Science has been, and shall always be, my thing. Currently, I study the history of Life on Earth from an organismal perspective, in search for a theory of sustainability by trying to answer the question: How come life never got extinct in the last 4x109 years? I do this relentlessly, all the time. Besides that, I help many colleagues solving the quantitative challenges that permeate their research.
After decades of collaborating with graduate students, I grew increasingly concerned with how much the undergraduate education is misaligned with the quantitative demands of modern research and of today's world. To try to do something about it, I get involved as much as I can afford with new educational projects, collaborating with a rather wide set of academic institutions in Portugal and beyond.
Drawing is another thing I do, as well as walking around...
Graduate Programmes
I played a coordinating role in the design and management of three graduate programmes:
Master's in Integrative and Systems Immunology. ICBAS, University of Porto.
PhD Programme in Integrative Biology and Biomedicine, IGC, Oeiras.
PhD Programme in Computational Biology, IGC, Oeiras.
Teaching
A random set of courses I have taught ...
Mathematical Models in Biomedicine. Instituto Superior Técnico, Lisbon Together with Jorge Tiago and Jessica King.
Systems Biology: Conceptual and Hands-on Introduction. UNAM, Mexico City and Cuernavaca,Mexico
Tooling Up For Systems Biology. UNAM, Mexico City, Mexico
Hypothesis Driven Research Course. PhD Programme in Integrative Biology and Biomedicine. GIMM, Oeiras
Systems Biology Course. Instituto Serrapilheira, São Paulo, Brazil.
Computational Systems Biology. Advanced Techniques in Biochemistry. ITQB NOVA, Oeiras
Lectures, Seminars, etc.
A few examples of the things I talk (or handwave) about...
How biochemistry evolved into systems biology: lessons from studying the immune system. Lecture in the context of the XI Jornadas da Bioquímica. Organised by the NEBQUP (University of Porto Biochemistry Student Association). ICBAS, April 18, 2026
Round table on "The Role of AI in the 3Rs" within the meeting "The 3Rs Framework for Intelligent Use of In Vitro, In Vivo, and NAMs" organised by MPS NOVA. Moderated by Anna Olsson (I3S) featured Gabriela Silva (NMS), João Conde (NMS), Ana Isabel Moura Santos (NMS), Ricardo Henriques (ITQB NOVA), and Jorge Carneiro (ITQB NOVA). February 26, 2026.
"Quantifying and modelling cellular heterogeneity in the immune system: does multimodality reflect multiple stable states?" University of Strathclyde, Glasgow, June 25, 2025.
"An uncanny valley in gamete mating choice during broadcast spawning." Institutional Seminar Instituto de Biotecnologia, UNAM, Cuernavaca, Mexico. May 26, 2025.
"Why is it so hard to exploit the immunobiology of regulatory T cells in disease therapies." Instituto Biotecnologia Experimental-IBET, Oeiras, Portugal. March 21, 2025.
Scientific Articles
Sandoval-Hernández, M.A. , N.A. Fierro, J.I. Veytia-Bucheli, D.A. Alvarado-Velázquez, E. Alemán-Navarro, E. Melchy-Pérez, C. Auvynet, I. Imaz-Rosshandler, J. Carneiro, E. Perez-Rueda, and Y. Rosenstein. (2024) Differential Impact of CD43 and CD28 on T-Cell Differentiation Depending on the Order of Engagement with the TCR. Int. J. Mol. Sci. 25, 3135.[doi]
Munõz, E. and J. Carneiro. (2022) ant-microbe symbiosis widens the habitability range of the Daisyworld. J Theor Biol 554, 111275.[doi] [preprint]
Carrasquel Martínez, G., A. Aldana, J. Carneiro, C. L. Treviño,, and A. Darszon. (2022)Acrosomal alkalinization occurs during human sperm capacitation. Mol. Human Reprod. 28, gaac005. [doi]
Aldana, A., J. Carneiro, G. Martinez-Mekler, and A. Darszon. (2021) Discrete Dynamic Model of the Mammalian Sperm Acrosome Reaction: The Influence of Acrosomal pH and Physiological Heterogeneity. Front. Physiol. 12, 682790. [doi]
Louro, M., M. Bettencourt-Dias, and J. Carneiro. (2021) A first-takes-all model of centriole copy number control based on cartwheel elongation. PLoS Comput. Biol. 17(5): e1008359. [doi][preprint]
Nabais, C., D. Pessoa, J. de-Carvalho, T. van Zanten, P. Duarte, S. Mayor, J. Carneiro, I.A. Telley, M. Bettencourt-Dias. (2021) Plk4 triggers autonomous de novo centriole biogenesis and maturation. J. Cell Biol. 220, e202008090. [doi] [preprint]
Louro, M., M. Bettencourt-Dias, and J. Carneiro. A first-takes-all model of centriole copy number control. bioRxiv [preprint]
Gomes, M.G.M., R.M. Corder, J.G. King, K.E. Langwig, C. Souto-Maior, J. Carneiro, G. Goncalves, C. Penha-Goncalves, M.U. Ferreira, R. Aguas. (2020) Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. medRxiv [preprint]
Nabais, C., D. Pessoa, J. de-Carvalho, T. van Zanten, P. Duarte, S. Mayor, J. Carneiro, I.A. Telley, M. Bettencourt-Dias. (2020) Plk4 triggers autonomous de novo centriole biogenesis and maturation. bioRxiv [preprint]
Ramos, C.V., L. Balesteros-Arias, J.G. Silva, J. Carneiro, E. Gjini, V.C. Martins. (2020) Cell competition, the kinetics of thymopoiesis, and thymus cellularity are regulated by double-negative 2 to 3 early thymocytes. Cell Reports. 32, 107910. [doi]
Guzella, T., V. Barreto, J. Carneiro. Partitioning stable and unstable expression level variation in cell populations: a theoretical framework and its application to the T cell receptor. PLoS Comput. Biol. 16, e1007910. [doi] [preprint]
Ramirez-Gomez, H.V., V. Jimenez-Sabinina, M. Velazquez-Perez, C. Beltran, J. Carneiro, C.D. Wood, I. Tuval, A. Darzon and A. Guerrero. (2020) Sperm chemotaxis is driven by the slope of the chemoattractant concentration field. eLife 9, e50532. [doi]
Priego-Espinosa, D., A. Darzon, A. Guerrero, A.L. Gonzalez-Cota, T. Nishigaki, Martinez-Mekler and J. Carneiro. (2020) Modular analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaV channels in sea urchin sperm. PLoS Comput. Biol. 16, e1007605. [doi]
Sepúlveda, N., J. Carneiro, E. Lacerda, L. Nacul. (2018) Myalgic Encephalomyelitis/Chronic Fatigue Syndrome as a hyper-regulated immune system driven by an interplay between regulatory T cells and chronic human herpesvirus infections.Front. Immunol. 10:2684. [doi]
Mendes, N.D., R. Henriques, E. Remy, J. Carneiro, P.T. Monteiro and C. Chaouiya. (2018) Estimating Attractor Reachability in Asynchronous Logical Models. Front. Physiol. 9, 1161. [doi]
Lopes, C.A., S.C. Jana, I. Cunha-Ferreira, S. Zitouni, I. Bento, P. Duarte, S. Gilberto, F. Freixo, A. Guerrero, M. Francia, M. Lince-Faria, J. Carneiro, M. Bettencourt-Dias. (2015) PLK4 trans-Autoactivation Controls Centriole Biogenesis in Space. Dev. Cell. 35(2):222-235. [pdf]
González-Cota, A.L., P.A. Silva , J. Carneiro, A. Darzon. (2015) Single cell imaging reveals that the motility regulator speract induces a flagellar alkalinization that precedes and is independent of Ca²⁺ influx in sea urchin spermatozoa. FEBS Lett. 589(16):2146-54. [pdf]
Tarapore, D., P. Lima, J. Carneiro, and A.L. Christensen. (2015) To err is robotic, to tolerate immunological: fault detection in multirobot systems. Bioinspir. Biomim. 10, 016014. [doi] [pdf]
Weber, T.S., I. Jaehnert, C. Schichor, M. Or-Guil and J. Carneiro. (2014) Quantifying the length and variance of the eukaryotic cell cycle phases by a stochastic model and dual nucleoside pulse labelling. PLoS Comput. Biol. 10, e1003616. [doi] [pdf]
Trancoso, I., M. Bonnet, R. Gardner, J. Carneiro, V.M. Barreto, J. Demengeot and L.M. Sarmento (2013) A Novel Quantitative Fluorescent Reporter Assay for RAG Targets and RAG Activity. Front Immunol. 4:110. [pdf ]
Guerrero A., J. Espinal, C.W. Wood, J. Carneiro, G. Martínez-Mekler and A. Darzon. (2012) Niflumic acid disrupts marine spermatozoan chemotaxis without impairing the spatiotemporal decoding of chemoattractant gradients. J. Cell Science 126, 1477-1487 [pdf]
Tarapore, D., A.L. Christensen, P.U. Lima and J. Carneiro. (2012) Environment classification in multiagent systems inspired by the adaptive immune system. Artificial Life 13, 275–282 [pdf 676Kb]
Pimentel, A., J. Carneiro, A. Darzon, and G. Corkidi. (2012) A Segmentation Algorithm for Automated Tracking of Fast Swimming Unlabelled Cells in Three-dimensions. J. Microscopy. 245, 72-81. [pdf 468Kb]
Serrano, M., G. Real, J. Santos, J. Carneiro, C.P. Moran Jr., and A. O. Henriques. (2011) A Negative Feedback Loop that Limits the Ectopic Activation of a Cell Type-Specific Sporulation Sigma Factor of Bacillus subtilis. PLoS Genetics. 7, e1002220. [pdf 1.5Mb]
Vélez de Mendizábal, N., J. Carneiro, R.V. Solé, J. Goñi , J. Bragard, I. Martinez-Forero, S. Martinez-Pasamar, J. Sepulcre , J. Torrealdea, F. Bagnato, J. Garcia-Ojalvo, and P. Villoslada. (2011) Modeling the effector - regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis. BMC Systems Biology 5, 114. [pdf 2.8Mb]
Guerrero, A., J. Carneiro, A. Pimentel, C.D. Wood , G. Corkidi, A. Darzon. (2011) Strategies for locating the female gamete: the importance of measuring sperm trajectories in three spatial dimensions. Mol. Hum. Reprod. 17, 511-23. [pdf 488Kb]
Sepulveda, N. and J. Carneiro. (2011) Repertoire dynamics of peripheral regulatory and effector T cells competing for antigen presenting cells. In: Mathematical Models and Immune Cell Biology (Editors: Lythe and Molina-Paris). Elsevier.
Guerrero, A., C.D. Wood CD, T. Nishigaki, J. Carneiro, and A. Darzon. (2010) Tuning sperm chemotaxis. Biochem. Soc. Trans. 38, 1270-1273. [pdf 304Kb]
Naldi, A., J. Carneiro, C. Chaouiya, and D. Thieffry. (2010) Diversity and plasticity of Th cell types predicted from regulatory network modelling. PLoS Comp. Biol. 6, e1000912. [pdf 528Kb]
Guerrero, A., T. Nishigaki, J. Carneiro, Y. Tatsu, C.D. Wood, and A. Darzon. (2010) Tuning sperm chemotaxis by calcium burst timing. Dev. Biol. 344, 52-65. [pdf 1Mb]
Sepulveda, N., C.D. Paulino, and J. Carneiro. (2010) Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models. J. Immunol. Methods. 353, 124-137. [pdf 2.6Mb]
Carneiro J., L. Duarte, and E. Padovan (2009) Limiting dilution analysis of antigen-specific T cells. Methods Mol. Biol. 514, 95-105. [pdf 292Kb]
Certal, A.C., R.B. Almeida, E. Wong, N. Moreno, Carneiro J., J. Rodriguez-Leon, H.-M. Wu, A.Y. Cheung, and J. Feijo. (2008). Differential exclusion of proton ATPases from the apical membrane is associated with cell polarity and apical growth in pollen tubes. Plant Cell 20, 614-34 [pdf 1.4Mb]
Leon, K., K. Garcia, J. Carneiro, and A. Lage. (2007). How regulatory CD25+CD4+T cells impinge on tumor immunobiology: On the differential response of tumors to therapies. J. Immunol. 179, 5659-5668. [pdf 288Kb]
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 99, 173-84. [pdf 208Kb]
Paixao, T., T.P. Carvalho, D.P. Calado, and J. Carneiro. (2007). Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunol. Cell. Biology 85, 315-322. [pdf 280Kb]
Léon, 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. 247, 122-137. [pdf 362Kb]
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 216, 48-68. [pdf 2.9Mb]
Milutinovic, D., J. Carneiro, M.Athans, and P. Lima (2007) Modeling Dynamics of Cell Population Molecule Expression Distribution. Nonlinear Analysis Hybrid Systems 1, 81-94. [pdf 792Kb]
Boucontet, L., N. Sepúlveda, J. Carneiro, & P. Pereira. (2005). Mechanisms controlling termination of V-J recombination at the TCR-γ locus: Implications for allelic and isotypic exclusion of TCR-γ chains. J. Immunol. 174, 3912-3919.
Sepúlveda, N., L. Boucontet, P. Pereira, & J. Carneiro. (2005). Stochastic modeling of T cell receptor γ gene rearrangement. J. Theor. Biol. 234, 153-165.
Carneiro, J., T. Paixão, D. Milutinovic, J. Sousa, K. Leon, R. Gardner & J. Faro. (2005). Immunological Self-Tolerance: Lessons from Mathematical Modeling. J. Comp. Appl. Math. 184, 77-100.
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.
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.
Léon, K., A. Lage, & J. Carneiro. (2003). Tolerance and immunity in a mathematical model of T cell mediated suppression. J. Theor. Biol. 225, 107-126.
Becker, J., L.C. Boavida, J. Carneiro, M. Haury, & J.A. Feijó (2003). Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. Plant Physiol. 133, 713-725.
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. and J. Carneiro. (2000) Mathematical Analysis of TCR serial triggering and downregulation. Eur. J. Immunol. 30, 3219-3227.
Brissac, C., A. Nobrega, J. Carneiro, and 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.
Faro, J., J., J. Carneiro, & S. Velasco. (1997). Further studies on the immune network modelling. J. Theor. Biol. 184, 405-421.
Carneiro, J., J., A. Coutinho, and 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, and 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., J. Stewart, A. Coutinho, and G. Coutinho. (1995). The ontogeny of class-regulation of CD4+ T lymphocyte populations. Int. Immunol. 7, 1265-1277.
Faro, J. and 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. and 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.
Theses Supervised
Tulumello, E. (2020) Robust tolerance out of volatile regulatory T cells. Lessons form mathematical modelling. Ph.D. Thesis. ITQB University Nova.
Pessoa, D. (2019) How to make a single product per cell ? Lessons from X chromosome inactivation and antigen receptor gene recombination. Ph.D. Thesis. ITQB University Nova.
Silva, P.A. (2017) Quantitative image analysis of cells using morphodynamical models: Sea urchin spermatozoa as case study. Ph.D. Thesis. ITQB University Nova
Louro, M. (2016) A Stochastic Model of Centriole Assembly.M.Sc. Thesis. University of Lisbon.
Guzella, T (2013) Variation in Protein Expression Levels in Cell Populations. Ph.D. Thesis. ITQB University Nova.
Weber, T (2013) Optimal Timing of Phase Resolved Cell Cycle Progression. Ph.D Thesis. Humboldt University Berlin.
Silva, P.A. (2011) Supervised and unsupervised spermatozoa detection, classification and tracking in imaging data. MSc. Thesis. University of Lisbon.
Sepúlveda, N. (2009) How is the T-cell repertoire shaped ? Ph.D. thesis. University of Porto. [pdf 6Mb]
Vilares, I. (2008) Interaction between microorganisms and the innate and adaptive immune systems: a mathematical view. MSc in Applied Maths. Department of Maths of the Instituto Superior de Agronomia. Technical University of Lisbon.
Paixão, T. (2007) The Stochastic Basis of Somatic Variation. Ph.D. Thesis. University of Porto. [pdf 5.2Mb]
Sousa, J. (2003) Modeling the antigen and cytokine receptors signaling processes and their propagation to lymphocyte population dynamics. Ph.D. Thesis. University of Porto.
Leon, K. (2002) A quantitative approach to dominant tolerance. Ph.D. Thesis. University of Porto.