Publications

Publications related to complex systems can also be found on ISC-PIF

Integrative Immunology I2D3  team publications

• Thomas-Vaslin, V., Altes, H. K., de Boer, R. J., and Klatzmann, D. (2008). Comprehensive assessment and mathematical modeling of T cell population dynamics and homeostasis. J Immunol 180, 2240-2250.
• Boudinot, P., Marriotti-Ferrandiz, M. E., Pasquier, L. D., Benmansour, A., Cazenave, P. A. & Six, A. New perspectives for large-scale repertoire analysis of immune receptors. Mol. Immunol. 45, 2437-2445 (2008).
• Lavelle, C., H. Berry, G. Beslon, F. Ginelli, J. Giavitto, Z. Kapoula, A. Le Bivic, N. Peyrieras, O. Radulescu, A. Six, V. Thomas-Vaslin and P. Bourgine (2008). “From molecules to organisms: towards multiscale integrated models of biological systems.” Theoretical Biology Insights 1: 13-22.
•  C. H. McEwan, H. Bersini, D. Klatzmann, V. Thomas-Vaslin, A. Six. A computational technique to scale mathematical models towards complex heterogeneous systems (2011), COSMOS 2011 Conference Proceeding of the 2011workshop on complex systems modeling and simulation Luniver press. IBSN 978-1-905986-32-3
•   C. H. McEwan, H. Bersini, D. Klatzmann, V. Thomas-Vaslin, A. Six. A Refitting Harel statecharts for systemic mathematical models in computational immunology (2011) 10th International Conference on Artificial Immune Systems (ICARIS) Pietro Lió, Giuseppe Nicosia and Thomas Stibor ed.
• Thomas-Vaslin, V., A. Six, H. P. Pham, C. Dansokho, W. Chaara, B. Gouritin, B. Bellier and D. Klatzmann (2011). Immunodepression & Immunosuppression in aging mice Immunosuppression. M. B. Portela. Brazil, InTech open acces publisher.
• Saadoun, D., M. Rosenzwajg, F. Joly, A. Six, F. Carrat, V. Thibault, D. Sene, P. Cacoub and D. Klatzmann “Regulatory T-cell responses to low-dose interleukin-2 in HCV-induced vasculitis.”(2011) N Engl J Med 365(22): 2067-77.
• Blazewicz, J., M. Borowski, W. Chaara, P. Kedziora, D. Klatzmann, P. Lukasiak, A. Six, P. Wojciechowski. GeVaDSs – decision support system for novel Genetic Vaccine development process. BMC Bioinform. 13, 91 (2012).
• Pham, H.P., M. Manuel, N. Petit, D. Klatzmann, S. Cohen-Kaminsky, A. Six, G. Marodon. Half of the T-cell repertoire combinatorial diversity is genetically determined in humans and humanized mice. Eur. J. Immunol. 42, 760-770 (2012).
• Terrier, B., G. Geri, W. Chaara, Y. Allenbach, M. Rosenzwajg, N. Costedoat-Chalumeau, P. Fourret, L. Musset, O. Benveniste, A. Six, D. Klatzmann, D. Saadoun and P. Cacoub. Interleukin-21 modulates Th1 and Th17 responses in Giant Cell Arteritis. Arth. & Rheum. 64, 2001-2011 (2012).
• Silva, H.M., M.C.S. Takenanka, P.M.M. Moraes-Vieira, S.M. Monteiro, M.O. Hernandez, W. Chaara, A. Six, F. Agena, P. Sesterheim, F.M. Barbé-Tuana, D. Saitovitch, F. Lemos, J. Kalil and V. Coelho (2012) Preserving the B cell compartment favors operational tolerance in human renal transplantation. Mol. Med. In press (DOI: 10.2119/molmed.2011.00281).
• Pham, H.P., N. Dérian, W. Chaara, B. Bellier, D. Klatzmann and A. Six. A novel strategy for molecular signature discovery based on independent component analysis. Int. J. Data Mining Bioinform. In press.
• Adrien Six, Bertrand Bellier, Véronique Thomas-Vaslin and David Klatzmann. Systems Biology in Vaccine Design. Microb Biotechnol. 2012, 5:295-304.
• Bersini H., D. Klatzmann, A. Six, V. Thomas-Vaslin. State-Transition Diagrams for Biologists. PLoS ONE. 2012, 7:e41165
• Bellier, B., A. Six, V. Thomas-Vaslin and D. Klatzmann (2013). Systems Immunology, Novel Evaluation of Vaccine. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 2089-2092 http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_107
  • Bellier, B., A. Six, V. Thomas-Vaslin and D. Klatzmann (2013). Immunomonitoring. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1003-1003 http://dx.doi.org/10.1007/978-1-4419-9863-7_716
  • Bellier, B., A. Six, V. Thomas-Vaslin and D. Klatzmann (2013). Vaccinomics. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 2335-2336 http://dx.doi.org/10.1007/978-1-4419-9863-7_718
  • Bellier, B., A. Six, V. Thomas-Vaslin and D. Klatzmann (2013). Reverse Vaccinology. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1856-1856 http://dx.doi.org/10.1007/978-1-4419-9863-7_717
• Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Lymphocyte Dynamics and Repertoires, Biological Methods. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1145-1149 http://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-9863-7_95
• Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Lymphocytes dynamics repertoires, modeling. Encyclopedia of Systems Biology. W. O. Dubitzky W, Springer, Heidelberg NewYork. http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_96
  •  Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Organism State, Lymphocyte. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1611-1612 http://dx.doi.org/10.1007/978-1-4419-9863-7_710
  • Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Lymphocyte Labeling, Cell Division Investigation. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1152-1154 http://dx.doi.org/10.1007/978-1-4419-9863-7_708
  • Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Life Span, Turnover, Residence Time. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1125-1126 http://dx.doi.org/10.1007/978-1-4419-9863-7_712
  • Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Modeling, Cell Division and Proliferation. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1430-1434 http://dx.doi.org/10.1007/978-1-4419-9863-7_714
  • Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Lymphocyte Population Kinetics. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1154-1155 http://dx.doi.org/10.1007/978-1-4419-9863-7_713
  • Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Quantifying Lymphocyte Division, Methods. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1804-1806 http://dx.doi.org/10.1007/978-1-4419-9863-7_711
  • Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Modeling Formalisms, Lymphocyte Dynamics and Repertoires. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 1429-1430 http://dx.doi.org/10.1007/978-1-4419-9863-7_715
  • Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Immune Repertoire Diversity. Encyclopedia of Systems Biology. W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota, Springer New York: 996-997 http://dx.doi.org/10.1007/978-1-4419-9863-7_709

  * Abi Haidar, A., A. Six, et al. (2013). The Artificial Immune Systems Domain: Identifying Progress and Main Contributors Using Publication and Co-Authorship Analyses. Advances in Artificial Life, ECAL. 12: 1206–1217 %U http://mitpress.mit.edu/sites/default/files/titles/content/ecal1213/ch1185.html.
  * Thomas-Vaslin, V., A. Six, J. G. Ganascia and H. Bersini (2013). “Dynamical and mechanistic reconstructive approaches of T lymphocyte dynamics:Using visual modelling languages to bridge the gap between immunologists, theoreticians and programmers.” Frontiers in Immunology http://www.frontiersin.org/Journal/Abstract.aspx?s=1177&name=t_cell_biology&ART_DOI=10.3389/fimmu.2013.00300

• Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham H-P, Lefranc M-P, Mora T, Thomas-Vaslin V, Walczak AM and Boudinot P (2013) The past, present, and future of immune repertoire biology – the rise of next-generation repertoire analysis. Front. Immunol. 4:413. doi: 10.3389/fimmu.2013.00413  http://www.frontiersin.org/t_cell_biology/10.3389/fimmu.2013.00413/abstract
• THOMAS-VASLIN, V. (2014). “A complex immunological idiotypic network for maintenance of tolerance.” Frontiers in Immunology 5.http://journal.frontiersin.org/Journal/10.3389/fimmu.2014.00369/full
• Thomas-Vaslin, V. (2014). Evaluation de la résilience et des perturbations des systèmes complexes. La lettre de l’inSHS du CNRS. Paris, CNRS. http://www.cnrs.fr/inshs/Lettres-information-INSHS/lettre_infoinshs_32hd.pdf
• Rémondet, M., F. Jacquemart, Thomas-Vaslin, L. Coutellec, J. Blondel, N. Bouleau, P. Gaudray, C. Larrère and A. F. Schmid (2014). Pour une évaluation globale des OGM : Des perspectives épistémologiques renouvelées pour l’analyse des risques programme « EvaGlo » dans le cadre du programme « RiskOgm » (rapport complet), Ministère de l’écologie et du développement durable, https://hal.archives-ouvertes.fr/hal-01300736.
• Thomas-Vaslin, V. (2015) Complexité multi-échelle du système immunitaire: Evolution, du chaos aux fractales. Le vivant critique et chaotique. E. matériologiques . http://www.materiologiques.com/Le-vivant-critique-et-chaotique
• THOMAS-VASLIN, V. (2015). Understanding and modeling the complexity of the immune system. First Complex Systems Digital Campus World E-Conference 2015, Tempe, United States, Springer.https://hal.archives-ouvertes.fr/hal-01291113/documentvideo : http://cs-dc-15.org/papers/organisms/cognitive-immune-sys/understanding-and-modelling-the-complexity-of-the-immune-system/
• Jacquemart, F. and V. Thomas-Vaslin (2016). “L’évaluation globale des technologies.” La Fièvre de l’évaluation 196. http://www.septentrion.com/fr/livre/?GCOI=27574100998460
  https://hal.archives-ouvertes.fr/hal-01291113/document
• Jacquemart, F., V. Thomas-Vaslin and L. Coutellec (2016). Pour une évaluation globale des OGM : Des perspectives épistémologiques renouvelées pour l’analyse des risques http://www.rechercheriskogm.fr/fr/page/evaglo
• THOMAS-VASLIN, V. (2016). Contribution à une évaluation globale des systèmes complexes et des perturbations: l’exemple du système immunitaire- site APR RIskOGM 2010 projet Evaglo Contribution à une évaluation globale des OGM : des perspectives épistémologiques renouvelées pour l’analyse des risques. http://www.rechercheriskogm.fr/fr/page/evaglo#contributions
• Thomas-Vaslin, V., & Jacquemart, F. (2016). Approche de la résilience et perturbations des systèmes complexes par une évaluation globale. Congrès mondial pour la pensée complexe: Les défis d’un monde globaliséreseau-canope.fr/congres-mondial-pour-la-pensee-complexe/pensee-complexe.html#bandeauPtf. https://www.reseau-canope.fr/fileadmin/user_upload/Projets/pensee_complexe/thomas_vaslin_jacquemart_approche_resilience_perturbations_systemes_complexes.pdf https://hal.archives-ouvertes.fr/hal-01427233
• Thomas-Vaslin, V. (2017). Questionnements et connaissance de la complexité.  p 251-256. In Editions Matériologiques Qu’est ce que la science… pour vous? Textes rassemblés par Marc Silberstein. Paris. ISBN 78-2-37361-107-6 http://materiologiques.com/sciences-philosophie-2275-9948/244-qu-est-ce-que-la-science-pour-vous–9782373611076.html    . hal-01499478, v1
• Vibert, J. and V. Thomas-Vaslin (2017). “Modelling T Cell Proliferation: Dynamics Heterogeneity, Depending on Cell Differentiation, Age, and Genetic Background.” PLos Comput Biol 13 (3): e1005417. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.10054

https://iscpif.fr/2017/03/plos-modelling-t-cell-proliferation-dynamics-heterogeneity-depending-on-cell-differentiation-age-and-genetic-background/

• Thomas-Vaslin, V. (2017). Le rôle des traces dans le système immunitaire : des anticorps au corps (B. Galinon-Mélénec Ed. Paris CNRS éditions ed. Vol. 4).HAL Id: hal-01565303 https://hal.archives-ouvertes.fr/hal-01565303

https://iscpif.fr/2017/08/lhomme-trace-des-traces-du-corps-au-corps-trace/

• Thomas-Vaslin, V. (2020). “Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes.” Acta Biotheor Volume 68 (Issue 1, March 2020 Special Issue: Proceedings of the XXXVIIIth Seminar of the French‑Speaking Society for Theoretical Biology; Saint‑Flour (Cantal), France, 11–13 June, 2018): 171-199.read the paper in Acta Biotheoretica 2019Individuation and the organization in complex living ecosystem: recursive integration and self-assertion by holon-lymphocytes.pdf
• Pastor, D., Beurier, E., & Thomas-Vaslin, V. (2022). A multiplicity of statistical models for modeling the degeneracy of living communicating holons. EPJ Web of Conferences, 263(8th Complexity-Disorder Days 2021), 010006. doi:https://doi.org/10.1051/epjconf/202226301006

Participation to roadmap and related publications

Feuille de route 2017

https://roadmap.iscpif.fr/2017/06/19/complexity-of-the-immune-system/

https://iscpif.fr/2017/07/compte-rendu-feuille-de-route/

Cargese Roadmaps 2008
•    ASSYST Science of Complex Systems Roadmap Workshop, 28th January 2010
•    Lavelle, C., H. Berry, G. Beslon, F. Ginelli, J. Giavitto, Z. Kapoula, A. Le Bivic, N. Peyrieras, O. Radulescu, A. Six, V. Thomas-Vaslin and P. Bourgine (2008). “From molecules to organisms: towards multiscale integrated models of biological systems.” Theoretical Biology Insights 1: 13-22.

Data repository
SIDR : Standards-based Infrastructure with Distributed Resources- Data Repository for multi-assay studies (CNRS-INIST) project leader M. Roux

T cell dynamics and aging

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