Publications

E. Amblard, V. Bertrand, L. M. Pena, S. Karkar et al.. A robust workflow to benchmark deconvolution of multi-omic data, Genome Biology November 2025

F. Pittion, B. Jumentier, A. Nakamura, J. Lepeule et al.. hdmax2, an R package to perform high dimension mediation analysis, September 2024

M. Richard, Y. Blum, J. Guinney, G. Stolovitzky et al.. AI Competitions and Benchmarks, Practical issues: Proposals, grant money, sponsors, prizes, dissemination, publicity, arXiv January 2024

S. Karkar, A. Sharma, C. Herrmann, Y. Blum et al.. DECOMICS, a shiny application for unsupervised cell type deconvolution and biological interpretation of bulk omic data, Bioinformatics Advances, January 2024

C. Saillard, F. Delecourt, B. Schmauch, O. Moindrot et al.. Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma, Nature Communications, June 2023

M. Vasse, S. Bonhoeffer, A. Frenoy. Ecological effects of stress drive bacterial evolvability under sub-inhibitory antibiotic treatments, ISME Communications, December 2022

M. Vasse, S. Bonhoeffer, A. Frenoy. Ecological effects of stress drive bacterial evolvability under sub-inhibitory antibiotic treatments, ISME communications, September 2022

Z. Xu, S. Escalera, A. Pavão, M. Richard et al.. Codabench: Flexible, easy-to-use, and reproducible meta-benchmark platform, Patterns, June 2022

A. L. Decrulle, A. Frénoy, T. A. Meiller-Legrand, A. Bernheim et al.. Engineering gene overlaps to sustain genetic constructs in vivo, PLOS Computational Biology, October 2021

A. L. Decrulle, A. Frénoy, T. A. Meiller-Legrand, A. Bernheim et al.. Engineering gene overlaps to sustain genetic constructs in vivo, PLOS Computational Biology, October 2021

C. Decamps, A. Arnaud, F. Petitprez, M. Ayadi et al.. DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification, BMC bioinformatics, October 2021

HADACA consortium, C. Decamps, F. Privé, R. Bacher et al.. Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software, BMC Bioinformatics, December 2020

M. Richard, C. Decamps, F. Chuffart, E. Brambilla et al.. PenDA, a rank-based method for personalized differential analysis: Application to lung cancer, PLOS Computational Biology, May 2020

J. Lehman, J. Clune, D. Misevic, C. Adami et al.. The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities, Artificial Life, 2020

M. DAlessandro, M. Richard, C. Stigloher, V. Gache et al.. CRELD1 is an evolutionarily-conserved maturational enhancer of ionotropic acetylcholine receptors, eLife, November 2018

A. Frenoy, S. Bonhoeffer. Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria, PLOS Biology, May 2018

A. Frenoy, S. Bonhoeffer. Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria, PLoS biology, May 2018

J. Salignon, M. Richard, E. Fulcrand, H. Duplus-Bottin et al.. Genomics of cellular proliferation in periodic environmental fluctuations, Molecular Systems Biology, March 2018

M. Richard, F. Chuffart, H. Duplus-Bottin, F. Pouyet et al.. Assigning function to natural allelic variation via dynamic modeling of gene network induction, Molecular Systems Biology, January 2018

B. Tepekule, H. Uecker, I. Derungs, A. Frenoy et al.. Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies, PLoS computational biology, September 2017

A. Frénoy, F. Taddei, D. Misevic. Second-order cooperation: Cooperative offspring as a living public good arising from second-order selection on non-cooperative individuals, Evolution; International Journal of Organic Evolution, July 2017

A. Mathieu, S. Fleurier, A. Frénoy, J. Dairou et al.. Discovery and Function of a General Core Hormetic Stress Response in E. coli Induced by Sublethal Concentrations of Antibiotics, Cell Reports, September 2016

F. Chuffart, M. Richard, D. Jost, C. Burny et al.. Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects, PLOS Genetics, August 2016

D. Misevic, A. Frénoy, A. B. Lindner, F. Taddei. Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations, Evolution; International Journal of Organic Evolution, March 2015

M. Richard, G. Yvert. How does evolution tune biological noise?, Frontiers in Genetics, 2014

M. Richard, T. Boulin, V. J. P. Robert, J. E. Richmond et al.. Biosynthesis of ionotropic acetylcholine receptors requires the evolutionarily conserved ER membrane complex, Proceedings of the National Academy of Sciences, March 2013

A. Frénoy, F. Taddei, D. Misevic. Genetic architecture promotes the evolution and maintenance of cooperation, PLoS computational biology, 2013

K. Legent, J. Steinhauer, M. Richard, J. E. Treisman. A screen for X-linked mutations affecting Drosophila photoreceptor differentiation identifies Casein kinase 1α as an essential negative regulator of wingless signaling, Genetics, February 2012