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Jorge Carneiro is a theoretical biologist, who uses mathematical models to understand the dynamical behaviour of cells and cellular collectives. He is currently a visiting scientist in the laboratory of Bacterial Development lab at the ITQB NOVA. He got his degree in Biochemistry from the University of Porto, Portugal, in 1991. He prepared his PhD at the Pasteur Institute in Paris, where he developed immune network models incorporating B and T lymphocytes with John Stewart. He got his PhD in 1997 from the University of Porto. After a short postdoc at the University of Utrecht, with Rob de Boer, he became an independent researcher at the Instituto Gulbenkian de Ciência in April 1998. In 2010, he did a sabbatical at the Institute of Biotechnology of the UNAM, Mexico, with Alberto Darszon. Jorge's group was at the forefront of theoretical and quantitative studies on the dynamics of regulatory T cells, the cells that prevent of autoimmune pathologies in healthy individuals. Together with his collaborators, he predicted the mechanism of action and repertoire selection of these cells, embodied in the Crossregulation Model. His vision of the way the immune system tolerates the organism's tissues and rejects extraneous or pathogen-infected tissues was successfully implemented as spam detection algorithms and fault-robust multiagent systems. Jorge gained interest in modelling the form and morphodynamics of cells and tissues during development, and on the quantitative imaging techniques necessary to assess these models. Jorge is active in the scientific community at large. He often organises workshops and courses on scientific topics such as biostatistics, mathematical and computational biology, immunology and imaging, as well as topics that are relevant for (young) scientists such as career development and entrepreneurship. Between 1998 and 2004, he was a member of direction of the Portuguese Society of Immunology, acting as Secretary General and Vice-President in the first and second triennia, respectively. He participated in the organisation of and fundraising for the PhD Program in Computational Biology and eventually became its Director. This pilot programme was launched in 2005 and trained more than 40 PhD students. It was the first programme of its kind being supported by the non-profit FCG and institutions of public (FCT and FCCN) and private (Siemens SA and Fundação PT Portugal Telecom) sectors. From 2013 to 2018, Jorge was Deputy the Director for Science of the Instituto Gulbenkian de Ciência. From September 2020 to March 2013 he was the Director of the PhD Programme in Integrative Biology and Biomedicine of the Instituto Gulbenkian de Ciência and ITQB NOVA.
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Identification

Personal identification

Full name
Jorge Carneiro

Citation names

  • Carneiro, Jorge

Author identifiers

Ciência ID
1B1F-46C3-9359
ORCID iD
0000-0002-7520-3406

Email addresses

  • jcarneiro@itqb.unl.pt (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Upper intermediate (B2) Advanced (C1) Intermediate (B1) Upper intermediate (B2)
Spanish; Castilian Upper intermediate (B2) Advanced (C1) Intermediate (B1) Upper intermediate (B2)
Education
Degree Classification
1997/05/13
Concluded
 Ciências Biomédicas (Doutoramento)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal

Institut Pasteur, France
1991
Concluded
 Bioquímica (Licenciatura)
Universidade do Porto, Portugal
Affiliation

Science

Category
Host institution 		Employer
2024/02 - Current Researcher (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1998/04/01 - 2023/03/31 Principal Investigator (Research) Instituto Gulbenkian de Ciência, Portugal
2010/04 - 2010/09 Invited Principal Investigator (Research) Universidad Nacional Autónoma de México Instituto de Biotecnología, Mexico

Positions / Appointments

Category
Host institution 		Employer
2020/07 - 2023/03/31 Director PhD Programme in Integrative Biology and Biomedicine Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Instituto Gulbenkian de Ciência, Portugal
2013/11/01 - 2018/03/31 Deputy Director for Science Fundação Calouste Gulbenkian, Portugal
2006/04 - 2009/03 Director PhD Programme in Computational Biology Instituto Gulbenkian de Ciência, Portugal
Projects

Contract

Designation Funders
2010/02/01 - 2013/05/31 Robótica Colectiva: Da Inspiração Biológica à Inspiração Institucionalista
PTDC/EEA-CRO/104658/2008
Universidade de Lisboa Instituto Superior Técnico, Portugal

Fundação Calouste Gulbenkian, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2007/09/01 - 2010/12/31 Repertório de receptores da célula T no geração e manutenção da tolerância imunológica: Requisitos qualitativos e quantitativos.
PTDC/SAU-MII/71402/2006
Fundação Calouste Gulbenkian, Portugal

Instituto Gulbenkian de Ciência, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005/06/01 - 2007/12/31 T cell production in HIV immunodeficiency
POCI/SAU-MMO/60333/2004
Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal

Fundação Calouste Gulbenkian, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Bersini, H.; Carneiro, J.. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface. 2006.
  2. Carneiro, J.; Stewart, J.. Self and nonseld revisited: Lessons from modelling the immune network. 1995.
    10.1007/3-540-59496-5_315
Conference paper
  1. Tarapore, D.; Christensen, A.L.; Lima, P.U.; Carneiro, J.. "Abnormality detection in multiagent systems inspired by the adaptive immune system". 2013.
  2. Antunes, M.; Correia, M.; Carneiro, J.. "Towards an immune-inspired temporal anomaly detection algorithm based on tunable activation thresholds". 2009.
Journal article
  1. Priego Espinosa, Daniel; Espinal-Enríquez, Jesús; Aldana, Andrés; Aldana, Maximino; Martínez-Mekler, Gustavo; Carneiro, Jorge; Darszon, Alberto. "Reviewing mathematical models of sperm signaling networks". Molecular Reproduction and Development 91 8 (2024): http://dx.doi.org/10.1002/mrd.23766.
    10.1002/mrd.23766
  2. Monserrat Alba Sandoval-Hernández; Nora A Fierro; José Ignacio Veytia-Bucheli; Den Alejandro Alvarado-Velázquez; Estefanía Alemán-Navarro; Erika Melchy-Pérez; Constance Auvynet; et al. "Differential Impact of CD43 and CD28 on T-Cell Differentiation Depending on the Order of Engagement with the TCR". International Journal of Molecular Sciences (2024): http://dx.doi.org/10.3390/ijms25063135.
    10.3390/ijms25063135
  3. Estefanía Muñoz; Jorge Carneiro. "Plant–microbe symbiosis widens the habitability range of the Daisyworld". Journal of Theoretical Biology (2022): https://doi.org/10.1016/j.jtbi.2022.111275.
    10.1016/j.jtbi.2022.111275
  4. Marco António Dias Louro; Attila Csikász-Nagy; Mónica Bettencourt-Dias; Jorge Carneiro. "A first-takes-all model of centriole copy number control based on cartwheel elongation". PLOS Computational Biology 17 5 (2021): e1008359-e1008359. https://doi.org/10.1371/journal.pcbi.1008359.
    10.1371/journal.pcbi.1008359
  5. Thiago S. Guzella; Vasco M. Barreto; Jorge Carneiro. "Partitioning stable and unstable expression level variation in cell populations: A theoretical framework and its application to the T cell receptor". PLOS Computational Biology (2020): https://doi.org/10.1371/journal.pcbi.1007910.
    10.1371/journal.pcbi.1007910
  6. Camila V. Ramos; Luna Ballesteros-Arias; Joana G. Silva; Rafael A. Paiva; Marta F. Nogueira; Jorge Carneiro; Erida Gjini; Vera C. Martins. "Cell Competition, the Kinetics of Thymopoiesis, and Thymus Cellularity Are Regulated by Double-Negative 2 to 3 Early Thymocytes". Cell Reports (2020): https://doi.org/10.1016/j.celrep.2020.107910.
    10.1016/j.celrep.2020.107910
  7. Héctor Vicente Ramírez-Gómez; Vilma Jimenez Sabinina; Martín Velázquez Pérez; Carmen Beltran; Jorge Carneiro; Christopher D Wood; Idan Tuval; Alberto Darszon; Adán Guerrero. "Sperm chemotaxis is driven by the slope of the chemoattractant concentration field". eLife 9 (2020): https://doi.org/10.7554/eLife.50532.
    10.7554/eLife.50532
  8. Daniel A. Priego-Espinosa; David Umulis; Alberto Darszon; Adán Guerrero; Ana Laura González-Cota; Takuya Nishigaki; Gustavo Martínez-Mekler; Jorge Carneiro. "Modular analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaV channels in sea urchin sperm". PLOS Computational Biology 16 3 (2020): e1007605-e1007605. https://doi.org/10.1371/journal.pcbi.1007605.
    10.1371/journal.pcbi.1007605
  9. Sepulveda, Nuno; Carneiro, Jorge; Lacerda, Eliana; Nacul, Luis. "Myalgic Encephalomyelitis/Chronic Fatigue Syndrome as a Hyper-Regulated Immune System Driven by an Interplay Between Regulatory T Cells and Chronic Human Herpesvirus Infections". Frontiers in Immunology (2019): http://dx.doi.org/10.3389/fimmu.2019.02684.
    10.3389/fimmu.2019.02684
  10. Mendes, Nuno D.; Henriques, Rui; Remy, Elisabeth; Carneiro, Jorge; Monteiro, Pedro T.; Chaouiya, Claudine. "Estimating Attractor Reachability in Asynchronous Logical Models". Frontiers in Physiology 9 (2018): http://dx.doi.org/10.3389/fphys.2018.01161.
    10.3389/fphys.2018.01161
  11. "Modular mathematical analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaV channels in sea urchin sperm". bioRxiv (2018): https://www.biorxiv.org/content/early/2018/10/18/415687.
    10.1101/415687
  12. González-Cota, A.L.; Silva, P.Â.; Carneiro, J.; Darszon, A.. "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 Letters 589 16 (2015): 2146-2154. http://www.scopus.com/inward/record.url?eid=2-s2.0-84937637227&partnerID=MN8TOARS.
    10.1016/j.febslet.2015.06.024
  13. Tarapore, D.; Lima, P.U.; Carneiro, J.; Christensen, A.L.. "To err is robotic, to tolerate immunological: Fault detection in multirobot systems". Bioinspiration and Biomimetics 10 1 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84922470045&partnerID=MN8TOARS.
    10.1088/1748-3190/10/1/016014
  14. Lopes, C.A.M.; Jana, S.C.; Cunha-Ferreira, I.; Zitouni, S.; Bento, I.; Duarte, P.; Gilberto, S.; et al. "PLK4 trans-Autoactivation Controls Centriole Biogenesis in Space". Developmental Cell 35 2 (2015): 222-235. http://www.scopus.com/inward/record.url?eid=2-s2.0-84945134296&partnerID=MN8TOARS.
    10.1016/j.devcel.2015.09.020
  15. Weber, T.S.; Jaehnert, I.; Schichor, C.; Or-Guil, M.; Carneiro, J.. "Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling". PLoS Computational Biology 10 7 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84905457962&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1003616
  16. Guerrero, A.; Espinal, J.; Wood, C.D.; Rendón, J.M.; Carneiro, J.; Martínez-Mekler, G.; Darszon, A.. "Niflumic acid disrupts marine spermatozoan chemotaxis without impairing the spatiotemporal detection of chemoattractant gradients". Journal of Cell Science 126 6 (2013): 1477-1487. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877903604&partnerID=MN8TOARS.
    10.1242/jcs.121442
  17. Trancoso, I.; Bonnet, M.; Gardner, R.; Carneiro, J.; Barreto, V.M.; Demengeot, J.; Sarmento, L.M.. "A novel quantitative fluorescent reporter assay for RAG targets and RAG activity". Frontiers in Immunology 4 MAY (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84883809486&partnerID=MN8TOARS.
    10.3389/fimmu.2013.00110
  18. Pimentel, J.A.; Carneiro, J.; Darszon, A.; Corkidi, G.. "A segmentation algorithm for automated tracking of fast swimming unlabelled cells in three dimensions". Journal of Microscopy 245 1 (2012): 72-81. http://www.scopus.com/inward/record.url?eid=2-s2.0-83055184384&partnerID=MN8TOARS.
    10.1111/j.1365-2818.2011.03545.x
  19. Tarapore, D.; Christensen, A.L.; Lima, P.U.; Carneiro, J.. "Clonal expansion without self-replicating entities". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 7597 LNCS (2012): 191-204. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866397837&partnerID=MN8TOARS.
    10.1007/978-3-642-33757-4_15
  20. Tarapore, D.; Christensen, A.L.; Lima, P.U.; Carneiro, J.. "Environment classification in multiagent systems inspired by the adaptive immune system". Artificial Life 13: Proceedings of the 13th International Conference on the Simulation and Synthesis of Living Systems, ALIFE 2012 (2012): 275-282. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874740415&partnerID=MN8TOARS.
  21. Guerrero, A.; Carneiro, J.; Pimentel, A.; Wood, C.D.; Corkidi, G.; Darszon, A.. "Strategies for locating the female gamete: The importance of measuring sperm trajectories in three spatial dimensions". Molecular Human Reproduction 17 8 (2011): 511-523. http://www.scopus.com/inward/record.url?eid=2-s2.0-80055075654&partnerID=MN8TOARS.
    10.1093/molehr/gar042
  22. Vélez de Mendizábal, N.; Carneiro, J.; Solé, R.V.; Goñi, J.; Bragard, J.; Martinez-Forero, I.; Martinez-Pasamar, S.; et al. "Modeling the effector - Regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis". BMC Systems Biology 5 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79960554264&partnerID=MN8TOARS.
    10.1186/1752-0509-5-114
  23. Serrano, M.; Real, G.; Santos, J.; Carneiro, J.; Moran Jr., C.P.; Henriques, A.O.. "A negative feedback loop that limits the ectopic activation of a cell type-specific sporulation sigma factor of bacillus subtilis". PLoS Genetics 7 9 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80053435145&partnerID=MN8TOARS.
    10.1371/journal.pgen.1002220
  24. Sepúlveda, N.; Paulino, C.D.; Carneiro, J.. "Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models". Journal of Immunological Methods 353 1-2 (2010): 124-137. http://www.scopus.com/inward/record.url?eid=2-s2.0-77649270288&partnerID=MN8TOARS.
    10.1016/j.jim.2009.11.009
  25. Guerrero, A.; Nishigaki, T.; Carneiro, J.; Yoshiro Tatsu; Wood, C.D.; Darszon, A.. "Tuning sperm chemotaxis by calcium burst timing". Developmental Biology 344 1 (2010): 52-65. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955054097&partnerID=MN8TOARS.
    10.1016/j.ydbio.2010.04.013
  26. Naldi, A.; Carneiro, J.; Chaouiya, C.; Thieffry, D.. "Diversity and plasticity of Th cell types predicted from regulatory network modelling". PLoS Computational Biology 6 9 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78049424847&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1000912
  27. Guerrero, A.; Wood, C.D.; Nishigaki, T.; Carneiro, J.; Darszon, A.. "Tuning sperm chemotaxis". Biochemical Society Transactions 38 5 (2010): 1270-1274. http://www.scopus.com/inward/record.url?eid=2-s2.0-77957278723&partnerID=MN8TOARS.
    10.1042/BST0381270
  28. Carneiro, J.; Duarte, L.; Padovan, E.. "Limiting dilution analysis of antigen-specific T cells.". Methods in molecular biology (Clifton, N.J.) 514 (2009): 95-105. http://www.scopus.com/inward/record.url?eid=2-s2.0-62449083705&partnerID=MN8TOARS.
  29. Certal, A.C.; Almeida, R.B.; Carvalho, L.M.; EricWong; Moreno, N.; Michard, E.; Carneiro, J.; et al. "Exclusion of a proton ATPase from the apical membrane is associated with cell polarity and tip growth in Nicotiana tabacum pollen tubes". Plant Cell 20 3 (2008): 614-634. http://www.scopus.com/inward/record.url?eid=2-s2.0-48249113807&partnerID=MN8TOARS.
    10.1105/tpc.106.047423
  30. Leon, K.; Garcia, K.; Carneiro, J.; Lage, A.. "How regulatory CD25+CD4+T cells impinge on tumor immunobiology: The differential response of tumors to therapies". Journal of Immunology 179 9 (2007): 5659-5668. http://www.scopus.com/inward/record.url?eid=2-s2.0-38349154060&partnerID=MN8TOARS.
    10.4049/jimmunol.179.9.5659
  31. Carneiro, J.; Leon, K.; Caramalho, Í.; Van Den Dool, C.; Gardner, R.; Oliveira, V.; Bergman, M.-L.; et al. "When three is not a crowd: A Crossregulation Model of the dynamics and repertoire selection of regulatory CD4+ T cells". Immunological Reviews 216 1 (2007): 48-68. http://www.scopus.com/inward/record.url?eid=2-s2.0-33947192440&partnerID=MN8TOARS.
    10.1111/j.1600-065X.2007.00487.x
  32. Milutinovic, D.; Carneiro, J.; Athans, M.; Lima, P.. "Modeling dynamics of cell population molecule expression distribution". Nonlinear Analysis: Hybrid Systems 1 1 (2007): 81-94. http://www.scopus.com/inward/record.url?eid=2-s2.0-36549037637&partnerID=MN8TOARS.
    10.1016/j.nahs.2006.04.003
  33. Sepúlveda, N.; Paulino, C.D.; Carneiro, J.; Penha-Gonçalves, C.. "Allelic penetrance approach as a tool to model two-locus interaction in complex binary traits". Heredity 99 2 (2007): 173-184. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547151518&partnerID=MN8TOARS.
    10.1038/sj.hdy.6800979
  34. Leon, K.; Garcia, K.; Carneiro, J.; Lage, A.. "How regulatory CD25+CD4+T cells impinge on tumor immunobiology? On the existence of two alternative dynamical classes of tumors". Journal of Theoretical Biology 247 1 (2007): 122-137. http://www.scopus.com/inward/record.url?eid=2-s2.0-34249024527&partnerID=MN8TOARS.
    10.1016/j.jtbi.2007.01.029
  35. Paixão, T.; Carvalho, T.P.; Calado, D.P.; Carneiro, J.. "Quantitative insights into stochastic monoallelic expression of cytokine genes". Immunology and Cell Biology 85 4 (2007): 315-322. http://www.scopus.com/inward/record.url?eid=2-s2.0-34249941342&partnerID=MN8TOARS.
    10.1038/sj.icb.7100057
  36. Sepúlveda, N.; Boucontet, L.; Pereira, P.; Carneiro, J.. "Stochastic Modeling of T cell receptor ¿ gene rearrangement". Journal of Theoretical Biology 234 2 (2005): 153-165. http://www.scopus.com/inward/record.url?eid=2-s2.0-14744292687&partnerID=MN8TOARS.
    10.1016/j.jtbi.2004.11.018
  37. Boucontet, L.; Sepúlveda, N.; Carneiro, J.; Pereira, P.. "Mechanisms controlling termination of V-J recombination at the TCR¿ locus: Implications for allelic and isotypic exclusion of TCR¿ chains". Journal of Immunology 174 7 (2005): 3912-3919. http://www.scopus.com/inward/record.url?eid=2-s2.0-15444362020&partnerID=MN8TOARS.
  38. Carneiro, J.; Paixão, T.; Milutinovic, D.; Sousa, J.; Leon, K.; Gardner, R.; Faro, J.. "Immunological self-tolerance: Lessons from mathematical modeling". Journal of Computational and Applied Mathematics 184 1 (2005): 77-100. http://www.scopus.com/inward/record.url?eid=2-s2.0-23344444120&partnerID=MN8TOARS.
    10.1016/j.cam.2004.10.025
  39. León, K.; Faro, J.; Carneiro, J.. "A general mathematical framework to model generation structure in a population of asynchronously dividing cells". Journal of Theoretical Biology 229 4 (2004): 455-476. http://www.scopus.com/inward/record.url?eid=2-s2.0-3042718026&partnerID=MN8TOARS.
    10.1016/j.jtbi.2004.04.011
  40. León, K.; Faro, J.; Lage, A.; Carneiro, J.. "Inverse correlation between the incidences of autoimmune disease and infection predicted by a model of T cell mediated tolerance". Journal of Autoimmunity 22 1 (2004): 31-42. http://www.scopus.com/inward/record.url?eid=2-s2.0-17044454394&partnerID=MN8TOARS.
    10.1016/j.jaut.2003.10.002
  41. León, K.; Lage, A.; Carneiro, J.. "Tolerance and immunity in a mathematical model of T-cell mediated suppression". Journal of Theoretical Biology 225 1 (2003): 107-126. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347572864&partnerID=MN8TOARS.
    10.1016/S0022-5193(03)00226-1
  42. Becker, J.D.; Boavida, L.C.; Carneiro, J.; Haury, M.; Feijó, J.A.. "Transcriptional Profiling of Arabidopsis Tissues Reveals the Unique Characteristics of the Pollen Transcriptome". Plant Physiology 133 2 (2003): 713-725. http://www.scopus.com/inward/record.url?eid=2-s2.0-0142152461&partnerID=MN8TOARS.
    10.1104/pp.103.028241
  43. Sousa, A.E.; Carneiro, J.; Meier-Schellersheim, M.; Grossman, Z.; Victorino, R.M.M.. "CD4 T cell depletion is linked directly to immune activation in the pathogenesis of HIV-1 and HIV-2 but only indirectly to the viral load". Journal of Immunology 169 6 (2002): 3400-3406. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037105617&partnerID=MN8TOARS.
    10.4049/jimmunol.169.6.3400
  44. León, K.; Peréz, R.; Lage, A.; Carneiro, J.. "Three-cell interactions in T cell-mediated suppression? A mathematical analysis of its quantitative implications". Journal of Immunology 166 9 (2001): 5356-5365. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035340973&partnerID=MN8TOARS.
    10.4049/jimmunol.166.9.5356
  45. León, K.; Peréz, R.; Lage, A.; Carneiro, J.. "Modelling T-cell-mediated suppression dependent on interactions in multicellular conjugates". Journal of Theoretical Biology 207 2 (2000): 231-254. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034700299&partnerID=MN8TOARS.
    10.1006/jtbi.2000.2169
  46. Sousa, J.; Carneiro, J.. "A mathematical analysis of TCR serial triggering and down-regulation". European Journal of Immunology 30 11 (2000): 3219-3227. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033737310&partnerID=MN8TOARS.
    10.1002/1521-4141(200011)30:11<3219::AID-IMMU3219>3.0.CO;2-7
  47. Sousa, J.; Carneiro, J.. "A mathematical analysis of TCR serial triggering and down-regulation". European Journal of Immunology 30 11 (2000): 3219-3227. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033737310&partnerID=MN8TOARS.
    10.1002/1521-4141(200011)30:11<3219::AID-IMMU3219>3.0.CO;2-7
  48. Brissac, C.; Nobrega, A.; Carneiro, J.; Stewart, J.. "Functional diversity of natural IgM". International Immunology 11 9 (1999): 1501-1507. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032870206&partnerID=MN8TOARS.
    10.1093/intimm/11.9.1501
  49. León, K.; Carneiro, J.; Peréz, R.; Montero, E.; Lage, A.. "Natural and induced tolerance in an immune network model". Journal of Theoretical Biology 193 3 (1998): 519-534. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032493615&partnerID=MN8TOARS.
    10.1006/jtbi.1998.0720
  50. Faro, J.; Carneiro, J.; Velasco, S.. "Further studies on the problem of immune network modelling". Journal of Theoretical Biology 184 4 (1997): 405-421. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031581728&partnerID=MN8TOARS.
    10.1006/jtbi.1996.0252
  51. Carneiro, J.; Coutinho, A.; Faro, J.; Stewart, J.. "A model of the immune network with B-T cell co-operation. I-Prototypical structures and dynamics". Journal of Theoretical Biology 182 4 (1996): 513-529. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030597113&partnerID=MN8TOARS.
    10.1006/jtbi.1996.0192
  52. Carneiro, J.; Coutinho, A.; Stewart, J.. "A model of the immune network with B-T cell co-operation. II - The simulation of ontogenesis". Journal of Theoretical Biology 182 4 (1996): 531-547. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030597105&partnerID=MN8TOARS.
    10.1006/jtbi.1996.0193
  53. Faro, J.; Carneiro, J.; Cohn, M.. "A commentary on Cohn's reply". Scandinavian Journal of Immunology 43 1 (1996): 6-8. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030063084&partnerID=MN8TOARS.
  54. Carneiro, J.; Coutinho, A.; Fargo, J.; Stewart, J.. "Erratum: A model of the immune network with B-T cell co-operation. I - Prototypical structures and dynamics (Journal of Theoretical Biology (1996) 182 No.4)". Journal of Theoretical Biology 183 1 (1996): http://www.scopus.com/inward/record.url?eid=2-s2.0-0029826525&partnerID=MN8TOARS.
    10.1006/jtbi.1996.0207
  55. Carneiro, J.; Stewart, J.; Coutinho, A.; Coutinho, G.. "The ontogeny of class-regulation of CD4+ T lymphocyte populations". International Immunology 7 8 (1995): 1265-1277. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029102015&partnerID=MN8TOARS.
    10.1093/intimm/7.8.1265
  56. Faro, J.; Carneiro, J.. "The two-signal model and 'self'-reactivity: Are they really incompatible?". Scandinavian Journal of Immunology 41 6 (1995): 519-522. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029035571&partnerID=MN8TOARS.
    10.1111/j.1365-3083.1995.tb03601.x
  57. Carneiro, J.; Stewart, J.. "Rethinking 'shape space': Evidence from simulated docking suggests that steric shape complementarity is not limiting for antibody-antigen recognition and idiotypic interactions". Journal of Theoretical Biology 169 4 (1994): 391-402. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028168537&partnerID=MN8TOARS.
    10.1006/jtbi.1994.1161
  58. Vilanova, M.; Ribeiro, A.; Carneiro, J.; Arala-Chaves, M.. "II. The effects of thalidomide treatment on Autoimmune-Prone NZB and MRL mice are consistent with stimulation of the central immune system". Scandinavian Journal of Immunology 40 5 (1994): 543-548. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028171418&partnerID=MN8TOARS.
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Preprint
  1. "Plk4 triggers autonomous de novo centriole biogenesis and maturation". 2020. http://dx.doi.org/10.1101/2020.04.29.068650.
    10.1101/2020.04.29.068650

Other

Other output
  1. Discrete dynamic model of the mammalian sperm acrosome reaction: the influence of acrosomal pH and biochemical heterogeneity. 2021. Andrés Aldana; Jorge Carneiro; Gustavo Martínez-Mekler; Alberto Darszon. https://doi.org/10.1101/2021.03.07.434290.
    10.1101/2021.03.07.434290
  2. Plk4 triggers autonomous de novo centriole biogenesis and maturation. 2021. Catarina Nabais; Delphine Pessoa; Jorge de-Carvalho; Thomas van Zanten; Paulo Duarte; Satyajit Mayor; Jorge Carneiro; Ivo Telley; Monica Bettencourt-Dias. https://doi.org/10.1083/jcb.202008090.
    10.1083/jcb.202008090
  3. A first-takes-all model of centriole copy number control. 2020. Marco António Dias Louro; Mónica Bettencourt-Dias; Jorge Carneiro. https://doi.org/10.1101/2020.09.23.309567.
    10.1101/2020.09.23.309567
  4. Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. 2020. Gomes, MGM; Corder, RM; King, JG; Langwig, KE; Souto-Maior, C; Carneiro, Jorge; Goncalves, G; et al. http://dx.doi.org/10.1101/2020.04.27.20081893.
    10.1101/2020.04.27.20081893
  5. Partitioning stable and unstable expression level variation in cell populations: a theoretical framework with application to the T cell receptor. 2019. Thiago S. Guzella; Vasco M. Barreto; Jorge Carneiro. https://doi.org/10.1101/527663.
    10.1101/527663
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2015/09 - 2020/07 Robust tolerance out of volatile Regulatory T cells Lessons from mathematical modelling
Supervisor
 Biologia Integrativa e Biomedicina (PhD)
Instituto Gulbenkian de Ciência, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014 - 2019/05 How to make a single product per cell ? Lessons from X chromosome inactivation and antigen receptor gene recombination
Supervisor
 Biologia Integrativa e Biomedicina (PhD)
Instituto Gulbenkian de Ciência, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2012/01 - 2017/05 Quantitative image analysis of cells using morphodynamical models: Sea urchin spermatozoa as case study
Supervisor
 Biologia (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2015 - 2016 A Stochastic Model of Centriole Assembly
Supervisor
 Bioinformatica e Biologia Computacional (Master)
Instituto Gulbenkian de Ciência, Portugal

Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2009/07 - 2013/12 Variation in Protein Expression Levels in Cell Populations
Supervisor
 Biologia Integrativa e Biomedicina (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Instituto Gulbenkian de Ciência, Portugal
2009/01 - 2013/04 Optimal Timing of Phase Resolved Cell Cycle Progression
Supervisor
Humboldt Universität zu Berlin Institute for Theoretical Biology, Germany
2010/10 - 2011/11 Supervised and unsupervised spermatozoa detection, classification and tracking in imaging data
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2005/01 - 2009/09 How is the T cell repertoire shaped?”
Supervisor
 Ciências Biomédicas
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal

Instituto Gulbenkian de Ciência, Portugal
2007/10 - 2008/10 Interaction between microorganisms and the innate and adaptive immune systems: a mathematical view
Supervisor
 Matemática Aplicada às Ciências Biológicas (Master)
Universidade de Lisboa Instituto Superior de Agronomia, Portugal
2003/04 - 2007/09 The Stochastic Basis of Somatic Variation
Supervisor
 Ciências Biomédicas (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal

Instituto Gulbenkian de Ciência, Portugal
1998/04 - 2003/12 Modeling the antigen and cytokine receptors signaling processes and their propagation to lymphocyte population dynamics
Supervisor
 Bioquímica (PhD)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
1999/04 - 2002/10 A quantitative approach to dominant tolerance
Supervisor
 Ciências Biomédicas (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal

Association member

Society Organization name Role
2003 - 2006 Portuguese Society of Immunology | Sociedade Portuguesa de Imunologia Vice-President
1998 - 2003 Portuguese Society of Immunology | Sociedade Portuguesa de Imunologia Secretary General and Scientific Secretary