Mining Concepts from Large SAGE Gene Expression Matrices. - François Rioult; Céline Robardet; Sylvain Blachon; Bruno Crémilleux; Olivier Gandrillon; Jean-François Boulicaut (KDID, 2003)

Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. - Céline Keime; Francesca Damiola; Dominique Mouchiroud; Laurent Duret; Olivier Gandrillon (BMC Bioinform., 2004)

Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. - Hédi Soula; Céline Robardet; François Perrin; Sébastien Gripon; Guillaume Beslon; Olivier Gandrillon (BMC Bioinform., 2005)

Mining Plausible Patterns from Genomic Data. - Jirí Kléma; Arnaud Soulet; Bruno Crémilleux; Sylvain Blachon; Olivier Gandrillon (CBMS, 2006)

Unexpected observations after mapping LongSAGE tags to the human genome. - Céline Keime; Marie Sémon; Dominique Mouchiroud; Laurent Duret; Olivier Gandrillon (BMC Bioinform., 2007)

Clustering Formal Concepts to Discover Biologically Relevant Knowledge from Gene Expression Data. - Sylvain Blachon; Ruggero G. Pensa; Jérémy Besson; Céline Robardet; Jean-François Boulicaut; Olivier Gandrillon (Silico Biol., 2007)

Modélisation cellulaire pour l'émergence de structures multiprotéiques auto-organisées. - Antoine Coulon; Hédi Soula; Olivier Mazet; Olivier Gandrillon; Guillaume Beslon (Tech. Sci. Informatiques, 2007)

SQUAT: A web tool to mine human, murine and avian SAGE data. - Johan Leyritz; Stéphane Schicklin; Sylvain Blachon; Céline Keime; Céline Robardet; Jean-François Boulicaut; Jérémy Besson; Ruggero G. Pensa; Olivier Gandrillon (BMC Bioinform., 2008)

Constraint-Based Knowledge Discovery from SAGE Data. - Jirí Kléma; Sylvain Blachon; Arnaud Soulet; Bruno Crémilleux; Olivier Gandrillon (Silico Biol., 2008)

Learning Constrained Edit State Machines. - Laurent Boyer 002; Olivier Gandrillon; Amaury Habrard; Mathilde Pellerin; Marc Sebban (ICTAI, 2009)

Extracting Signature Motifs from Promoter Sets of Differentially Expressed Genes. - Ieva Mitasiunaite; Christophe Rigotti; Stéphane Schicklin; Laurène Meyniel; Jean-François Boulicaut; Olivier Gandrillon (Silico Biol., 2009)

Using a Solver Over the String Pattern Domain to Analyze Gene Promoter Sequences. - Christophe Rigotti; Ieva Mitasiunaite; Jérémy Besson; Laurène Meyniel; Jean-François Boulicaut; Olivier Gandrillon (Inductive Databases and Constraint-Based Data Mining, 2010)

On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter. - Antoine Coulon; Olivier Gandrillon; Guillaume Beslon (BMC Syst. Biol., 2010)

Extraction sous contraintes d'ensembles de cliques homogènes. - Pierre-Nicolas Mougel; Marc Plantevit; Christophe Rigotti; Olivier Gandrillon; Jean-François Boulicaut (EGC, 2011)

Finding Collections of k-Clique Percolated Components in Attributed Graphs. - Pierre-Nicolas Mougel; Christophe Rigotti; Olivier Gandrillon (PAKDD (2), 2012)

Multiscale Modeling of the Early CD8 T-Cell Immune Response in Lymph Nodes: An Integrative Study. - Sotiris A. Prokopiou; Loïc Barbarroux; Samuel Bernard; Julien Mafille; Yann Leverrier; Christophe Arpin; Jacqueline Marvel; Olivier Gandrillon; Fabien Crauste (Comput., 2014)

Finding maximal homogeneous clique sets. - Pierre-Nicolas Mougel; Christophe Rigotti; Marc Plantevit; Olivier Gandrillon (Knowl. Inf. Syst., 2014)

Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts. - Peggy Cellier; Thierry Charnois; Marc Plantevit; Christophe Rigotti; Bruno Crémilleux; Olivier Gandrillon; Jirí Kléma; Jean-Luc Manguin (J. Biomed. Semant., 2015)

IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC: a multiscale modeling study. - Xuefeng Gao; Christophe Arpin; Jacqueline Marvel; Sotiris A. Prokopiou; Olivier Gandrillon; Fabien Crauste (BMC Syst. Biol., 2016)

A Cloud-aware Autonomous Workflow Engine and Its Application to Gene Regulatory Networks Inference. - Arnaud Bonnaffoux; Eddy Caron; Hadrien Croubois; Olivier Gandrillon (CLOSER, 2018)

SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. - Nan Papili Gao; S. M. Minhaz Ud-Dean; Olivier Gandrillon; Rudiyanto Gunawan (Bioinform., 2018)

WASABI: a dynamic iterative framework for gene regulatory network inference. - Arnaud Bonnaffoux; Ulysse Herbach; Angélique Richard; Anissa Guillemin; Sandrine Gonin-Giraud; Pierre-Alexis Gros; Olivier Gandrillon (BMC Bioinform., 2019)

Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts. - Ronan Duchesne; Anissa Guillemin; Fabien Crauste; Olivier Gandrillon (Silico Biol., 2019)

Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. - Ronan Duchesne; Anissa Guillemin; Olivier Gandrillon; Fabien Crauste (BMC Bioinform., 2021)

Modeling and characterization of inter-individual variability in CD8 T cell responses in mice. - Chloe Audebert; Daphné Laubreton; Christophe Arpin; Olivier Gandrillon; Jacqueline Marvel; Fabien Crauste (Silico Biol., 2021)

Kernel-Based Testing for Single-Cell Differential Analysis. - Anthony Ozier-Lafontaine; Camille Fourneaux; Ghislain Durif; Céline Vallot; Olivier Gandrillon; Sandrine Giraud; Bertrand Michel; Franck Picard (CoRR, 2023)

scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data. - Maxime Lepetit; Mirela Diana Ilie; Marie Chanal; Gerald Raverot; Philippe Bertolino; Christophe Arpin; Franck Picard; Olivier Gandrillon (Silico Biol., 2023)

One model fits all: Combining inference and simulation of gene regulatory networks. - Elias Ventre; Ulysse Herbach; Thibault Espinasse; Gérard Benoit; Olivier Gandrillon (PLoS Comput. Biol., 2023)

TopoDoE: a design of experiment strategy for selection and refinement in ensembles of executable gene regulatory networks. - Matteo Bouvier; Souad Zreika; Elodie Vallin; Camille Fourneaux; Sandrine Gonin-Giraud; Arnaud Bonnaffoux; Olivier Gandrillon (BMC Bioinform., 2024)

Modeling relaxation experiments with a mechanistic model of gene expression. - Maxime Estavoyer; Marion Dufeu; Grégoire Ranson; Sylvain Lefort; Thibault Voeltzel; Véronique Maguer-Satta; Olivier Gandrillon; Thomas Lepoutre (BMC Bioinform., 2024)