Post-Doctoral Fellow / Research Engineer position in: Machine Learning and Image Analysis for Neurodegenerative Diseases @Pasteur Institute

A friend group at the Institut Pasteur (Unit of Membrane Traffic and Pathogenesis lead by Prof. Chiara Zurzolo) is hiring a Post-Doctoral Fellow or Research Engineer to join them in our efforts to study the brain using big-data electron microscopy image volumes, machine-learning, and virtual reality:

Post-Doctoral Fellow / Research Engineer position in:

Machine Learning and Image Analysis for Neurodegenerative Diseases @Pasteur Institute

Principal Investigators:

Chiara ZURZOLO, Membrane Traffic and Pathogenesis (MTP) Department of Cell Biology and Infection, Institut Pasteur

Jean-Baptiste MASSON, Decision and Bayesian Computation (DBC) Department of Neuroscience & Computational Biology, Institut Pasteur

Abstract

Tunneling nanotubes (TNTs) are thin connections that gained international scientific attention as novel mechanisms of intercellular communication for providing a continuous cytoplasmic bridge between cells. By allowing versatile cell-to-cell transport of cargo (e.g. organelles, viruses, and proteins), TNTs have been associated to a wide range of physiological processes and pathological conditions. Our group has pioneered the TNT field by showing that TNTs mediate the spreading of amyloid proteins linked with neurodegeneration. Unfortunately, due to a lack of a TNT-specific marker, evidence that these structures exist in vivo is scarce. With most studies failing to establish whether the function of TNTs in vitro translate in complex organisms, there is a pressing need to confirm their existence in tissue before their role in pathology can be addressed. In order to overcome this barrier, this project proposes to combine the use of serial sectioning scanning electron microscopy connectomics, machine learning, and virtual reality for the annotation and identification of TNT-like structures in vivo.

The project is a collaboration between the labs of C. Zurzolo and J.B. Masson at the Pasteur Institute, and is based on solid preliminary data and pre-established international collaborations (with Jeff Lichtman @ Harvard University and Jan Funke @ Janelia Research Campus). This and the combination of our two labs’ areas of expertise, [Zurzolo: cell biology, advanced imaging, and image analysis of TNTs (https://research.pasteur.fr/en/member/chiara-zurzolo/) and Masson: computational/Bayesian inference and VR approaches (https://research.pasteur.fr/en/member/jean-baptiste-masson/)], assure the success of this project. This work will be valuable for future research on TNTs’ structure/function, while our implementation of machine learning will generate a framework for inter- disciplinary research in the life sciences.

We are seeking for a young, highly motivated scientist with an interest in data visualization and analysis. We are open to hire a Post-Doctoral Fellow, Research engineer, or an early career applicant who wishes to pursue a PhD at the interface between Mathematic, Physics, and Computational Biology. Experience in cellular biology is NOT required; however, coding abilities are necessary. A background in applied mathematics, computational biology, and or image analysis is desirable.

This position is open 1st of January 2020 and is funded for one to two years (with possible extension).

Candidates should apply by sending a CV, a brief outline of current research/status, scientific interests, and career goals, as well as the name and contact details of at least two academic references to Chiara Zurzolo: zurzolo@pasteur.fr and dcordero@pasteur.fr

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