Model Repository¶
Note: if you wish to add your model, please add it directly on GitHub or simply contact us.
| Model name | Taxon - all terms | Process - all terms | Year | Author(s) |
|---|---|---|---|---|
| Lysis vs lysogeny decision in the phage lambda | Phage Lambda | Lysis-lysogeny decision | 1995 | Thieffry, Denis and Thomas, René |
| Gap Model | D. melanogaster | Segmentation, Development | 2001 | Sánchez, Lucas and Thieffry, Denis |
| The pair-rule cross-regulatory module | D. melanogaster | Segmentation, Development | 2003 | Sánchez, Lucas and Thieffry, Denis |
| Controlling tryptophan biosynthesis | E. Coli, Bacterium | Tryptophan biosythesis | 2005 | Simão, E. and Remy, E. and Thieffry, D. and Chaouiya, C. |
| DV boundary formation of the Wing imaginal disc | D. melanogaster | Wing Imaginal disk, Development | 2006 | González, Aitor and Chaouiya, Claudine and Thieffry, Denis |
| Restriction point control of the mammalian cell cycle | Mammal | Cell cycle | 2006 | Fauré, Adrien and Naldi, Aurélien and Chaouiya, Claudine and Thieffry, Denis |
| TCR signalisation | Mammal | Differentiation | 2006 | Klamt, Steffen and Saez-Rodriguez, Julio and Lindquist, Jonathan A and Simeoni, Luca and Gilles, Ernst D |
| Control of Th1/Th2 cell differentiation | Mammal | Differentiation | 2006 | Mendoza, Luis |
| Budding yeast cell cycle (Orlando et al. 2008) | Yeast, Budding yeast | Cell cycle | 2009 | Fauré, Adrien and Thieffry, Denis |
| The Anterior-Posterior Boundary (Gonzalez et al. 2008) | D. melanogaster | Wing Imaginal disk, Development | 2008 | González, Aitor and Chaouiya, Claudine and Thieffry, Denis |
| Segment polarity module (Sánchez et al. 2008) | D. melanogaster | Segmentation, Development | 2008 | Sanchez, Lucas and Chaouiya, Claudine and Thieffry, Denis |
| Fission Yeast Cell Cycle (Davidich and Bornholdt, 2008) | Yeast, Fission yeast | Cell cycle | 2009 | Fauré, Adrien and Thieffry, Denis |
| Network model of survival signaling in large granular lymphocyte leukemia (Zhang et al 2008) | Mammal, Blood cells, T lymphocytes | Cell fate decision | 2008 | Zhang, Ranran and Shah, Mithun Vinod and Yang, Jun and Nyland, Susan B. and Liu, Xin and Yun, Jong K. and Albert, Réka and Loughran, Thomas P. |
| Budding yeast cell cycle (adapted from Irons, 2009) | Yeast, Budding yeast | Cell cycle | 2009 | Fauré, Adrien and Thieffry, Denis |
| Core engine controlling the budding yeast cell cycle | Yeast, Budding yeast | Cell cycle, Core engine | 2009 | Fauré, Adrien and Naldi, Aurélien and Lopez, Fabrice and Chaouiya, Claudine and Ciliberto, Andrea and Thieffry, Denis |
| Budding yeast cell cycle (Fauré et al. 2009) | Yeast, Budding yeast | Cell cycle | 2009 | Fauré, Adrien and Naldi, Aurélien and Lopez, Fabrice and Chaouiya, Claudine and Ciliberto, Andrea and Thieffry, Denis |
| Budding yeast exit module | Yeast, Budding yeast | Mitosis exit control, Cell cycle | 2009 | Fauré, Adrien and Naldi, Aurélien and Lopez, Fabrice and Chaouiya, Claudine and Ciliberto, Andrea and Thieffry, Denis |
| Morphogenetic checkpoint of the budding yeast cell cycle | Yeast, Budding yeast | Cell cycle, Morphogenetic checkpoint | 2009 | Fauré, Adrien and Naldi, Aurélien and Lopez, Fabrice and Chaouiya, Claudine and Ciliberto, Andrea and Thieffry, Denis |
| ERBB receptor-regulated G1/S transition | Human | Cell cycle | 2009 | Sahin, Özgür and Fröhlich, Holger and Löbke, Christian and Korf, Ulrike and Burmester, Sara and Majety, Meher and Mattern, Jens and Schupp, Ingo and Chaouiya, Claudine and Thieffry, Denis and Poustka, Annemarie and Wiemann, Stefan and Beissbarth, Tim and Arlt, Dorit |
| p53-Mdm2 network involved in DNA repair | Mammal | Cancer, DNA repair | 2009 | Abou-Jaoudé, Wassim and Ouattara, Djomangan A. and Kaufman, Marcelle |
| Cell-Fate Decision in Response to Death Receptor Engagement | Mammal | Cell fate decision | 2010 | Calzone, Laurence and Tournier, Laurent and Fourquet, Simon and Thieffry, Denis and Zhivotovsky, Boris and Barillot, Emmanuel and Zinovyev, Andrei |
| Control of Th1/Th2/Th17/Treg cells differentiation | Mammal | Differentiation | 2010 | Naldi, Aurélien and Carneiro, Jorge and Chaouiya, Claudine and Thieffry, Denis |
| Drosophila cell cycle | D. melanogaster | Cell cycle | 2009 | Fauré, Adrien and Thieffry, Denis |
| miR-9 and timing of neurogenesis (Coolen 2012) | Zebrafish | Development, Differentiation | 2012 | Coolen, Marion and Thieffry, Denis and Drivenes, \Oyvind and Becker, Thomas S. and Bally-Cuif, Laure |
| Specification of vulval precursor cells and cell fusion control in C. elegans | C. elegans | Differentiation | 2013 | Weinstein, Nathan and Mendoza, Luis |
| Drosophila FGF Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila JAK/STAT Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila Dpp Signalling pathway | D. melanogaster | Wing Imaginal disk, Development, Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila EGF Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila Hh Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila Notch Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila SPATZLE Processing pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila Toll Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila VEGF Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| Drosophila Wg Signalling pathway | D. melanogaster | Signalling | 2013 | Mbodj, Abibatou and Junion, Guillaume and Brun, Christine and Furlong, Eileen E. M. and Thieffry, Denis |
| MAPK network | Mammal | Signalling | 2013 | Grieco, Luca and Calzone, Laurence and Bernard-Pierrot, Isabelle and Radvanyi, François and Kahn-Perlès, Brigitte and Thieffry, Denis |
| Drosophila eggshell patterning | D. melanogaster | Development | 2014 | Fauré, Adrien and Vreede, Barbara M. I. and Sucena, Élio and Chaouiya, Claudine |
| Mast cell activation | Mammal, Blood cells | Signalling | 2014 | Niarakis, Anna and Bounab, Yacine and Grieco, Luca and Roncagalli, Romain and Hesse, Anne-Marie and Garin, Jérôme and Malissen, Bernard and Daëron, Marc and Thieffry, Denis |
| Senescence onset at the G1/S cell cycle checkpoint | Mammal | Senescence, Cell cycle, Cell fate decision | 2014 | Mombach, José CM and Bugs, Cristhian A and Chaouiya, Claudine |
| Control of Th1/Th2/Th17/Treg/Tfh/Th9/Th22 cell differentiation | Mammal, Blood cells, T lymphocytes | Differentiation | 2015 | Abou-Jaoudé, Wassim and Monteiro, Pedro T. and Naldi, Aurélien and Grandclaudon, Maximilien and Soumelis, Vassili and Chaouiya, Claudine and Thieffry, Denis |
| Mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis | Mammal, Human | Cancer, Signalling, Cell fate decision | 2015 | Remy, Elisabeth and Rebouissou, Sandra and Chaouiya, Claudine and Zinovyev, Andrei and Radvanyi, François and Calzone, Laurence |
| Cell fate decision network in the AGS gastric cancer cell line (Flobak et al 2015) | Mammal | Cancer | 2015 | Flobak, Åsmund and Baudot, Anaïs and Remy, Elisabeth and Thommesen, Liv and Thieffry, Denis and Kuiper, Martin and Lægreid, Astrid |
| Molecular Pathways Enabling Tumour Cell Invasion and Migration | Mammal, Human | Cancer, Signalling | 2015 | Cohen, David P. A. and Martignetti, Loredana and Robine, Sylvie and Barillot, Emmanuel and Zinovyev, Andrei and Calzone, Laurence |
| Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk | Mammal, Stem cells, Haematopoietic stem cells, Mesenchymal stem cells | Cell fate decision | 2015 | Desterke, Christophe and Martinaud, Christophe and Ruzehaji, Nadira and Le Bousse-Kerdilès, Marie-Caroline |
| Drosophila mesoderm specification | D. melanogaster | Development, Signalling | 2016 | Mbodj, Abibatou and Gustafson, E. Hilary and Ciglar, Lucia and Junion, Guillaume and Gonzalez, Aitor and Girardot, Charles and Perrin, Laurent and Furlong, Eileen E. M. and Thieffry, Denis |
| Multilevel mammalian cell cycle model | Mammal | Cell cycle | 2016 | Traynard, Pauline and Fauré, Adrien and Fages, François and Thieffry, Denis |
| Boolean model of geroconversion | Mammal | Senescence | 2016 | Verlingue, Loic and Dugourd, Aurélien and Stoll, Gautier and Barillot, Emmanuel and Calzone, Laurence and Londoño-Vallejo, Arturo |
| Communication pathways between Hematopoietic Stem Progenitor Cells (HSPCs) and Mesenchymal Stromal Cells (MSCs) | Mammal, Blood cells | Cell fate decision | 2016 | Enciso, Jennifer and Mayani, Hector and Mendoza, Luis and Pelayo, Rosana |
| Primary sex determination of placental mammals | Mammal | Development, Sex determination | 2016 | Sánchez, Lucas and Chaouiya, Claudine |
| Asymmetric Cell Division in Caulobacter Crescentus | C. Crescentus, Bacterium | Asymmetric cell division, Cell cycle | 2017 | Sánchez-Osorio, Ismael and Hernández-Martínez, Carlos A. and Martínez-Antonio, Agustino |
| Lymphoid and myeloid cell specification and transdifferentiation | Mammal, Blood cells | Differentiation | 2017 | Collombet, Samuel and van Oevelen, Chris and Sardina Ortega, Jose Luis and Abou-Jaoudé, Wassim and Di Stefano, Bruno and Thomas-Chollier, Morgane and Graf, Thomas and Thieffry, Denis |
| Primary sex determination of chicken gonads | Mammal, Bird | Development, Sex determination | 2018 | Sánchez, Lucas and Chaouiya, Claudine |
| TCR and TLR5 merged Boolean model | Mammal | T-cell activation | 2019 | Rodríguez-Jorge, Otoniel and Kempis-Calanis, Linda A. and Abou-Jaoudé, Wassim and Gutiérrez-Reyna, Darely Y. and Hernandez, Céline and Ramirez-Pliego, Oscar and Thomas-Chollier, Morgane and Spicuglia, Salvatore and Santana, Maria A. and Thieffry, Denis |
| Comprehensive Boolean model of the mammalian cell cyle control network | Mammal, Human | Cell cycle, Signalling | 2025 | Noël, Vincent and Naldi, Aurélien and Calzone, Laurence and Paulevé, Loic and Thieffry, Denis |
| Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation | Mammal, Human | T-cell activation | 2019 | Sánchez-Villanueva, José Antonio and Rodríguez-Jorge, Otoniel and Ramírez-Pliego, Oscar and Rosas Salgado, Gabriela and Abou-Jaoudé, Wassim and Hernandez, Céline and Naldi, Aurélien and Thieffry, Denis and Santana, María Angélica |
| T-lymphocyte specification | Mammal | Differentiation, Signalling, Development | 2020 | Cacace, Elisabetta and Collombet, Samuel and Thieffry, Denis |
| Regulation of p21-dependent senescence-apoptosis switch by the ATM/miR-34a-5p axis in non-small cell lung cancer | Mammal | DNA repair, Cell cycle | 2020 | Shantanu Gupta and Daner A. Silveira and Jose Carlos M. Mombach |
| Differential expression of IL17 isoforms A and F in helper T Lymphocytes | Mammal | differentiation | 2021 | Corral-Jara, Karla Fabiola and Chauvin, Camille and Abou-Jaoudé, Wassim and Grandclaudon, Maximilien and Naldi, Aurélien and Soumelis, Vassili and Thieffry, Denis |
| Microenvironment control of hybrid Epithelial-Mesenchymal phenotypes | Mammal | Cancer | 2020 | Selvaggio, Gianluca and Canato, Sara and Pawar, Archana and Monteiro, Pedro T. and Guerreiro, Patrícia S. and Brás, M. Manuela and Janody, Florence and Chaouiya, Claudine |
| Immune checkpoints | Mammal, Human | T-cell activation | 2020 | Kondratova, Maria and Barillot, Emmanuel and Zinovyev, Andrei and Calzone, Laurence |
| Immunogenic Cell Death | Mammal | Cancer | 2020 | Checcoli, Andrea and Pol, Jonathan G. and Naldi, Aurelien and Noel, Vincent and Barillot, Emmanuel and Kroemer, Guido and Thieffry, Denis and Calzone, Laurence and Stoll, Gautier |
| Control of proliferation by oncogenes and tumor suppressors | Mammal | Cancer | 2018 | G.T. Zañudo, Jorge and Steinway, Steven N. and Albert, Réka |
| T cells response to CTLA4 and PD-1 checkpoint inhibitors | Mammal | Differentiation | 2020 | Hernandez, Céline and Thomas-Chollier, Morgane and Naldi, Aurélien and Thieffry, Denis |
| Logical model of the regulatory network controlling dorsal-ventral axis specification in the sea urchin P. lividius | Sea Urchin | Development | 2020 | Floc'hlay, Swann and Molina, Maria Dolores and Hernandez, Céline and Haillot, Emmanuel and Thomas-Chollier, Morgane and Lepage, Thierry and Thieffry, Denis |
| Response to BRAF treatment in melanoma and colorectal cancer | Mammal, Human | Cancer | 2021 | Béal, Jonas and Pantolini, Lorenzo and Noël, Vincent and Barillot, Emmanuel and Calzone, Laurence |
| Differentiation of Monocytes to Dendritic Cells | Mammal, Human | Differentiation | 2021 | Nuñez-Reza, Karen J. and Naldi, Aurélien and Sánchez-Jiménez, Arantza and Leon-Apodaca, Ana V. and Santana, M. Angélica and Thomas-Chollier, Morgane and Thieffry, Denis and Medina-Rivera, Alejandra |
| Signalling in prostate cancer | Mammal, Human | Cancer | 2022 | Montagud, Arnau and Béal, Jonas and Tobalina, Luis and Traynard, Pauline and Subramanian, Vigneshwari and Szalai, Bence and Alföldi, Róbert and Puskás, László and Valencia, Alfonso and Barillot, Emmanuel and Saez-Rodriguez, Julio and Calzone, Laurence |
| Logical model of the early differentiation and aging of Hematopoietic Stem Cells (HCS) | Mammal | Differentiation | ||
| Logical model of the regulatory network underlying Retinoic Acid resistance in Acute Promyelocytic Leukaemia | Mammal | Cancer | 2024 | Sánchez-Villanueva J and N'Guyen L and Poplineau M and Duprez E and Remy É and Thieffry D |