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You are here: Home / Teams / Systems Biology of Decision Making - O. Gandrillon / Publications (not up to date)

Publications (not up to date)

This folder holds the following references to publications, sorted by year and author.

There are 107 references in this bibliography folder.

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.

Dussiau, C, Boussaroque, A, Gaillard, M, Bravetti, C, Zaroili, L, Knosp, C, Friedrich, C, Asquier, P, Willems, L, Quint, L, Bouscary, D, Fontenay, M, Espinasse, T, Plesa, A, Sujobert, P, Gandrillon, O, and Kosmider, O (2022).
Hematopoietic differentiation is characterized by a transient peak of entropy at a single-cell level
BMC Biol, 20(1):60.

Todorov, H, Prieux, M, Laubreton, D, Bouvier, 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 cell generation is a continuous process
iScience, 25(9):104927.

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 Biol, 20(1):155.

Audebert, C, Laubreton, D, Arpin, C, Gandrillon, O, Marvel, J, and Crauste, F (2021).
Modeling and characterization of inter-individual variability in CD8 T cell responses in mice
In Silico Biol, 14(1-2):13–39.

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(1):478.

Jeanpierre, S, Arizkane, K, Thongjuea, S, Grockowiak, E, Geistlich, K, Barral, L, Voeltzel, T, Guillemin, A, Gonin-Giraud, S, Gandrillon, O, Nicolini, FE, Mead, AJ, Maguer-Satta, V, and Lefort, S (2021).
The quiescent fraction of chronic myeloid leukemic stem cells depends on BMPR1B, Stat3 and BMP4-niche signals to persist in patients in remission
Haematologica, 106(1):111–122.

Ventre, E, Espinasse, T, hier, CE, Calvez, V, Lepoutre, T, and Gandrillon, O (2021).
Reduction of a stochastic model of gene expression: Lagrangian dynamics gives access to basins of attraction as cell types and metastabilty
J Math Biol, 83(5):59.

Bonnaffoux, A, Herbach, U, Richard, A, Guillemin, A, Gonin-Giraud, S, Gros, PA, and Gandrillon, O (2019).
WASABI: a dynamic iterative framework for gene regulatory network inference
BMC Bioinformatics, 20(1):220.

Duchesne, R, Guillemin, A, Crauste, F, and Gandrillon, O (2019).
Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts
In Silico Biol, 13(1-2):55–69.

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, 10:230.

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.

Angulo, O, Gandrillon, O, and Crauste, F (2018).
Investigating the role of the experimental protocol in phenylhydrazine-induced anemia on mice recovery
J Theor Biol, 437:286–298.

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(1):92.

Papili Gao, N, Ud-Dean, SMM, Gandrillon, O, and Gunawan, R (2018).
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
Bioinformatics, 34(2):258–266.

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 Syst, 4(3):306-317.e4.

Herbach, U, Bonnaffoux, A, Espinasse, T, and Gandrillon, O (2017).
Inferring gene regulatory networks from single-cell data: a mechanistic approach
BMC Syst Biol, 11(1):105.

Moussy, A, Cosette, J, Parmentier, R, da Silva, C, Corre, G, Richard, A, Gandrillon, O, Stockholm, D, and ldi, 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.

Gao, X, Arpin, C, Marvel, J, Prokopiou, SA, 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 Syst Biol, 10(1):77.

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.

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.

Cellier, P, Charnois, T, Plantevit, M, Rigotti, C, Cremilleux, B, Gandrillon, O, Klema, J, and Manguin, J (2015).
Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts.
J Biomed Semantics, 6:27.

Chatagnon, A, Veber, P, Morin, V, Bedo, J, Triqueneaux, G, Semon, M, Laudet, V, d'Alche-Buc, F, and Benoit, G (2015).
RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements.
Nucleic Acids Res, 43(10):4833-54.

Crauste, F, Terry, E, Mercier, IL, 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.

Eymard, N, Bessonov, N, Gandrillon, O, Koury, MJ, and Volpert, V (2015).
The role of spatial organization of cells in erythropoiesis.
J Math Biol, 70(1-2):71-97.

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