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Elements of Coevolution in Biological Sequences

Olivier Rivoire
Physical Review Letters, 2013, 110, pp.178102. ⟨10.1103/PHYSREVLETT.110.178102⟩
Article dans une revue hal-00961061v1

Computational design of a minimal catalyst using colloidal particles with programmable interactions

Maitane Muñoz-Basagoiti , Olivier Rivoire , Zorana Zeravcic
Soft Matter, 2023, 19 (21), pp.3933-3939. ⟨10.1039/D3SM00194F⟩
Article dans une revue hal-04060620v1

Modulation of kinetic barriers under chemical constraints: a role for allostery in enzyme catalysis

Olivier Rivoire
2023
Pré-publication, Document de travail hal-04270054v1

Landscape of solutions in constraint satisfaction problems

Marc Mezard , Matteo Palassini , Olivier Rivoire
Physical Review Letters, 2005, 95, pp.200202
Article dans une revue hal-00013933v1

Glass models on Bethe lattices

Olivier Rivoire , Giulio Biroli , Olivier C. Martin , Marc Mézard
The European Physical Journal B: Condensed Matter and Complex Systems, 2004, 37, pp.55-78
Article dans une revue hal-00002292v1

Random multi-index matching problems

O. C. Martin , M. Mezard , Olivier Rivoire
Journal of Statistical Mechanics: Theory and Experiment, 2005, 1, pp.P09006
Article dans une revue hal-00008996v1

A model for the generation and transmission of variations in evolution.

Olivier Rivoire , Stanislas Leibler
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (19), pp.E1940-9. ⟨10.1073/pnas.1323901111⟩
Article dans une revue hal-00998067v1

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

Roadmap on biology in time varying environments

Arvind Murugan , Kabir Husain , Michael Rust , Chelsea Hepler , Joseph Bass , et al.
Physical Biology, 2021, 18 (4), pp.041502. ⟨10.1088/1478-3975/abde8d⟩
Article dans une revue hal-03392195v1
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Properties of atypical graphs from negative complexities

Olivier Rivoire
Journal of Statistical Physics, 2004, 117, pp.453
Article dans une revue hal-00000970v2

Hierarchy and extremes in selections from pools of randomized proteins

Sébastien Boyer , Dipanwita Biswas , Anandakumar Soshee , Natate Scaramozzino , Clément Nizak , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2016, ⟨10.1073/pnas.1517813113⟩
Article dans une revue hal-01301847v1

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

The cavity method for large deviations

Olivier Rivoire
Journal of Statistical Mechanics: Theory and Experiment, 2005, 1, pp.P04007
Article dans une revue hal-00008983v1

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
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Sex as information processing: Optimality and evolution

Anton Zadorin , Olivier Rivoire
Physical Review E , 2021, 103 (6), ⟨10.1103/PhysRevE.103.062413⟩
Article dans une revue hal-03392182v1
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On the exclusion of exponential autocatalysts by sub-exponential autocatalysts

Yann Sakref , Olivier Rivoire
2023
Pré-publication, Document de travail hal-04357368v1
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Natural Selection beyond Life? A Workshop Report

Sylvain Charlat , André Ariew , Pierrick Bourrat , María Ferreira Ruiz , Thomas Heams , et al.
Life, 2021, 11 (10), pp.1051. ⟨10.3390/life11101051⟩
Article dans une revue hal-03418757v1
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On Kinetic Constraints That Catalysis Imposes on Elementary Processes

Yann Sakref , Maitane Muñoz-Basagoiti , Zorana Zeravcic , Olivier Rivoire
2023
Pré-publication, Document de travail hal-04358160v1
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Phases vitreuses, optimisation et grandes déviations

Olivier Rivoire
Analyse de données, Statistiques et Probabilités [physics.data-an]. Université Paris Sud - Paris XI, 2005. Français. ⟨NNT : ⟩
Thèse tel-00009956v1

Parsimonious evolutionary scenario for the origin of allostery and coevolution patterns in proteins

Olivier Rivoire
Physical Review E , 2019, 100 (3), ⟨10.1103/PhysRevE.100.032411⟩
Article dans une revue hal-02333986v1

Evolution of sparsity and modularity in a model of protein allostery

Mathieu Hemery , Olivier Rivoire
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, 2015, ⟨10.1103/PhysRevE.91.042704⟩
Article dans une revue hal-01301839v1

Statistical mechanics of error exponents for error-correcting codes

Thierry Mora , Olivier Rivoire
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, 2006, 74, pp.056110
Article dans une revue hal-00115544v1
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Multilevel selection in the evolution of sexual dimorphism in phenotypic plasticity

Anton Zadorin , Olivier Rivoire
Proceedings of the Royal Society B: Biological Sciences, 2023, 290 (1999), pp.20230634. ⟨10.1098/rspb.2023.0634⟩
Article dans une revue hal-04060592v1

Assessing in vivo the impact of gene context on transcription through DNA supercoiling

Ihab Boulas , Lisa Bruno , Sylvie Rimsky , Olivier Espeli , Ivan Junier , et al.
Nucleic Acids Research, 2023, 51 (18), pp.9509-9521. ⟨10.1101/2022.10.31.514473⟩
Article dans une revue hal-03836731v1

Geometry and Flexibility of Optimal Catalysts in a Minimal Elastic Model

Olivier Rivoire
Journal of Physical Chemistry B, 2020, ⟨10.1021/acs.jpcb.0c00244⟩
Article dans une revue hal-03019086v1

The Value of Information for Populations in Varying Environments

Olivier Rivoire , Stanislas Leibler
Journal of Statistical Physics, 2011, 142, pp.1124-1166. ⟨10.1007/S10955-011-0166-2⟩
Article dans une revue hal-00961034v1

Emergence of single- versus multi-state allostery

Eric Rouviere , Rama Ranganathan , Olivier Rivoire
PRX Life, 2023, 1 (2), pp.023004. ⟨10.48550/arXiv.2111.09377⟩
Article dans une revue hal-03830469v1
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Undersampling and the inference of coevolution in proteins

Yaakov Kleeorin , William Russ , Olivier Rivoire , Rama Ranganathan
Cell Systems, 2023, 14 (3), pp.210-219.e7. ⟨10.1016/j.cels.2022.12.013⟩
Article dans une revue hal-03392190v1
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Parameters and determinants of responses to selection in antibody libraries

Steven Schulz , Sébastien Boyer , Matteo Smerlak , Simona Cocco , Rémi Monasson , et al.
PLoS Computational Biology, 2021, 17 (3), pp.e1008751. ⟨10.1371/journal.pcbi.1008751⟩
Article dans une revue hal-03190048v2
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A frozen glass phase in the multi-index matching problem

O. C. Martin , M. Mezard , Olivier Rivoire
Physical Review Letters, 2004, 93, pp.217205
Article dans une revue hal-00002281v1