Sepulveda, N., C.D. Paulino, J. Carneiro, C. Penha-Goncalves. (2007) Allelic Penetrance Approach As a Tool To Model Two-Locus Interaction in Complex Binary Traits. Heredity. In press.

Paixao, T., T.P. Carvalho, D.P. Calado, and J. Carneiro. (2007). Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunol. Cell. Biology. In Press.

Leon, K., K. Garcia, J. Carneiro, and A. Lage. (2007). How regulatory CD25+CD4+T cells impinge on tumor immunobiology? On the existence of two alternative dynamical classes of tumors. J. Theor. Biol. In Press.

Carneiro, J., K. Leon, I. Caramalho, C. van den Dool, R. Gardner, V. Oliveira, M.-L. Bergman, N. Sepulveda, T. Paixao, J. Faro, and J. Demengeot. (2007) When three is not a crowd: A crossregulation model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunol. Reviews . In press

Milutinovic, D., J- Carneiro, M. Athans, P. Lima (2006) Modeling Dynamics of Cell Population Molecule Expression Distribution Journal of Hybrid Systems and Applications. In press.

Or-Guil, M., F. Luciani, J. Carneiro. (2005). Clonal expansion of cytotoxic T cell clones: The role of the Immunoproteasome. In: BIOMAT 2005, Proceedings of the International Symposium on Mathematical and Computational Biology (Eds. Dil‹o R and Mondaini R). World Scientific Publishing.

Boucontet, L., N. Sepúlveda, J. Carneiro, P. Pereira. (2005). Stochastic modeling of T cell receptor gene rearrangement. J. Immunol. 174, 3912-3919. [PDF 312Kb]

Sepúlveda, N., L. Boucontet, P. Pereira, J. Carneiro. (2005). Stochastic modeling of T cell receptor gene rearrangement. J. Theor. Biol. 234, 153-165. [PDF 396Kb]

Carneiro, J., T. Paixão, D. Milutinovic, J. Sousa, K. Léon, R. Gardner, J. Faro (2005). Immunological Self-Tolerance: Lessons from Mathematical Modeling. J. Comp. Appl. Math. 184, 77-100. [PDF 412Kb]

Léon, K., J. Faro, J. Carneiro. (2004). A general mathematical framework to model generation structure in a population of asynchronously dividing cells. J.Theor.Biol. 229, 455-476. [PDF 188KB]

Léon, K., J. Faro, A. Lage, J. Carneiro. (2004). Inverse Correlation between the Incidences of Autoimmune Disease and Infection Predicted by a Model of T cell mediated Tolerance. J.Autoimmunity. 22, 31-42. [PDF 948KB]

Becker, J., L.C.Boavida, J.Carneiro, M.Haury, J.A.Feijo (2003) Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. Plant Physiology. 133, 713-725.

Léon, K., A.Lage, J.Carneiro. (2003). Tolerance and immunity in a mathematical model of T-cell mediated suppression. J. Theor. Biol. 255, 107-126.

Sepúlveda, N., P. Pereira, and J. Carneiro. (2003). À procura do mecanismo de rearranjo dos genes gama do receptor dos linfócitos T gama delta. (Eds. Brito, P., Figueiredo, A., Teles, P. and Rosado, F.), p. 609-618. Edições SPE, Lisboa.

Sousa, A., J.Carneiro, M. Meier-Schellersheim, Z.Grossman, & R.M.M. Victorino (2002). CD4 T cell depletion is directly linked to immune activation in the pathogenesis of HIV1 and HIV2 but only indirectly to the viral load. J. Immunol. 169, 3400-3406.

Léon, K., R.Perez, A.Lage & J.Carneiro, (2001). Three-cell interactions in T cell mediated suppression? A mathematical analysis of its quantitative implications. J. Immunol. 166, 5356-5365.

Léon, K., R.Perez, A.Lage & J.Carneiro, (2000). Modelling T cell mediated suppression dependent on interactions in multicellular conjugates. J.Theor.Biol. 207, 231-254.

Sousa, J. & J.Carneiro. (2000) Mathematical Analysis of TCR serial triggering and downregulation. Eur. J. Immunol. 30, 3219-3227.

Brissac,C., A.Nobrega, J.Carneiro, & J.Stewart (1999). Functional Diversity of Natural IgM. Int. Immunol. 11, 1501-1507.

Léon, K., J.Carneiro, R.Perez, E.Montero & A.Lage. (1998). Natural and induced tolerance in an immune network model. J.Theor.Biol. 193, 519-534.

Stewart, J. & J.Carneiro (1998). The central and the peripheral immune system: What is the relationship? In: Artificial Immune Systems and their Applications. (Ed. D.Dasgupta). Springer-Verlag. pp. 47-64.

Carneiro, J. (1997). Towards a comprehensive view of the immune system. Ph.D. Thesis, University of Porto.

Faro, J., J.Carneiro, & S.Velasco. (1997). Further studies on the immune network modelling. J. Theor. Biol. 184, 405-421.

Carneiro, J., A.Coutinho, & J.Stewart. (1996). A model of the immune network with B-T cell co-operation. II-The simulation of ontogenesis. J. Theor. Biol. 182, 531-547.

Carneiro, J., J.Faro, A.Coutinho, & J.Stewart. (1996). A model of the immune network with B-T cell co-operation. I-Prototypical Structures and Dynamics. J. Theor. Biol. 182, 513-529.

Carneiro, J. (1996). The Burnetian revolution and the foundations of the immunological matrix. Revista da Sociedade Portuguesa de Imunologia. 182, 513-529.

Carneiro, J., J.Stewart, A.Coutinho, & G.Coutinho. (1995). The ontogeny of class-regulation of CD4+ T lymphocyte populations. Int.Immunol. 7, 1265-1277.

Carneiro, J. & J.Stewart. (1995). Self and Nonself Revisited: Lessons From Modelling The Immune Network. In: Advances in Artificial Life. Proceedings of the Third European Conference on Artificial Life. Springer, Berlin. pp. 406-420.

Faro, J. & J.Carneiro. (1995). The two signal model and autoreactivity: are they really incompatible? Scand.J.Immunol.  41, 519-522.

Vilanova, M., A.Ribeiro, J.Carneiro, & M.Arala-Chaves. (1994). II. The effects of Thalidomide treatment on autoimmune-prone NZB and MRL mice are consistent with stimulation of the central immune system. Scand.J.Immunol.  40, 543-548.

Carneiro,J. & J.Stewart. (1994). Rethinking "Shape Space": Evidence from simulated docking suggests that steric shape complementarity is not limiting for antibody-antigen recognition and idiotypic interactions. J.Theor.Biol. 169, 391-402.