Statistical Modeling and Estimation of Molecule Diffusion in Fluorescence Microscopy

_Le descriptif de l’offre ci-dessous est en Anglais_

**Type de contrat**: CDD

**Contrat renouvelable**: Oui

**Niveau de diplôme exigé**: Thèse ou équivalent

**Fonction**: Chercheur contractuel

**Niveau d'expérience souhaité**: De 5 à 12 ans

**Contexte et atouts du poste**:
Understanding the molecular interactions and intracellular transport mechanisms in space and time is central in fundamental cell biology to characterize cellular functions, and crucial to the treatment and cure of human disease. In that context, it is of primary interest for biologists to be able to visualize and estimate molecular mobility within the cell.

To address this issue, we have developed a novel Eulerian method inspired from previous works [1, 2 ,3, 4] that allows to estimate the diffusion and drift parameters attached to moving biomolecules within cells from 2D/3D individual trajectories. In the first step, the method estimates both drift and diffusion in local neighborhoods centered on trajectory points. The local spatiotemporal kernel estimators correspond to weighted averages of the trajectory elements. Unlike existing methods, the estimation of two or three-dimensional drift vector and the diffusion coefficient are performed on trajectory-sliding kernels, calculated at coordinates corresponding exactly to the coordinates given by the preliminary particle tracking. In the second step, each particle track point is labeled into three motion categories: confined motion (subdiffusion), Brownian motion (free diffusion), and directed motion (superdiffusion). The method is currently tested in several biological studies such as dynamics of transcription factors in the nucleus, MReB proteins in bacteria walls.

**Bibliography**
- BRIANE, M. VIMOND, C. KERVRANN. An overview of diffusion models for intracellular dynamics analysis, Briefings in Bioinformatics 21, 4, July 2020, p. 1136-1150, [doi:10.1093/bib/bbz052], [hal:hal-02424761].
- BRIANE, C. KERVRANN, M. VIMOND. Statistical analysis of particle trajectories in living cells, Physical Review E 97, 6, June 2018, p. 1-20, [doi:10.1103/PhysRevE.97.062121], [hal:hal-01961971].
- BRIANE, M. VIMOND, C.A. VALADES-CRUZ, A. SALOMON, C. WUNDER, C. KERVRANN. A sequential algorithm to detect diffusion switching along intracellular particle trajectories, Bioinformatics 36, 1, June 2019, p. 317-329, [doi:10.1093/bioinformatics/btz489], [hal: hal-02424777].
- SALOMON, C.A. VALADES-CRUZ, L. LECONTE, C. KERVRANN. Dense mapping of intracellular diffusion and drift from single-particle tracking data analysis, in : ICASSP 2020 - IEEE International Conference on Acoustics, Speech and Signal Processing, IEEE, p. 1-5, Barcelona, Spain, May 2020, [hal:hal-03087048].
- PRIGENT, C. A. VALADES -CRUZ, L. LECONTE, L. MAURY, J. SALAMERO, C. KERVRANN. BioImageIT: Open-source framework for integration of image data-management with analysis, Nature Methods, [doi: 10.1038/s41592-022-01642-9], [hal: hal-03474512], 2022.

**Mission confiée**:
**Principales activités**:

- Develop a method and an algorithm to estimate the Hurst exponent, in space and time, for trajectory classification.
- Evaluate the method on artificial and real datasets.
- Ensure interoperability with BioImageIT plateform.
- Present the advancements to collaborators.

**Compétences**:
Technical skills and level required:
Languages:
Relational skills:
Other valued appreciated:
**Avantages**:

- Subsidized meals
- Partial reimbursement of public transport costs
- Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
- Possibility of teleworking (after 6 months of employment) and flexible organization of working hours
- Professional equipment available (videoconferencing, loan of computer equipment, etc.)
- Social, cultural and sports events and activities
- Access to vocational training
- Social security coverage

**Informations générales**:

- **Thème/Domaine**: Optimisation, apprentissage et méthodes statistiques
Biologie et santé, Sciences de la vie et de la terre (BAP A)
- **Ville**: Rennes
- **Centre Inria**: Centre Inria de l'Université de Rennes
- **Date de prise de fonction souhaitée**: 2025-02-01
- **Durée de contrat**: 10 mois
- **Date limite pour postuler**: 2025-02-07

**Consignes pour postuler**:
**Sécurité défense**:
Ce poste est susceptible d’être affecté dans une zone à régime restrictif (ZRR), telle que définie dans le décret n°2011-1425 relatif à la protection du potentiel scientifique et technique de la nation (PPST). L’autorisation d’accès à une zone est délivrée par le chef d’établissement, après avis ministériel favorable, tel que défini dans l’arrêté du 03 juillet 2012, relatif à la PPST. Un avis ministériel défavorable pour un poste affecté dans une ZRR aurait pour conséquence l’annulation du recrutement.

**Politique de recrutement**:
Dans le cadre de sa politique diversité, tous les postes Inria sont ac