Publications

2024

• Estavoyer, M., Dufeu, M., Ranson, G., Lefort, S., Voeltzel, T., Maguer-Satta, V., Gandrillon, O. and Lepoutre, T. (2024). Modeling relaxation experiments with a mechanistic model of gene expression. BioRxiv 

• Nguyen, T. N. T., Martin, M., Arpin, C., Bernard, S., Gandrillon, O. and Crauste, F. (2024). In silico modelling of CD8 T cell immune response links genetic regulation to population dynamics. bioRxiv

• Ozier-Lafontaine, A., Fourneaux, C., Durif, G., Vallot, C., Gandrillon, O., Giraud, S., Michel, B. and Picard, F. (2024). Kernel-Based Testing for Single-Cell Differential Analysis. Genome Biology, in the press.

• Ryad Belhakem, R., Picard, F., Rivoirard, V. and Roche, A. (2024). Minimax estimation of Functional Principal Components from noisy discretized functional data.  Scandinavian Journal of Statistics, in the press.

• Koshkin, A., Herbach, U., Martínez, M. R., Gandrillon, O. and Crauste, F. (2024). Stochastic modeling of a gene regulatory network driving B cell development in germinal centers. PLoS ONE, 19(3): e0301022.

• Fourneaux*, C., Racine*, L., Koering, C., Dussurgey, S., Vallin, E., Moussy, A., Parmentier, R., Brunard, F., Stockholm, D., Modolo, L., Picard, F., Gandrillon, O., Paldi, A., and Gonin-Giraud, S. (2024). Differentiation is accompanied by a progressive loss in transcriptional memory. BMC Biology 22, 58 

• Wang, S., Prieux, M., de Bernard, S., Dubois, M., Laubreton, D., Djebali, S., Zala, M., Arpin, C., Genestie, L., Leverrier, Y., Gandrillon, O., Crauste, F., Jiang, W. and Marvel, J. (2024). Exogenous IL-2 delays the generation of memory precursor cells and is essential for the generation of memory cells with increased effector functions.  Iscience 24, 109411

2023

• Arpin, C., Picard, F. and Gandrillon, O. (2023). In silico single-cell metabolism analysis unravels a new transition stage of CD8 T cells 4 days post-infection. bioRxiv

• Bouvier, M., Zreika, S., Vallin, E., Fourneaux, C., Gonin-Giraud, S., Bonnaffoux, A. and Gandrillon, O. (2023). TopoDoE: A Design of Experiment strategy for selection and refinement in ensembles of executable Gene Regulatory Networks. bioRxiv

• Baradat, A. and Ventre, E. (2022). Convergence of the Sinkhorn algorithm when the Schrödinger problem has no solution. Annales de la Faculté des Sciences de Toulouse (In the press).

• Aslan*, K. M., Fourneaux*, C*, Yilmaz, A., Stavros, S., Parmentier, R., Paldi, A., Gonin-Giraud, S., deMello, J A. , and Gandrillon, O. (2023). An Image-Guided Microfluidic System for Single-Cell Lineage Tracking. PLoS ONE 18(8): e0288655

• Poulet-Benedetti*, J., Tonnerre-Doncarli*, C., Valton, A.-L., Laurent, M., Gérard, M., Barinova, N., Parisi, N., Florian Massip, F., Picard, F. and Prioleau, M.-N. (2023). Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates. Nat Commun; 14: 4843.

• Gao, N.P., Gandrillon, O., Paldi, A., Herbach, U. and Gunawan, R. (2023). Single-cell transcriptional uncertainty landscape of cell differentiation. F1000Research 12:426.

• Ventre*, E., Herbach*, U., Espinasse, T., Benoit, G. and Gandrillon, O. (2023). One model fits all: combining inference and simulation of gene regulatory networks. PLoS Comput Biol 19(3): e1010962

• Lepetit, M., Ilie, M.D., Chanal, M., Raverot, G., Bertolino, P., Arpin, C., Picard, F., and Gandrillon, O. (2023). scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data. In Silico Biology  15, 11-21.

2022

• van Assel, H., Espinasse, T., Chiquet, J. and Picard, F. (2022). A probabilistic Graph Coupling View of Dimension Reduction. in Advances in Neural Information Processing System

• Bonnet, A., Lacour, C., Picard, F. and Rivoirard, V. (2022). Uniform Deconvolution of Poisson Point Processes. Journal of Machine Learning Research. 23, 1-36.

• Todorov*, H., Prieux*, M., Laubreton, D., Bouvie, M., Wang, S., de Bernard, S., Arpin, C., Cannoodt, R., Saelens, W., Bonnaffoux, A., Gandrillon, O., Crauste, F., Saeys, Y., and Marvel, J. (2022). CD8 memory precursor cells generation is a continuous process.  iScience. 25, 104927.

• Dussiau, C., Boussaroque, A., Gaillard, M., Bravetti, C., Zaroili, L., Knosp, C., Friedrich, C., Asquier, P., Willems, L., Quint, L., Fontenay, M., Espinasse, T., Plesa, A., Sujobert, P., Gandrillon, O. and Kosmider, O. (2022). Hematopoietic differentiation is characterized by a transient peak of cell-to-cell gene expression variability in normal and pathological conditions. BMC Biology 20, Article number: 60 

• Zreika*, S., Fourneaux*, C., Vallin, E. , Modolo, L., Seraphin, R., Moussy, A., Ventre, E., Bouvier, M., Ozier-Lafontaine, A., Bonnaffoux, A., Picard, F., Gandrillon, O. and Gonin-Giraud, S. (2022). Evidence for close molecular proximity between reverting and undifferentiated cells. BMC Biology 20, Article number: 155

2021

• Gandrillon, O., Gaillard, M., Espinasse, T., Garnier, N.B., Charles Dussiau, C., Kosmider, O. and Sujobert, P. (2021). Entropy as a measure of variability and stemness in single-cell transcriptomics. Current opinion in Systems Biology. 27, 100348

• Ventre, E. (2021) Reverse engineering of a mechanistic model of gene expression using metastability and temporal dynamics. In Silico Biology, 14, pp. 89-113.

• Ventre, E., Espinasse, T., Brehier, C.-E., Calvez, V., Lepoutre,T. and Gandrillon, O. (2021). Reduction of a stochastic model of gene expression: Lagrangian dynamics gives acces to basins of attraction as cell types and metastability.  Journal of Mathematical Biology, 83, Article number: 59.

• Duchesne, R., Guillemin, A., Gandrillon, O. and Crauste, F. (2021). Practical Identifiability in the Frame of Nonlinear Mixed Effects Models: the Example of the in vitro Erythropoiesis. BMC Bioinformatics 22, Article number: 478.

2020

• Audebert, C., Laubreton, D., Arpin, C., Gandrillon, O., Marvel, J. and Crauste, F. (2020). Investigation of Inter-Individual Variability in CD8 T Cell Responses with Nonlinear Mixed Effects Models. In Silico Biology. 14, 13-39.

• Jeanpierre, S., Arizkane, K., Thongjuea, S., Grockowiak, E., Geistlich, K., Barral, L., Voeltzel, T., Guillemin, A., Gonin-Giraud, S., Gandrillon, O., Nicolini, F.-E., Mead, A. J., Maguer-Satta, V. and Lefort, S. (2020). The quiescent fraction of chronic myeloid leukemic stem cells depends on BMPR1B, Stat3 and BMP4-niche signals to persist in patients in remission. Haematologica. 2020; 105.

2019

• Guillemin, A.,Duchesne, R., Crauste, F., Gonin-Giraud, S. and Gandrillon, O. (2019). Drugs modulating stochastic gene expression affect the erythroid differentiation process.  Plos ONE 14(11): e0225166.

• Richard, A., Vallin, E., Romestaing, C., Roussel, D., Gandrillon, O., and Gonin-Giraud, S. (2019). Erythroid differentiation displays a peak of energy consumption concomitant with glycolytic metabolism rearrangements.  Plos ONE 14(9): e0221472.

• Girel, S. Arpin, C., Marvel, J., Gandrillon, O. and Crauste, F. (2019). Model-based assessment of the role of uneven partitioning of molecular content on heterogeneity and regulation of differentiation in CD8 T-cell immune responses. Front. Immunol. 10, article 230.

• Bonnaffoux, A, Herbach, U, Richard, A, Guillemin, A, Gonin-Giraud, S, Gros, P.A. and Gandrillon, O (2019). WASABI: a dynamic iterative framework for gene regulatory network inference. BMC Bioinformatics 20:220. 

• Duchesne, R., Guillemin, A., Gandrillon, O. and Crauste, F. (2019). Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts. In Silico Biology 13, pp. 55-69. 

2018

• Leduc, M., Gautier, E.F., Guillemin, A., Broussard, C., Salnot, V., Lacombe, C., Gandrillon, O., Guillonneau, F. and Mayeux, P. (2018). Deep proteomic analysis of chicken erythropoiesis. BioRxiv.

• Guillemin, A., Richard, A., Gonin-Giraud, S. and Gandrillon, O. (2018). Automated cell cycle and cell size measurements for single-cell gene expression studies. BMC Res Notes 11:92  

• Angulo, O. Gandrillon, O. and Crauste, F. (2018) Investigating the role of the experimental protocol in phenylhydrazine-induced anemia on mice recovery, Journal of Theoretical Biology, Volume 437, Pages 286-298.

2017

• Herbach, U., Bonnaffoux, A., Espinasse, T., and Gandrillon, O. (2017). Inferring gene regulatory networks from single-cell data: a mechanistic approach. BMC Systems Biology 11:105 .

• Gao, N.P., Ud-Dean, S.M.M., Gandrillon, O. and Gunawan, R. (2017). SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. Bioinformatics, btx575.

• Moussy, A., Cosette, J., Parmentier, R., da Silva, C., Corre, G., Richard, A., Gandrillon, O., Stockholm, D., Páldi, A. (2017). Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment. PLoS Biol 15(7): e2001867.

• Crauste, F., Mafille, J., Boucinha, L., Djebali, S., Gandrillon, O., Marvel, J. and Arpin, C. (2017). Identification of nascent Memory CD8 T cells and modeling of their ontogeny. Cell Systems 4, pp.306-317

2016

• Richard, A, Boullu, L, Herbach, U, Bonnafoux, A, Morin, V, Vallin, E, Guillemin, A, Papili Gao, N, Gunawan, R, Cosette, J, Arnaud, O, Kupiec, J, Espinasse, T, Gonin-Giraud, S, and Gandrillon, O (2016). Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process. PLoS Biol, 14(12):e1002585.

• Gao, X., Arpin, C., Marvel, J., Prokopiou, S.A., Gandrillon, O. and Crauste, F. (2016). IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC : a multiscale modeling study. BMC Systems Biology (2016) 10:77 DOI 10.1186/s12918-016-0323-y 

2015

• Arnaud, O., Meyer, S., Vallin, E., Beslon, G. and Gandrillon, O. (2015). Temperature-induced variation in gene expression burst size in metazoan cells. BMC Mol. Biol. 16:20

• Crauste, F., Terry, E., Mercier, I.L., Mafille, J., Djebali, S., Andrieu, T., Mercier, B., Kaneko, G., Arpin, C., Marvel, J. and Gandrillon, O. (2015). Predicting pathogen-specific CD8 T cell immune responses from a modeling approach. J Theor Biol. 374, 66–82

• Cellier, P., Charnois, T., Plantevit, M., Rigotti, C., Crémilleux, B., Gandrillon, O., Kléma, J. and Manguin, J.-L. (2015). Sequential Pattern Mining for Discovering Gene Interactions and their Contextual Information from Biomedical Texts. Journal of Biomedical Semantics;  6:27

• Eymard, N., Bessonov, N., Gandrillon, O., Koury, M.J. and Volper, V. (2015). The role of spatial organization of cells in erythropoiesis. J. Math. Biol. 70, 71-97

2014

• Corre, G., Stockholm, D., Arnaud, O., Kaneko, G., Viñuelas, J., Yamagata, Y., Neildez-Nguyen, T. M. A., Kupiec, J.-J., Beslon, G., Gandrillon, O., and Paldi, A. (2014). Stochastic fluctuations and distributed control of gene expression impact cellular memory. Plos ONE (0115574)

• Prokopiou, S.A., Barbarroux, L., Bernard, S., Mafille, J., Leverrier, Y., Arpin, C., Marvel, J., Gandrillon, O. and Crauste, F. (2014). Multiscale modeling of the early CD8 T cell immune response in lymph nodes : an integrative study. Computation 2, 159-181.

2013

• Joly-Tonetti, N., Viñuelas, J., Gandrillon, O. and Lamartine, J. (2013). Differential miRNA expression profiles in proliferating or differentiated keratinocytes in response to gamma irradiation. BMC Genomics 14:184.

• Viñuelas*, J., Kaneko*, G., Coulon, A., Vallin, E., Morin, V., Mejia-Pous, C., Kupiec, J.-J., Beslon, G. and Gandrillon, O. (2013). Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts. BMC Biology 11:15. * equal contributors

• Nguyen-Lefebvre, A.T., Leprun, G., Morin, V., Viñuelas, J., Couté, Y., Madjar, J.-J., Gandrillon, O. and Gonin-Giraud, S. (2013). V-erbA generates ribosomes devoid of RPL11 and regulates translational activity in avian erythroid progenitors. Oncogene: 33, pages1581

• Mougel, P-N., Rigotti, C., Plantevit, M. and Gandrillon, O. (2013). Finding Maximal Homogeneous Clique Sets. Knowledge and Information Systems (published online : 27 march 2013).

2012

• Gandrillon, O., Kolesnik-Antoine, D., Kupiec, J.J. and Beslon, G. (2012). Chance at the heart of the cell. Progress in Biophysics & Molecular Biology 110, pp 1-4.

• Viñuelas, J., Kaneko, G., Coulon, A., Beslon , G. and Gandrillon, O. (2012). Toward experimental manipulation of stochasticity in gene expression. Progress in Biophysics & Molecular Biology, 110, pp 44-53.

• Terry, E., Marvel, J., Arpin, C., Gandrillon, O. and Crauste F. (2012).Mathematical model of the primary CD8 T cell immune response : stability analysis of a nonlinear age-structured system. J. Math. Biol. 65, Number 2, Pages 263-291.

• Fischer, S., Kurbatova, P., Bessonov, N., Gandrillon, O., V. Volpert, V., and Crauste, F. (2012). Modelling erythroblastic islands : using a hybrid model to assess the function of central macrophage. Journal of Theoretical Biology, 298, 92–106.

2011

• Pellerin, M. and Gandrillon, O. (2011). Querying formal concepts containing transcription factors : a case study using multiple databases. Journal of Computational Biology and Bioinformatics Research 3(6), pp. 83-90.

• Mejia-Pous, C., Damiola, F. and Gandrillon, O. (2011). The cholesterol synthesis-related enzyme oxidosqualene cyclase is required to maintain self-renewal in primary erythroid progenitors. Cell Proliferation, 44, 441-452.

2010

• Royer, C., Briolay, J., Garel, A., Brouilly, P., Sasanuma, S.-I., Sasanuma, M., Shimomura, M., Keime, C., Gandrillon, O., Huang, Y., Chavancy, G., Mita, K. and Couble P. (2010). Novel genes differentially expressed between posterior and median Silk gland identified by SAGE-aided transcriptome analysis. Insect Biochemistry and Molecular Biology, 41:118-24.

• Nguyen-Lefebvre, A.-T., Gonin-Giraud, S., Scherl, A., Arboit, P., Granger, L., Sanchez, J.-C., Diaz J.-J., Gandrillon, O. and Jean-Jacques Madjar, J.-J. (2010). Identification of human, rat and chicken ribosomal proteins by a combination of two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. Journal of Proteomics 74:167-85.

• Crauste, F., Demin, I., Gandrillon, O. and Volpert, V. (2010). Mathematical study of feedback control roles and relevance in stress erythropoiesis. Journal of Theoretical Biology 263 : 303-316

• Coulon A., Gandrillon, O. and Beslon, G. (2010). On the spontaneous stochastic dynamics of a single gene : complexity of the molecular interplay at the promoter BMC Systems Biology,4:2.

• Demin, I., Crauste, F., Gandrillon, O. and Volpert, V. (2010). A multi-scale model of erythropoiesis. J. Biol. Dynamics, 4:59-70

2009

• Silberstein, M., Kupiec, J.-J. and Gandrillon, O. (2009). De la nécessité du hasard en biologie. Chapter in Le Hasard au coeur de la cellule, Éditions Matériologiques , 5-18.

• Coulon, A., Beslon, G., Chatelain, F., Fuchs, A., Gandrillon, O., Gineste, M., Kupiec, J.-J., Mejia-Perez, C. and Paldi A. (2009). Mécanismes moléculaires et fonction biologique de la variabilité de l’expression génique à l’échelle de la cellule unique : une approche systémique. Chapter in Le Hasard au coeur de la cellule, Éditions Matériologiques , 59-78.

• Mejia-Pous, C., Viñuelas, J., Faure, C., Koszela, J., Kawakami, K., Takahashi,, Y. and Gandrillon, O. (2009). A combination of transposable elements and magnetic cell sorting provides a very efficient transgenesis system for chicken primary erythroid progenitors BMC Biotechnology 2009, 9:81

• Boyer L., Gandrillon O., Habrard A., Pellerin M., Sebban M. "Learning Constraii ned Edit State Machines" Proceedings 21st IEEE Int. Conf. on Tools with Artificial Intelligence (ICTAI’09),, Newark, New Jersey, USA, November 2009.

• Crémilleux B., Soulet A., Klema J., Hébert C., Gandrillon O. Discovering Knowledge from Local Patterns in SAGE data. In Data Mining and Medical Knowledge Management : Cases and Applications, IGI Global publications, pp. 251-267, 2009.

2008

• Mitasiunaite, I., Rigotti, C., Schicklin, S., Meyniel, L., Boulicaut, J .-F. and Gandrillon, . O. (2008). Extracting signature motifs from promoter sets of differentially expressed genes. In Silico Biology, 8:0043.

• Leyritz, L., Schicklin, S., Blachon, S., Keime, C., Robardet, C., Boulicaut, J.-F., Besson, J., Pensa, R. G. and Gandrillon, O. (2008). SQUAT : a web tool to mine human, murine and avian SAGE data. BMC Bioinformatics 9:378.

• Hanriot*, L., Keime*, C., Gay, N., Faure, C., Dossat, C., Wincker, P., Scoté-Blachon, C., Peyron, C. and Gandrillon, O. (2008). A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome. BMC Genomics 9:418. * equal contributors

• Coulon A, Beslon G, Gandrillon O. (2008). Large multiprotein structures modeling and simulation : the need for mesoscopic models. Methods Mol Biol. 484:537-58.

• Gonin-Giraud S, Bresson-Mazet C, Gandrillon O. (2008). Involvement of the TGF-beta and mTOR/p70S6Kinase pathways in the transformation process induced by v-ErbA. Leuk Res. 32, 1878-1888

• Klema, J., Blachon, S., Soulet, A. , Cremilleux, B and Gandrillon, O. (2008). Constraint-Based Knowledge Discovery from SAGE Data In Silico Biology 8, 0014.

• Bresson, C., Gandrillon, O. and Gonin-Giraud, S. (2008). sca2 : a new gene involved in the self-renewal of erythroid progenitors. Cell Proliferation 41, 726-738.

• Crauste, F., Pujo-Menjouet, L., Génieys, S., Molina, C. and Gandrillon, O. (2008). Adding Self-Renewal in Committed ErythroidProgenitors Improves the Biological Relevanceof a Mathematical Model of Erythropoiesis. Journal of Theoretical Biology 250, 322-338.

2007

• Bresson, C., Keime, C., Faure, C., Letrillard, Y., Barbado, M., Sanfilippo, S., Benhra, N., Gandrillon, O. and Gonin-Giraud, S. (2007). Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action. BMC Genomics 8, 390.
• Blachon, S., Pensa, R.G., Besson, J., Robardet, C, Boulicaut, J.-F. and Gandrillon, O. (2007) Clustering formal concepts to discover biologically relevant knowledge from gene expression data. In Silico Biol. 7, 0033
• Keime, C., Sémon, M., Mouchiroud, D., Duret, L. and Gandrillon, O. (2007). Unexpected observations after mapping LongSAGE tags to the human genome. BMC Bioinformatics 2007, 8:154
• Coulon, A., Soula, H., Mazet, O., Gandrillon, O. and Beslon, G. (2007). Modélisation cellulaire pour l’émergence de structures multiprotéiques auto-organisées. Technique et Science Informatiques (TSI) 26, 123-148.

2006

• Rosinski-Chupin, I., Briolay, J., Brouilly, P., Perrot, S., Gomez, S.M., Chertemps, T., Roth, C.W., Keime, C., Gandrillon, O., Couble, P. and Brey, P.T. (2006). SAGE analysis of mosquito salivary gland transcriptomes during Plasmodium invasion. Cellular Microbiology 9, 708-724.
• Dazy, S., Gandrillon, O., Hyrien O. and Prioleau, M.-N. (2006). Activation of stage-specific DNA replication origins during metazoan cell differentiation. EMBO Rep 7, 806-811.

2005

• Soula, H. Robardet, C., Perrin, F., Gripon, S., Beslon, G. and Gandrillon O. (2005). Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a Multi-Agent-based Software. BMC Bioinformatics 6, 228.
• Huang, J., Miao, X., Jin, W., Couble, P., Mita, K., Zhang, Y., Liu, W., Zhuang, L, Shen, Y., Keime, C., Gandrillon, O., Brouilly, P., Briolay, J., Zhao, G. and Huang, Y. (2005). Serial analysis of gene expression (SAGE) in the silkworm, Bombyx mori. Genomics 86, 233-241.

2004

•  
• Keime, C., Damiola, F., Mouchiroud, D., Duret, L. and Gandrillon, O. (2004). Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. BMC Bioinformatics 5, 143
• Damiola, F., Keime, C., Gonin-Giraud, S., Dazy, S., and Gandrillon, O. (2004). Global transcription analysis of immature avian erythrocytic progenitors : from self-renewal to differentiation. Oncogene 23, 7628-7643.
• Blachon, S., Robardet, C., Boulicaut J.F. et Gandrillon, O. (2004). Extraction de connaissances dans les données d’expression SAGE humaines. Informatique pour l’Analyse du Transcriptome. Hermes Science, traité IC2 2004.
• Gandrillon, O., Houlgatte, R. (2004). Le transcriptome : Le nouveau monde ? Informatique pour l’Analyse du Transcriptome. Hermes Science, traité IC2 2004
• Benoit G., Malewicz M. and Perlmann T. Digging deep into the pockets of orphan nuclear receptors : insights from structural studies. Trends Cell Biol : 14, 369-76. 2004

2003

• Gandrillon, O. (2003). Les gènes du cancer. Sciences et Avenir Hors Série, 136 70-74.
• Dazy, S., Damiola, F., Parisey, N., Beug, H. and Gandrillon, O. (2003) The MEK-1/ ERKs signalling pathway is differentially involved in the self-renewal of early and late avian erythroid progenitor cells. Oncogene 22, 9205-9216.
• Rioult, F., Robardet, C., Blachon, S., Crémilleux, B., Gandrillon, O., Boulicaut J.F. (2003). Mining concepts from large SAGE gene expression matrices. Proceedings of the 2nd International Workshop on Knowledge Discovery in Inductive Databases KDID’03 co-located with ECML-PKDD 2003, Catvat-Dubrovnik (Croatia), September 22, 2003.

2002

• Becquet, C., Blachon, S., Jeudy, B., Boulicaut, J.F. and Gandrillon, O. (2002). Strong association rule mining for large gene expression data analysis : a case study on human SAGE data . Genome Biology 3, research0067.1-0067.16
• Gandrillon, O. (2002). The v-erbA oncogene. Assessing its differentiation-blocking ability using normal chicken erythrocytic progenitor cells. Methods Mol Biol 202, 91-107.

2001

• Braliou, G.G., Ciana, P., Klaassen, W., Gandrillon, O. and Stunnenberg, H.G. (2001). The v-ErbA oncoprotein quenches the activity of an erythroid-specific enhancer. Oncogene 20, 775-787.
• Bauer, A., Gandrillon, O., Samarut, J., and Beug, H. (2001). Nuclear receptors in hematopoietic development : cooperation with growth factor receptors in regulation of proliferation and differentiation. In Hematopoiesis : a developmental approach, L. Zon, ed. (New York : Oxford University Press), pp 368-390.

1999

• Gandrillon, O., Mey, A.. and Samarut, J. (1999). Plasticité insoupçonnée des progéniteurs érythrocytaires. Médecine/Science 15, 1295-1297.
• Gandrillon, O., Schmidt, U., Beug, H. and Samarut, J. (1999). TGFbeta cooperates with TGFalpha to induce the self-renewal of normal erythrocytic progenitors : Evidence for an autocrine mechanism. EMBO J. 18, 2764-2781.

Communications 

Gandrillon, O. (2016). Single-cell analyses reveal a link between cell-to-cell variability and irreversible commitment during differentiation. ICSB 2016

Gandrillon, O. (2012). Quantification of chromatin dynamics contribution to stochasticity in eukaryotic gene expression reveals a highly bursty regime with long quiet states. Journées pleinières du GDR 3070

Coulon, A., Chow, C. C., Gandrillon, O. and Beslon, G. (2011). Multi-timescale modeling of promoter chromatin dynamics and cofactor recruitment. Chromatin Dynamics, Keystone Symposia.
Coulon, A., Chow, C. C., Gandrillon, O. and Beslon, G. (2011). Modeling the dynamics of promoter chromatin and cofactor recruitment at various timescales. Mechanisms of eukaryotic transcription Cold Spring Harbor Laboratory.
Gandrillon, O. (2011). Chromatin dynamics is a key player in regulating gene expression stochasticity in higher eukaryotic cells. Semovi, Lyon
Gandrillon, O. (2011). La dynamique chromatinienne est un paramètre majeur de l’expression probabiliste des gènes. XXXIème Séminaire de la SFBT, Autrans.
Viñuelas, J., Kaneko, G., Morin, V., Vallin, E., Coulon, A., Mejia-Pous, C., Rouberol, B., Beslon, G. and Gandrillon, O.(2010). Chromatin is a major player in regulating gene expression stochasticity in higher eukaryotic cells. Gordon Research Conference, Stochastic Physics in Biology, Ventura.
Gandrillon, O. (2010). Relationship between chromosomal features and gene expression stochasticity in higher eukaryotic cells Noise in Life, Benasque
Gandrillon, O. (2010). Multi-scale modelling of the primary CD8 T-cell response System Biology and Immune Response Veyrier-du-lac
Gandrillon, O. (2010). Relationship between chromosomal features and gene expression stochasticity in higher eukaryotic cells.WCSB 2010, Luxembourg
Gandrillon, O. (2010). Relationship between chromosomal features and gene expression stochasticity in higher eukaryotic cells. Atelier interdisciplinaire « Du désordre moléculaire aux programmes cellulaires : microscopie et modélisation », Lile
Lefebvre, AT., Madjar, JJ., Gandrillon,O and Gonin-Giraud, S. (2009). The v-erbA oncogene induces variations in ribosomal protein gene expression. Protein Translation and Cancer, Coronado.
Viñuelas, J., Kaneko, G., Coulon, A, Beslon, G. and Gandrillon O (2009). Relationship between chromosomal features and gene expression stochasticity in higher eukaryotic cells. Integrative Post Genomics (IPG ‘09), Villeurbanne, France.
Gandrillon, O. (2009). A system’s biology approach to understand stochasticity in gene expression Edition 2009 de la Journée de l’IXXI, Grenoble
Mejia-Pous, C. and Gandrillon, O. (2009). Cholesterol synthesis, modulated by the Oxidosqualene Cyclase gene expression, maintains primary immature erythroid progenitors in a self-renewal state 16eme congrès du CHO, Giens
Gandrillon, O. (2009). A system’s biology approach to understand stochasticity in gene expression Modelling Complex Biological Systems in the Context of Genomics Nice
Gandrillon, O. (2008). A system’s biology approach to understand stochasticity in gene expression Workshop on heterogeneity and transcriptional noise in cell populations Cambridge.
Lefebvre, A.T., Gonin-Giraud, S., Madjar, J.J. and Gandrillon, O. (2008). The v-erbA oncogene induces variations in ribosomal protein gene expression. IPG’08, LYON, 20-21 Novembre 2008
Crauste, F., Pujo-Menjouet, L., Génieys, S. and Gandrillon, O. (2007). Adding Self-Renewal in Committed ErythroidProgenitors Improves the Biological Relevance of a Mathematical Model of Erythropoiesis. 14ème congrès du CHO Giens France.
Mejia-Perez, C., Damiola, F., Faure, C. and Gandrillon, O. (2007). Role of Cholesterol Synthesis in Avian Erythrocytic Progenitors Self-Renewal. 14ème congrès du CHO Giens France.
Leyritz, J., Keime, C., Blachon, S., Robardet, C., Boulicaut, J.F., Besson, J., Pensa, R.G. and Gandrillon, O. (2007). SQUAT : a web tool to browse chicken sage data. International Chick Meeting, Barcelona
Bresson, C., Keime, C., Faure, C., Letrillard, Y., Mitasiunaite, I., Rigotti, C., Boulicaut, J.F., Bendjeladi, A.,Benhra, , N., Gandrillon, O. and Gonin-Giraud, S. (2007). New mechanisms of v-ErbA oncogene action revealed by SAGE analysis. International Chick Meeting, Barcelona
Gandrillon, O. (2006).Quelques problèmes ouverts en Biologie (moléculaire) contemporaine. Laboratoire de Physique Nucléaire et de Hautes Energies Paris, France
Gandrillon, O. (2006). De l’intérèt des SMAs pour modéliser des structures biologiques et leur évolution dans le temps et l’espace. 11èmes journées de Gerland Lyon, France
Gandrillon, O. (2006) Le poulet : d’un modèle en cancérologie vers un modèle en biologie des systèmes. 32ème journées d’études scientifiques et techniques AFSTAL 2006. Bordeaux, France.
Bresson, C., Keime, C., Faure, C., Letrillard, Y., Mitasiunaite, I., Rigotti, C., Boulicaut, J.F., Bendjeladi, A.,Benhra, , N., Gandrillon, O. and Gonin-Giraud, S. (2006). New mechanisms of v-ErbA oncogene action revealed by SAGE analysis. IPG’06, Lyon, France.
Bresson, C., Keime, C., Faure, C., Bendjeladi, A., Benhra, N., Gandrillon, O. and Gonin-Giraud, S. (2006). Analyse du transcriptome de progéniteurs érythrocytaires exprimant l’oncogène v-erbA. 13ème congrès du CHO Giens France.
Dazy, S., Gandrillon, O., Hyrien, O. and Prioleau, M.-N. (2005). Activation of tissue specific origins at the chicken b-globin locus is coupled to gene activation and chromatin decondensation Workshop on chromosome duplication and segregation, 2-5 May, Trieste, Italy.
Bresson, C., Keime, C., Faure, C., Bendjeladi, A.,Benhra, , N., Gandrillon, O. and Gonin-Giraud, S. (2006).A better comprehension of the mechanisms underlying transformation by the v-erbA oncogene. Nuclear Receptors : Bench to Bedside Cold Spring Harbor, USA.
Klema, J., Soulet, A., Crémilleux, B., Blachon, S., Gandrillon, O. (2006). Mining Plausible Patterns from Genomic Data. In 19th IEEE International Symposium on Computer-Based Medical Systems , pages 90-101, Salt Lake City, Utah.
Dazy, S., Gandrillon, O., Hyrien, O. and Prioleau, M.-N. (2005). Plasticité de la réplication au cours de l’érythropoïèse. 6ème Colloque des 3R (Réplication, Réparation, Recombinaison), 19-22 Juin, Presqu’ile de Giens
Robardet, C., Soula, H., Frugier, K., Belin, S., Diaz, J.-J., Gandrillon, O., and Beslon, G. (2005). Multi-agent modeling of dynamic multi-protein cellular structures. JOBIM 2005, Lyon, France
Keime C., Duret L., Mouchiroud D. and Gandrillon O. (2005). Are transcriptomes evolutionary constrained ? : a comparative transcriptomic analysis using SAGE data. JOBIM 2005, Lyon, France
Blachon, S., Pensa, R., Besson, J., Robardet, C., Boulicaut J.-F. and Gandrillon, O. (2005). A complete scenario of extraction of formal concepts in SAGE data aimed at discovering new biological knowledge. JOBIM 2005, Lyon, France
Keime, C., Faure, C., Damiola, F., Dazy, S., Gonin-Giraud, S., Bresson, C. and Gandrillon, O. (2005). A study of self-renewal by transcriptome analysis of chicken erythrocytic progenitors Workshop on CHICKEN GENOMICS & DEVELOPMENT, Cold Spring Harbor Laboratory, USA
Dazy, S., Gandrillon, O., Hyrien, O. and Prioleau, M.-N. (2005). Activation of tissue specific origins at the chicken b-globin locus is coupled to gene activation and chromatin decondensation Workshop on chromosome duplication and segregation, 2-5 May, Trieste, Italy
Gonin-Giraud, S., Keime, C., Bresson, C., Faure, C. and Gandrillon, O. (2004). SAGE transcriptomic analysis of avian erythrocytic progenitors expressing the v-erbA oncogene. IPG’04, Lyon, France
Soula, H., Robardet, C., Frugier, K., Perrin, F., Gripon, S., Beslon, G. and Gandrillon, O. (2004). Evidence that multi-protein dynamic structures are formed and maintained by principles of self-organization through the use of 3DSpi, a Multi-Agent-based Software. IPG’04, Lyon, France
Dazy, S., Keime, C., Blachon, S., Damiola, F., Faure, C. and Gandrillon, O. (2004). A SAGE approach for the identification of MEK1/ERK target genes in chicken primary self-renewing erythroid progenitors. IPG’04, Lyon, France
Damiola, F. (2004). A SAGE approach to identify genes involved in self-renewal. SAGE sattelite meeting to IPG’04, Lyon, France
Keime, C., Damiola, F., Mouchiroud, D., Duret, L. et Gandrillon, O. (2004). Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. JOBIM 2004, Montréal, Canada.
Gonin-Giraud, S., Bresson, C. et Gandrillon, O. (2003). Interférence de l’oncogène v-erbA avec les voies de signalisation initiées par le TGFbeta dans des cellules souches érythrocytaires Première journée d’onco-hématologie et de thérapie cellulaire, Lyon, France, 3 Novembre 2003.
Dazy, S., Damiola, F., Keime, C. Faure, C. et Gandrillon, O. (2003). Utilisation d’une approche transcriptomique pour l’identification des cibles transcriptionnelles d’une voie de signalisation essentielle à un processus d’autorenouvellement Première journée d’onco-hématologie et de thérapie cellulaire, Lyon, France, 3 Novembre 2003.
Briolay, J., Brouilly, P., Keime, M., Gandrillon, O., Sanamura, S.I., Kasuey, M., Couble, P. (2003). SAGE-aided transcriptome analysis of the silk gland cells of Bombyx mori. Sixth International Workshop on the Molecular Biology and Genetics of Lepidoptera, Kolympari, Grèce, 24-30 Août 2003.
Damiola, F., Faure, C., Dazy, S., Keime, C., Gonin-Giraud, S., Robardet, C. Blachon, S., Derrington, E. and O. Gandrillon (2003). A global approach to identify the molecular basis of stem cell self-renewal. Colloque "Génomique des animaux d’élevage" Seignosse-le-Penon, France.
Damiola, F., Dazy S., Keime, C., Gonin-Giraud S., and O. Gandrillon (2003). A global approach to identify the molecular basis of avian erythrocytic stem cell self-renewal. SAGE 2003 Amsterdam, The Netherlands
Olivier Gandrillon, Jean-François Boulicaut, Céline Robardet, Sylvain Blachon, Jérémy Besson et Sophie Rome (2003). Recherche de groupes de gènes intéressants dans des données d’expression : apport des ensembles fréquents. EGC’ 2003 Lyon, France
Becquet, C., Jeudy, B., J.F. Boulicaut, J.F., S. Blachon, S., and Gandrillon, O. (2002). Strong association rule mining for large gene expression data analysis : a case study on human SAGE data. JPGD ’02 Villeurbanne, France
Damiola, F., Dazy, S. and Gandrillon, O. (2002) A global approach to identify the functions involved in erythocytic stem cells self-renewal. JPGD ’02 UCBL Villeurbanne, France
Becquet, C .,Charavay, C., Herr, A., Martin, T., Morle, F., Deandrea, A., Beslon, G. and Gandrillon, O. (2002). Modeling protein-protein interactions by using Multi-Agents Systems. JPGD ’02 UCBL Villeurbanne, France
Beslon, G., Charles, H., Fayard, J.M., Gandrillon, O. Mazet, O. and Soula, H. (2002). Functional Space Approach for Evolutionary Algorithms. JPGD ’02 UCBL Villeurbanne, France
Damiola F., Dazy S., Gonin-Giraud S., and Gandrillon O. (2002). Une approche globale pour l’identification des mécanismes moléculaires impliqués dans l’auto-renouvellement des cellules souches érythrocytaires. 9ème Congrès. du CHO Giens France
Beslon, G., Charles, H., Fayard, J.M., Gandrillon, O. and Mazet, O. (2002). Modeling evolution through a genetic regulation network. JPGD ’02 UCBL Villeurbanne, France
Dazy, S., Damiola, F., Briolay, J and Gandrillon, O. (2001). Contrôle moléculaire de l’autorenouvellement et de la différenciation de cellules souches érythrocytaires aviaires : une analyse globale par SAGE. JPGD ’01 UCBL Villeurbanne, France
Dazy, S. and Gandrillon, O. (2000). Changements d’identités : le transductosome dans tous ses états. 7ème congrés du CHO. Giens, France.
Gandrillon, O. and Dazy, S. (2000). Self-renewal versus Differentiation : Decision-making in an erythrocytic stem cell. 15e Colloque Franco-Japonais de Coopération en Recherche sur le Cancer. Strasbourg, France
Gandrillon, O. (2000). Autorenouvellement/Différenciation/Apoptose : la cellule souche dans tous ses états. 7ème congrés du CHO. Giens, France.
Dazy, S. and Gandrillon, O. (2000). Transduction d’un signal d’autorenouvellement et de différenciation dans des progéniteurs érythrocytaires normaux. 6èmes journées scientifiques de Gerland. Lyon, France.