{"id":83,"date":"2023-09-05T16:29:10","date_gmt":"2023-09-05T14:29:10","guid":{"rendered":"https:\/\/project.inria.fr\/gdtmathbio\/?page_id=83"},"modified":"2026-10-20T13:59:30","modified_gmt":"2026-10-20T11:59:30","slug":"journees-communes","status":"publish","type":"page","link":"https:\/\/project.inria.fr\/gdtmathbio\/journees-communes\/","title":{"rendered":"Journ\u00e9es communes"},"content":{"rendered":"<p><big style=\"font-family: Cambria;\"><big style=\"font-weight: bold;\">Journ\u00e9e 1 : mercredi 21 octobre 2026 \u00e0 Marseille 10h30-16h, Campus Saint-Charles.<\/big><br \/>\nFRUMAM building (<a href=\"https:\/\/osm.org\/go\/xVvjHyxQP?layers=N&#038;m=\">here<\/a>) in the 2nd floor lecture room.<br \/>\n<!--Inscription avant le 2 octobre : <a href=\"https:\/\/evento.renater.fr\/survey\/registration-for-the-workshop-modelisation-du-vivant-e6y4tryi\"> https:\/\/evento.renater.fr\/survey\/registration-for-the-workshop-modelisation-du-vivant-e6y4tryi<\/a>.<\/big>\n--><br \/>\n<strong> Orateurs confirm\u00e9s : <\/strong><\/p>\n<ul>\n<li>Pete Czuppon (I2M)<\/li>\n<li>Giada Fiandaca (INRIA &#8211; COMPO)<\/li>\n<li>Oksana Grente (BioSP &#8211; INRAE)<\/li>\n<li>Baptiste Oger (BioSP &#8211; INRAE)<\/li>\n<\/ul>\n<p><strong>Organisation de la journ\u00e9e : <\/strong><\/p>\n<ul>\n<li>10h : accueil caf\u00e9<\/li>\n<li>10h30 &#8211; 11h30 : Giada Fiandaca<\/li>\n<\/ul>\n<p>Title: Towards a Mechanistic Understanding of Tumour Phenotypic Heterogeneity Across Scales<\/p>\n<p>Abstract: Tumour phenotypic heterogeneity is a major contributor to treatment failure and disease recurrence. It manifests across biological scales, from differences in cellular states and responses within clonal populations to changes in population composition driven by cellular plasticity and reciprocal interactions with the microenvironment. Continuous phenotype-structured population models offer a framework for describing this diversity, but phenotypic states and transitions often remain phenomenological. Recent advances in single-cell transcriptomics and live-cell imaging provide complementary molecular and dynamical data, opening opportunities to ground these descriptions in intracellular regulation.mIn this talk, I will present two ongoing projects that motivate this research direction. The first investigates heterogeneous responses to TRAIL, a signalling protein that can trigger programmed cell death, in clonal cancer cell populations. Combining longitudinal single-cell measurements with mechanistic modelling of apoptotic signalling allows us to reconstruct a continuous intracellular landscape of sensitivity and tolerance. This provides a basis for investigating reversible tolerance and the recovery of sensitivity at the population level, and their interplay with spatial organisation during tumour spheroid growth. The second investigates plasticity between proliferative and quiescent states in patient-derived rhabdomyosarcoma organoids, where quiescent cells can evade chemotherapy and later re-enter the cell cycle. By combining mechanistic population modelling with mechanistic gene regulatory network inference from time-resolved single-cell transcriptomic data, we investigate the regulation of plasticity, with the aim of identifying potential targets to impair plasticity-mediated resistance. Alongside their biological aims, these projects motivate the longer-term objective of developing continuous phenotype-structured population models grounded in intracellular regulation. I will discuss the methodological challenges involved in pursuing this objective and possible approaches to address them.<\/p>\n<ul>\n<li>11h30 &#8211; 12h30 : Baptiste Oger<\/li>\n<\/ul>\n<p>Title: Predicting sugar beet yellows severity and large-scale disease spread from coupled field observations and remote sensing data<\/p>\n<p>Abstract: Beet yellows disease is currently a major threat to sugar beet production in Europe, following recent restrictions on neonicotinoids. Caused by four different viruses, the disease leads to leaf yellowing, reduced photosynthesis, and substantial yield losses. Monitoring its spatial and temporal dynamics remains challenging, as traditional field observations are sparse and costly. In this context, multispectral satellite imagery offers new opportunities to monitor disease severity across multiple spatial scales.<br \/>\nThis presentation introduces a two-step approach. First, a statistical framework based on random forests is used to predict beet yellows severity at the field scale from remote sensing data and field observations. Second, a semi-parametric spatio-temporal model is introduced to analyse epidemic dynamics at larger spatial and temporal scales. The proposed approaches are compared with reference methods to assess their predictive performance and ability to capture disease dynamics.<br \/>\nOverall, this work highlights the potential of combining remote sensing and field observations with flexible statistical models for monitoring plant epidemics.<\/p>\n<ul>\n<li>12h30 &#8211; 14h : D\u00e9jeuner<\/li>\n<li>14h &#8211; 15h : Peter Czuppon<\/li>\n<\/ul>\n<p>Title: Stochastic models of transposable element dynamics<\/p>\n<p>Abstract:<br \/>\nTransposable elements (TEs) are self-replicating genetic sequences that populate genomes. Their dynamics within a genome are governed by transposition events, where new TE copies are generated, and excision events, which remove TE copies. Moreover, TEs can have deleterious effects on the host, e.g. by inserting into coding genes. This can create negative effects for the host, resulting in TE numbers being counterselected on the population level. In this talk, I will talk about two models to describe TE dynamics. First, we study the mean and variance dynamics arising from individual-based descriptions. We extend the model from [1] to show that TE copy numbers are naturally overdispersed, i.e., the variance TE copy number is larger than the mean in a population and compare these results to data. In a second model, we investigate the interaction of autonomous and nonautonomous TEs, where the latter relies on the former for transposition, similar to a host-parasite system. We describe the stationary copy number distribution of the two TE types in a population.<\/p>\n<p>[1] Pfaffelhuber &amp; Wakolbinger, A diploid population model for copy number variation of genetic elements, Electronic Journal of Probability, 28:1-15, 2023<\/p>\n<ul>\n<li>15h &#8211; 16h : Oksana Grente<\/li>\n<\/ul>\n<p>Title: Modelling the effects of lethal control on wolf recolonization dynamics in France<\/p>\n<p>Abstract: The return of wolves to France since the 1990s has led to the resurgence of livestock attacks, particularly on sheep. To prevent livestock losses, the French government has authorized the lethal control of wolves for the past fifteen years. The intensity of this management measure has increased over the past seven years. Here, we aim to model the effects of lethal control on wolf recolonization dynamics in France. Does lethal control accelerate or slow down wolf recolonization? To address this question, we are developing a dynamic multi-state occupancy model using Bayesian inference. We will show the first results of this work in progress. We will discuss the main challenges associated with this modelling approach, including modelling a distribution that is not in an ecological equilibrium and accounting for reciprocal causation between lethal control and wolf presence.<\/p>\n<p>&nbsp;<\/p>\n<p><!--\n<big style=\"font-family: Cambria;\"><big style=\"font-weight: bold;\">Journ\u00e9e 3 \u00e0 Grenoble le 1 juin 2026 (10h -16h) <\/big>\n\n\n<ul>\n \t\n\n<li> Lieu : <strong>\/!\\ Changement de salle \/!\\ Institut Fourier, salle 4 le matin et amphi Chabauty l'apr\u00e8s-midi<\/strong><\/li>\n\n\n \t\n\n<li> Inscription : <a href=\"https:\/\/beta.framadate.org\/polls\/3455d2b7b01d7c8c9286\">https:\/\/beta.framadate.org\/polls\/3455d2b7b01d7c8c9286<\/a><\/li>\n\n\n \t\n\n<li> Programme :\n\n\n<ul>\n \t\n\n<li> 9h45 : Accueil<\/li>\n\n\n \t\n\n<li> 10h - 11h : <strong>Chlo\u00eb Mian <\/strong> (Institut Fourier, Grenoble), <em>Dynamique de deux esp\u00e8ces avec des interactions densit\u00e9-d\u00e9pendantes dans un contexte mutualiste<\/em>\n\n\n<p class=\"has-medium-font-size\">R\u00e9sum\u00e9 : Les interactions mutualistes sont tr\u00e8s r\u00e9pandues dans les \u00e9cosyst\u00e8mes et peuvent \u00e9voluer vers le parasitisme en fonction de la densit\u00e9 des esp\u00e8ces. Nous d\u00e9veloppons un mod\u00e8le d\u00e9terministe g\u00e9n\u00e9ral d\u00e9crivant deux populations en interaction qui int\u00e8gre \u00e0 la fois les co\u00fbts et les avantages du mutualisme par le biais d\u2019effets d\u00e9pendants de la densit\u00e9. En utilisant simplement des \u00e9quations diff\u00e9rentielles ordinaires et l\u2019analyse des portraits de phase, nous identifions les conditions g\u00e9n\u00e9rales conduisant \u00e0 diff\u00e9rents comportements dynamiques. En particulier, nous montrons que des cycles limites peuvent appara\u00eetre lorsque les interactions comportent des phases parasitaires, alors qu'ils sont absents dans les r\u00e9gimes strictement mutualistes. Ce cadre fournit une approche g\u00e9n\u00e9rale pour caract\u00e9riser la dynamique des populations d'esp\u00e8ces en interaction et met en \u00e9vidence l'effet des transitions du mutualisme vers le parasitisme dues \u00e0 la d\u00e9pendance \u00e0 la densit\u00e9.<\/p>\n\n\n<\/li>\n\n\n \t\n\n<li> 11h15 - 12h15 : <strong>Rebecca Tyson (University of British Columbia, Canada)<\/strong>, <em>Basculement sensible \u00e0 la phase dans les \u00e9cosyst\u00e8mes : Un nouveau m\u00e9canisme d'extinction<\/em>\n\n\n<p class=\"has-medium-font-size\">R\u00e9sum\u00e9 : Les syst\u00e8mes cycliques peuvent pr\u00e9senter des comportements tr\u00e8s inattendus lorsqu'ils sont soumis \u00e0 des for\u00e7ages externes. De nombreux syst\u00e8mes consommateur-ressource sont intrins\u00e8quement cycliques et soumis \u00e0 des for\u00e7ages climatiques qui peuvent \u00e9galement \u00eatre domin\u00e9s par certaines fr\u00e9quences. Dans ce projet de recherche, nous nous demandons si les changements pr\u00e9dits de la couleur et de la fr\u00e9quence du bruit environnemental pourraient mettre en p\u00e9ril les syst\u00e8mes cycliques consommateur-ressource. Nous \u00e9tudions cette question en analysant un mod\u00e8le pr\u00e9dateur-proie continu et un mod\u00e8le h\u00f4te-parasito\u00efde discret, tous deux int\u00e9grant un effet Allee, sous l'effet de for\u00e7ages climatiques mod\u00e9lis\u00e9s par des variations de la productivit\u00e9 des proies ou des h\u00f4tes.\nNotre analyse de ces mod\u00e8les r\u00e9v\u00e8le un comportement contre-intuitif, que nous appelons basculement de phase ou basculement de type P (P-tipping). Ce basculement se produit m\u00eame si le cycle consommateur-ressource existe et est stable pour toutes les valeurs des param\u00e8tres climatiques. Nous \u00e9tudions les m\u00e9canismes \u00e0 l'origine du basculement de type P et les similitudes et diff\u00e9rences entre les syst\u00e8mes continus et discrets. Nous examinons \u00e9galement la probabilit\u00e9 de ce basculement en fonction des projections de la stochasticit\u00e9 climatique.<\/p>\n\n\n<\/li>\n\n\n \t\n\n<li> 12h15 - 13h45 : Buffet (caf\u00e9t\u00e9ria de l'Institut Fourier)\n \t\n\n<li> 13h45 - 14h45 :  <strong>Vivien Lecomte<\/strong> (LiPhy, Grenoble), <em>Mapping thermodynamically feasible metabolic states<\/em>\n\n\n<p class=\"has-medium-font-size\"> R\u00e9sum\u00e9 : Thermodynamically, living cells are open systems, driven out of equilibrium by input fluxes (resources) and output fluxes (products, work, waste). A central question of systems biology is to understand the possible internal states of a cell from the knowledge of input\/output fluxes and other biological bounds. Chemical reaction networks (CRNs) are now widely known for many cells and offer a quantitative framework to tackle it. A Physicist\u2019s take of the problem consists in mapping the allowed values of internal reaction currents given the known constraints. At stationarity, the relation between internal reaction currents and external ones would be purely affine if it were not for an essential feature of biological CRNs: inside a cell, conservation of energy implies that reaction rates must satisfy detailed balance. The corresponding constraint on currents, named thermodynamic feasibility, renders the internal\/external currents' interdependency non-linear. In this work, we fully characterize the space of thermodynamically feasible currents by showing that they constitute the bounded chambers of a well-defined hyperplane arrangement. To achieve this, we make use of \u00abgeometric\u00bb concepts of (hyper)graph theory (such as cycles and cocycles), that generalize the notion of Kirchoff law(s) to CRNs.\nJoint work with Sara Dal Cengio and Delphine Ropers<\/p>\n\n\n<\/li>\n\n\n \t\n\n<li> 15h - 16h : <strong>Lena Kuwata<\/strong> (Inria Grenoble), <em>Mod\u00e9lisation de la croissance d'un champignon filamenteux<\/em>\n\n\n<p class=\"has-medium-font-size\">R\u00e9sum\u00e9 : Les champignons filamenteux jouent un r\u00f4le crucial dans le fonctionnement de nombreux \u00e9cosyst\u00e8mes. Ils sont constitu\u00e9s de filaments interconnect\u00e9s qui croissent et branchent pour former un r\u00e9seau, appel\u00e9 myc\u00e9lium. On mod\u00e9lise la croissance du r\u00e9seau myc\u00e9lien par un processus de naissance et de mort spatial dans lequel chaque filament est repr\u00e9sent\u00e9 par la position de son extr\u00e9mit\u00e9, dont la trajectoire est solution d\u2019une \u00e9quation diff\u00e9rentielle stochastique avec un terme de d\u00e9rive d\u00e9pendant de toutes les autres trajectoires. Le branchement peut s\u2019effectuer soit au niveau de l\u2019extr\u00e9mit\u00e9 soit le long d\u2019un filament \u00e0 des taux d\u00e9pendant de la position du point de branchement, et les filaments peuvent s\u2019arr\u00eater de cro\u00eetre \u00e0 un taux d\u00e9pendant en outre de la position des autres extr\u00e9mit\u00e9s. On \u00e9tudie la limite en grande population de ce processus et on caract\u00e9rise le processus limite comme la solution faible d\u2019une certaine \u00e9quation aux d\u00e9riv\u00e9es partielles.<\/p>\n\n\n<\/li>\n\n\n<\/ul>\n\n\n<\/li>\n\n\n<\/ul>\n\n\nJourn\u00e9e soutenue par Inria.--><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Journ\u00e9e 1 : mercredi 21 octobre 2026 \u00e0 Marseille 10h30-16h, Campus Saint-Charles. FRUMAM building (here) in the 2nd floor lecture room. Orateurs confirm\u00e9s : Pete Czuppon (I2M) Giada Fiandaca (INRIA &#8211; COMPO) Oksana Grente (BioSP &#8211; INRAE) Baptiste Oger (BioSP &#8211; INRAE) Organisation de la journ\u00e9e : 10h : accueil\u2026<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/project.inria.fr\/gdtmathbio\/journees-communes\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":2367,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_members_access_role":[],"_members_access_error":""},"class_list":["post-83","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages\/83","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/users\/2367"}],"replies":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/comments?post=83"}],"version-history":[{"count":142,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages\/83\/revisions"}],"predecessor-version":[{"id":680,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages\/83\/revisions\/680"}],"wp:attachment":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/media?parent=83"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}