Quantitative Organism Biology
Cells of multicellular organisms cooperate to ensure body development and maintenance throughout life.
They do this in a collective distributed manner, without any master or plan.
The Quantitative Organism Biology group studies the multilevel mechanisms that give rise to properties of the whole organism, in search for general principles of biological organisation and, eventually, the design of artificial systems.
One of our main research interests is the immune system, in which cells collectively ensure body housekeeping and homeostasis, avoid autoimmune diseases, and fight cancer and infections.
We also investigate the morphodynamics of cells and tissues during fertilisation and embryonic development of metazoan.
Our approach is two fold: on the one hand, we create mathematical models of specific exemplary systems aiming to uncover basic principles, and on the other hand, we develop the quantitative methods required to assess the properties and predictions of these models.
- Tarapore, D., Christensen, A.L., Lima, P.U., Carneiro, J. (2012) Environment classification in multiagent systems inspired by the adaptive immune system. Proceedings of the Thirteenth International Conference on Artificial L MIT Press:275–282
- Sepúlveda, N., Carneiro, J. (2011) Repertoire dynamics of peripheral regulatory and effector T cells competing for antigen presenting cells. In: Current Mathematical Models in T cell Biology (Editors: Lythe and Molina-Paris):Elsevier
- Guerrero, A., Carneiro, J., Pimentel, A., Wood, C.D., Corkidi, G., Darszon, A. (2011) Strategies for locating the female gamete: the importance of measuring sperm trajectories in three spatial dimensions. Mol Hum Reprod 17:511-523
- Naldi, A., Carneiro, J., Chaouiya, C., Thieffry, D. (2010) Diversity and plasticity of Th cell types predicted from regulatory network modeling. PLoS Comp. Biol 6:e1000912
- Sepúlveda, N, Paulino, C.D., Carneiro, J. (2010) Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models. J. Immunol. Methods 352:124-137
- Paixao, T., Carvalho, T.P., Calado, D.P., Carneiro, J. (2007) Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunol. Cell. Biology 85:315-322
- Carneiro, J., Léon, K., Caramalho, I., van den Dool, C., Gardner, R., Oliveira, V., Bergman, M.L., Sepúlveda, N., Paixão, T., Faro, J., Demengeot, J. (2007) When three is not a crowd: A crossregulation model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunol. Reviews 216:48-68
- Sepúlveda, N., Boucontet, L., Pereira, P., Carneiro, J. (2005) Stochastic modeling of T cell receptor γ gene rearrangement. J. Theor. Biol. 234:153-165
- Léon, K., Faro, J., Carneiro, J. (2004) A General Mathematical Framework to Model Generation Structure in a Population of Asynchronously Dividing Cells. J. Theor. Biol. 229:455-476
- Léon, K., Perez, R., Lage, A., Carneiro, J. (2000) Modelling T cell mediated suppression dependent on interactions in multicellular conjugates. J Theor Biol 207:231-254