Papers

Preprints

• G. Bunin, O. Rivoire. Evolutionary features in a minimal physical system: directionality, diversity, selection, growth, inheritance, and adaptation. arXiv preprint.

• E. Rouviere, O. Rivoire, R. Ranganathan. A unified view of allostery. arXiv preprint.

• S. Mahdavi, Y. Sakref, O. Rivoire. One-way catalysis: Insights from a solvable lattice model. arXiv preprint.

Publications

• Y. Sakref, O. Rivoire (2024). Design principles, growth laws, and competition of minimal autocatalysts. Comm. Chem. 7 : 239. [SI]

• J. Fernandez-de-Cossio-Diaz, G. Uguzzoni, K. Ricard, F. Anselmi, A. Pagnani, C. Nizak, O. Rivoire (2024). Inference and design of antibody specificity: from experiments to models and back. PLoS Comput. Biol. 20 : e1012522. [SI]

• O. Rivoire (2024). A role for conformational changes in enzyme catalysis. Biophys. J. 123 : 1-16. [SI]

• Y. Sakref, O. Rivoire (2024). On the exclusion of exponential autocatalysts by sub-exponential autocatalysts. J. Theoret. Bio. 579 : 111714.

• Y. Sakref, M. Muñoz-Basagoiti, Z. Zeravcic, O. Rivoire (2023). On kinetic constraints that catalysis imposes on elementary processes. J. Phys. Chem. B 127 : 10950. [SI]

• E. Rouviere, R. Ranganathan, O. Rivoire (2023) Emergence of single- versus multi-state allostery. PRX Life 1 : 023004. [SI]

• I. Boulas, L. Bruno, S. Rimsky, O. Espeli, I. Junier, O. Rivoire (2023). Assessing in vivo the impact of gene context on transcription through DNA supercoiling. Nucleic Acids Res. 51 : 9509–9521. [SI]

• O. Rivoire (2023). How flexibility can enhance catalysis. Phys. Rev. Lett. 131 : 088401. [SI]

• S. Charlat, T. Heams, O. Rivoire (2023). Is natural selection physical? Evolutionary Thinking Across Disciplines, Chapter 12 : 287-296, Springer.

• M. Muñoz-Basagoiti, O. Rivoire. Z. Zeravcic (2023). Computational design of a minimal catalyst using colloidal particles with programmable interactions. Soft Matter, 19 : 3933-3939.

• A. S. Zadorin, O. Rivoire (2023). Multilevel selection in the evolution of sexual dimorphism in phenotypic plasticity. Proc. R. Soc. B 290 : 20230634.

• D. Lacoste, O. Rivoire, D. S. Tourigny (2023). Cell behavior in the face of uncertainty. Economic Principles in Cell Biology, Chapter 13.

• Y. Kleeorin, W. P. Russ, O. Rivoire, R. Ranganathan (2023). Undersampling and the inference of coevolution in proteins. Cell Systems 14 : 210–219.

• S. Charlat et al. (2021). Natural selection beyond life? A workshop report. Life 11 : 1051.

• A. S. Zadorin, O. Rivoire (2021). Sex as information processing: optimality and evolution. Phys. Rev. E 103 : 062413.

• A. Murugan et al. (2021). Roadmap on biology in time varying environments. Phys. Biol. 18 : 041502.

• S. Schulz, S. Boyer, M. Smerlak, S. Cocco, R. Monasson, C. Nizak, O. Rivoire (2021). Parameters and determinants of responses to selection in antibody libraries. PLoS Comp Biol 17 : e1008751.

• O. Rivoire (2020). Geometry and flexibility of optimal catalysts in a minimal elastic model. J. Phys. Chem. B 124 : 807-813. [SI]

• A. F. Schober, A. D. Mathis, C. Ingle, J. O. Park, L. Chen, J. D. Rabinowitz, I. Junier, O. Rivoire, K. A. Reynolds (2019). A two-enzyme adaptive unit in bacterial folate metabolism. Cell Reports 27 : 3359-3370. [SI]

• O. Rivoire (2019). Parsimonious evolutionary scenario for the origin of allostery and coevolution patterns in proteins. Phys. Rev. E 100 : 032411.

• I. Junier, P. Frémont, O. Rivoire (2018). Universal and idiosyncratic characteristic lengths in bacterial genomes. Phys. Biol. 15 : 035001. [SI]

• A. Mayer, T. Mora, O. Rivoire, A. M. Walczak (2017). Transitions in optimal adaptive strategies for populations in fluctuating environments. Phys. Rev. E 96 : 032412.

• O. Rivoire, K. Reynolds, R. Ranganathan (2016). Evolution-based functional decomposition of proteins. PLoS Comput Biol 12 : e1004817. [SI]

• A. Mayer, T. Mora, O. Rivoire, A. M. Walczak (2016). Diversity of immune strategies explained by adaptation to pathogen statistics. PNAS 113 : 8630–8635. [SI]

• I. Junier, O. Rivoire (2016). Conserved units of co-expression in bacterial genomes: an evolutionary insight. PLoS ONE 11 : e0155740. [SI]

• S. Boyer, D. Biswas, A. K. Soshee, N. Scaramozzino, C. Nizak, O. Rivoire (2016). Hierarchy and extremes in selections from pools of randomized proteins. PNAS 113 : 3482-3487. [SI]

• O. Rivoire (2016). Informations in models of evolutionary dynamics. J. Stat. Phys. 162 : 1324–1352.

• M. Hemery, O. Rivoire (2015). Evolution of sparsity and modularity in a model of protein allostery. Phys. Rev. E 91 : 042704.

• O. Rivoire, S. Leibler (2014). A model for the generation and transmission of variations in evolution. PNAS 111 : E1940-E1949. [SI]

• O. Rivoire (2013). Elements of coevolution in biological sequences. Phys. Rev. Lett. 110 : 178102. [SI]

• O. Rivoire, S. Leibler (2011). The value of information for populations in varying environments. J. Stat. Phys. 142 : 1124-66.

• R. Smock, O. Rivoire, W. Russ, J. Swain, S. Leibler, R. Ranganathan, L. Gierasch (2010). An interdomain sector mediating allostery in HSP70 molecular chaperone. Mol. Syst. Biol. 6 : 414. [SI]

• J. S. Chuang, O. Rivoire, S. Leibler (2010). Cooperation and Hamilton’s rule in a simple synthetic microbial system. Mol. Syst. Biol. 6 : 398. [SI]

• N. Halabi, O. Rivoire, S. Leibler, R. Ranganathan (2009). Protein sectors: evolutionary units of three-dimensional structures. Cell 138 : 774-86. [SI]

• J. S. Chuang, O. Rivoire, S. Leibler (2009). Simpson’s paradox in a synthetic microbial system. Science 223 : 272-75. [SI]

• O. Rivoire, J. Barré (2006). Exactly solvable models of adaptive networks. Phys. Rev. Lett. 97: 148701.

• T. Mora, O. Rivoire (2006). Statistical mechanics of error exponents for error-correcting codes. Phys. Rev. E 74 : 056110.

• T. Mora, O. Rivoire (2006). Error exponents of low-density parity-check codes on the binary erasure channel. Proc. IEEE Information Theory Workshop (Chengdu) 81-85.

• M. Mézard, M. Palassini, O. Rivoire (2005). Landscape of solutions in constraint satisfaction problems. Phys. Rev. Lett. 95 : 200202.

• O. C. Martin, M. Mézard, O. Rivoire (2005). Random multi-index matching problems. J. Stat. Mech. P09006.

• O. Rivoire (2005). The cavity method for large deviations. J. Stat. Mech. P07004.

• O. C. Martin, M. Mézard, O. Rivoire (2004). Frozen glass phase in the multi-index matching problem. Phys. Rev. Lett. 93 : 21720.

• O. Rivoire (2004). Properties of atypical graphs from negative complexities. J. Stat. Phys. 117 : 453.

• O. Rivoire, G. Biroli, O. C. Martin, M. Mézard (2004). Glass models on Bethe lattices. Eur. Phys. J. B 37: 55-78.

• M. Cashen, O. Rivoire, L. Yatsenko, H. Metcalf (2002). Coherent exchange of momentum between atoms and light. J. Opt. B : Quantum Semiclass. Opt. 4 : 75-79.

• M. Cashen, O. Rivoire, V. Romanenko, L. Yatsenko, H. Metcalf (2001). Strong optical forces in frequency-modulated light. Phys. Rev. A 64 : 063411.