Publications

A robust workflow to benchmark deconvolution of multi-omic data

E. Amblard, V. Bertrand, L. M. Pena, S. Karkar, F. Chuffart, M. Ayadi, A. Baures, L. Armenoult, Y. Kermezli, J. Cros, Y. Blum, M. Richard

hdmax2, an R package to perform high dimension mediation analysis

F. Pittion, B. Jumentier, A. Nakamura, J. Lepeule, O. Francois, M. Richard

DECOMICS, a shiny application for unsupervised cell type deconvolution and biological interpretation of bulk omic data

S. Karkar, A. Sharma, C. Herrmann, Y. Blum, M. Richard

Bioinformatics Advances

Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma

C. Saillard, F. Delecourt, B. Schmauch, O. Moindrot, M. Svrcek, A. Bardier-Dupas, J. F. Emile, M. Ayadi, V. Rebours, L. de Mestier, P. Hammel, C. Neuzillet, J. B. Bachet, J. Iovanna, N. Dusetti, Y. Blum, M. Richard, Y. Kermezli, V. Paradis, M. Zaslavskiy, P. Courtiol, A. Kamoun, R. Nicolle, J. Cros

Nature Communications

Codabench: Flexible, easy-to-use, and reproducible meta-benchmark platform

Z. Xu, S. Escalera, A. Pavão, M. Richard, W.-W. Tu, Q. Yao, H. Zhao, I. Guyon

Patterns

DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification

C. Decamps, A. Arnaud, F. Petitprez, M. Ayadi, A. Baurès, L. Armenoult, HADACA consortium, S. Escalera, I. Guyon, R. Nicolle, R. Tomasini, A. de Reyniès, J. Cros, Y. Blum, M. Richard

BMC bioinformatics

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

HADACA consortium, C. Decamps, F. Privé, R. Bacher, D. Jost, A. Waguet, E. A. Houseman, E. Lurie, P. Lutsik, A. Milosavljevic, M. Scherer, M. G. B. Blum, M. Richard

BMC Bioinformatics

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer

M. Richard, C. Decamps, F. Chuffart, E. Brambilla, S. Rousseaux, S. Khochbin, D. Jost

PLOS Computational Biology

CRELD1 is an evolutionarily-conserved maturational enhancer of ionotropic acetylcholine receptors

M. D'Alessandro, M. Richard, C. Stigloher, V. Gache, T. Boulin, J. E. Richmond, J.-L. Bessereau

eLife

Genomics of cellular proliferation in periodic environmental fluctuations

J. Salignon, M. Richard, E. Fulcrand, H. Duplus-Bottin, G. Yvert

Molecular Systems Biology

Assigning function to natural allelic variation via dynamic modeling of gene network induction

M. Richard, F. Chuffart, H. Duplus-Bottin, F. Pouyet, M. Spichty, E. Fulcrand, M. Entrevan, A. Barthelaix, M. Springer, D. Jost, G. Yvert

Molecular Systems Biology

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

F. Chuffart, M. Richard, D. Jost, C. Burny, H. Duplus-Bottin, Y. Ohya, G. Yvert

PLOS Genetics

Biosynthesis of ionotropic acetylcholine receptors requires the evolutionarily conserved ER membrane complex

M. Richard, T. Boulin, V. J. P. Robert, J. E. Richmond, J.-L. Bessereau

Proceedings of the National Academy of Sciences

A screen for X-linked mutations affecting Drosophila photoreceptor differentiation identifies Casein kinase 1α as an essential negative regulator of wingless signaling

K. Legent, J. Steinhauer, M. Richard, J. E. Treisman

Genetics

AI Competitions and Benchmarks, Practical issues: Proposals, grant money, sponsors, prizes, dissemination, publicity

M. Richard, Y. Blum, J. Guinney, G. Stolovitzky, A. Pavao

DMLR

How does evolution tune biological noise?

M. Richard, G. Yvert

Frontiers in Genetics

hdmax2: R package hdmax2 performs high dimension mediation analysis

F. Pittion, M. Richard, O. Francois, B. Jumentier

decomics: DEConvolution of OMICS data

S. Karkar, Y. Blum, M. Richard