Post-Doctoral Research Visit F/M Post-Doctoral Position in computational biology and biomechanics

_Le descriptif de l’offre ci-dessous est en Anglais_ TYPE DE CONTRAT : CDD NIVEAU DE DIPLÔME EXIGÉ : Thèse ou équivalent FONCTION : Post-Doctorant CORPS D'ACCUEIL : Ingénieur de Recherche (IR) A PROPOS DU CENTRE OU DE LA DIRECTION FONCTIONNELLE Grenoble Rhône-Alpes Research Center groups together a few less than 650 people in 35 research teams and 8 research support departments. Staff is localized on 5 campuses in Grenoble and Lyon, in close collaboration with labs, research and higher education institutions in Grenoble and Lyon, but also with the economic players in these areas. Present in the fields of software, high-performance computing, Internet of things, image and data, but also simulation in oceanography and biology, it participates at the best level of international scientific achievements and collaborations in both Europe and the rest of the world. CONTEXTE ET ATOUTS DU POSTE Do we understand embryonic development? In 1994, the famous embryologist Lewis Wolpert wondered “WILL THE EGG BE COMPUTABLE?“ Can we today combine numerical models that embody the fundamental physical and chemical principles governing cell function with quantitative descriptions of the biochemical and spatio-temporal features of the system? Generic multiscale modelling frameworks are starting to link gene expression to morphogenesis [Delile 2017, Marin-Riera 2016], but the connection between these frameworks and accurate natural observations remains a major bottleneck, which severely impairs the parametrization of the models. In addition, in spite of spectacular improvements, OBSERVATIONS STILL CONTAIN EXPERIMENTAL ERRORS AND ONLY SAMPLE PART OF THE DEVELOPMENTAL PROGRAM “SPACE”: their temporal resolution is limited, the studied individuals incompletely represent natural diversity and many parameters remain impossible to measure. The objective of this project is to develop an INTEGRATED MODELING PLATFORM USING MULTI-SCALE DATA ASSIMILATION to overcome the challenges of morphogenesis modeling which integrates the molecular and genetic interaction networks with the cellular dynamics and tissue mechanics. This platform will contribute to a better understanding of the relative contributions of genetic and stochastic processes within cellular morphological processes [Little 2011]. This approach by data assimilation needs to integrate large amounts of multi-scale data describing the particularly simple and reproducible ascidian embryogenesis, from genome sequence to the dynamics of individual cell shapes. * The genetic program has been studied for the past 20 years, and the results are represented in the ANISEED world-wide ascidian model organism database, developed by the Lemaire team. * The morphogenetic program of multiple individual live embryos, observed with subcellular resolution with lightsheet microscopy, followed by image segmentation, which we have pioneered [Faure 2016, Guignard 2020]. * The experimental or computational inference of the cellular forces that drive morphogenesis, which we are describing in collaboration with the Asnacios (U. Paris, France), Mani (Northwestern U., USA) and Munro (U. Chicago, USA) teams. MISSION CONFIÉE The post-doc will be based at LIRMM (Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier) and will directly work under the supervision of E. Faure, with frequent interactions with the neighboring experimental and computational scientists of the Lemaire team. Both teams are well funded and have the required experimental and computational means to support the project. The recruited scientist is expected to also establish strong interactions with our national and international collaborators. The University of Montpellier has a vibrant interdisciplinary academic community. This recruitment is supported by the iSite Montpellier University of Excellence. PRINCIPALES ACTIVITÉS Faure Team : https://www.lirmm.fr/~efaure/, Lemaire Team : https://www.crbm.cnrs.fr/team/lemaire/?lang=en, LIRMM : https://www.lirmm.fr , CRBM : https://www.crbm.cnrs.fr, MorphoNet : https://morphonet.org, Aniseed : https://www.aniseed.cnrs.fr, MUSE : https://muse.edu.umontpellier.fr/en/muse-i-site, Montpellier City : https://www.montpellier.fr CONTACT: Please send CV, a motivation letter and two letters of recommendation to Dr. Emmanuel Faure (emmanuel.faure@lirmm.fr ) and Dr. Patrick Lemaire ( patrick.lemaire@crbm.cnrs.fr ). REFERENCES : * L. Wolpert, (1994). _Do we understand development? _Science. 266, 571–572 * J. R. Karr et al (2012). A _Whole-Cell Computational Model Predicts Phenotype from Genotype_. Cell. 150, 389–401 * J. Delile, M. Herrmann, N. Peyriéras, R. Doursat, (2017). _A cell-based computational model of early __embryogenesis coupling mechanical behaviour and gene regulation. _Nature Communications. 8, 13929 * Little S.C. & Wieschaus E.F. (2011) _Shifting patterns: merging molecules, morphogens, motility, and __methodology_. Developmental cell, 21(1):2-4. * M. Marin-Riera, et al (2016). _Computational modeling of development by epithelia, mesenchyme and their __interactions: a unified model. _Bioinformatics. 32, 219–225 * Guignard L. Fiúza UM et al (2020). _Contact Area-Dependent Cell Communication and the Morphological __Invariance of Ascidian Embryogenesis_. Science July 2020. * Faure, E., Savy, T., Rizzi, B. et al. (2016)_. A workflow to process 3D+time microscopy images of developing __organisms and reconstruct their cell lineage_. Nat Commun 7, 8674 (2016). * Leggio, B., Laussu, J., Carlier, A. et al. (2019). _MorphoNet: an interactive online morphological browser to __explore complex multi-scale data_. Nat Commun 10, 2812 * Leggio et al (2020) _Multiscale mechanical model for cell division orientation in developing biological __systems. _bioRxiv 785337; doi: 10.1101/785337 COMPÉTENCES Motivation to apply this knowledge to biology is required. Prior experience with biological data analysis. The candidates should have a PhD, or equivalent, with an excellent track record of achievement and less than 5 years of post-doctoral experience.. AVANTAGES According to the employer's benefits RÉMUNÉRATION According to the employer's salary scale : LIRMM UMR 5506