Inférence de réseaux de régulation génétique à partir de données du transcriptome non indépendamment et indentiquement distribuées (2009-2012)
Camille’s PhD was co-supervised with Christophe Ambroise (50%/50%), from 2009 to 2012.
Summary
This thesis develops statistical methods for inferring gene regulatory networks from transcriptomic data that violate the classical independent and identically distributed (iid) sampling assumption, in particular time-course and structured experimental designs. It proposes weighted-Lasso and cooperative-Lasso penalized estimators of Gaussian graphical models that incorporate prior structural information (temporal ordering, replicate structure) to improve network recovery, together with model selection procedures adapted to these dependent settings. The resulting methods are implemented in the SIMoNe R package and applied to real transcriptomic time-course data.
PhD manucript
2012
PhD thesis
Inférence de réseaux de régulation génétique à partir de données du transcriptome non indépendamment et identiquement distribuées
This thesis develops statistical methods for inferring gene regulatory networks from transcriptomic data that violate the classical independent and identically distributed (iid) sampling assumption, in particular time-course and structured experimental designs. It proposes weighted-Lasso and cooperative-Lasso penalized estimators of Gaussian graphical models that incorporate prior structural information (temporal ordering, replicate structure) to improve network recovery, together with model selection procedures adapted to these dependent settings. The resulting methods are implemented in the SIMoNe R package and applied to real transcriptomic time-course data.
Journal papers
2012
Ann Appl Stat
Sparsity in sign-coherent groups of variables via the cooperative-Lasso
@article{2012_AAS_chiquet,author={Chiquet, Julien and Grandvalet, Y. and Charbonnier, C.},title={Sparsity in sign-coherent groups of variables via
the cooperative-Lasso},journal={The Annals of Applied Statistics},year={2012},volume={6},number={2},pages={795--830},doi={10.1214/11-AOAS520},}
2010
SAGMB
Weighted-Lasso for structured network inference from time course data
C. Charbonnier, Julien Chiquet, and C. Ambroise
Statistical Applications in Genomics and Molecular Biology, 2010
@article{2010_SAGMB_Chiquet,author={Charbonnier, C. and Chiquet, Julien and Ambroise, C.},title={Weighted-Lasso for structured network inference from
time course data},journal={Statistical Applications in Genomics and Molecular
Biology},year={2010},volume={9},doi={1544-6115.1519},}
2014
Probabilistic graphical models dedicated to applications in genetics, genomics and postgenomics
M. Jeanmougin, C. Charbonnier, M. Guedj, and 1 more author