, 2015, 589 (20, A, SI), pp.2996-3004. ⟨10.1016/j.febslet.2015.07.002⟩
Article dans une revue hal-01528521v1
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Etude de systemes hors equilibre

 Ivan Junier
Matière Condensée [cond-mat]. Université Paris-Diderot - Paris VII, 2004. Français. ⟨NNT : ⟩
Thèse tel-00007153v1
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circHiC: circular visualization of Hi-C data and integration of genomic data

 Ivan Junier , Nelle Varoquaux
2021
Pré-publication, Document de travail hal-02945275v1
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Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions

 Ludovic Pelosi , Anne-Lise Ducluzeau , Laurent Loiseau , Frédéric Barras , Dominique Schneider , et al.
mSystems, 2016, 1 (4), pp.00091-16. ⟨10.1128/mSystems.00091-16⟩
Article dans une revue hal-01424513v1
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Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex

 Jean-Charles Walter , Thibaut Lepage , Jerome Dorignac , Frédéric Geniet , Andrea Parmeggiani , et al.
PLoS Computational Biology, 2021, 17 (4), pp.e1008869. ⟨10.1371/journal.pcbi.1008869⟩
Article dans une revue hal-03438826v1
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Intracellular positioning systems limit the entropic eviction of secondary replicons toward the nucleoid edges in bacterial cells

 Charlene Planchenault , Marine Pons , Caroline Schiavon , Patricia Siguier , Jérôme Rech , et al.
2019
Pré-publication, Document de travail hal-02366139v1

A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism

 A.F. Schober , A.D. Mathis , C. Ingle , J.O. Park , Lin Chen , et al.
Cell Reports, 2019, 27 (11), pp.3359-3370.e7. ⟨10.1016/j.celrep.2019.05.030⟩
Article dans une revue hal-02283154v1

Microscopic realizations of the trap model

 Ivan Junier , Jorge Kurchan
Journal of Physics A: Mathematical and Theoretical, 2004, 37 (13), pp.3945--3965
Article dans une revue hal-00160774v1
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