Job Offers

Clinical data manager for national consortium on epilepsy surgery – Aix-Marseille Université, Marseille, FRANCE

 

 A position for an experienced clinical data manager is open to create and maintain an epileptic patient database including registration, normalization and security issues and to ensure the communication with the key partners in the academic, clinical and industry sectors with the aim of generating individual Virtual Patient models using The Virtual Brain (TVB) platform as framework (see http://www.thevirtualbrain.org). This database will be generated in the context of the EPINOV (Improving EPilepsy surgery management and progNOsis using Virtual brain technology) project led by Professor Fabrice Bartolomei (http://fr.ap-hm.fr/service/neurophysiologie-clinique-hopital-timone) funded by the RHU programme.

 

 Qualification

 

 Candidates must be highly motivated to work on an interdisciplinary project and collaborate with the various members of the consortium. They should have a degree in biomedical engineering, medical informatics or equivalent level of knowledge. Candidates must possess a solid experience in management of clinical and/or research data and programming (C, MATLAB, Python). Experience with neuroimaging data (stereotactic EEG, MRI, DTI, MEG, EEG), clinical trials, neuroinformatics and its standard formats (for instance DICOM, XNAT, BIDS), machine learning and Big Data would be considered an advantage.

 

 The EPINOV project and consortium

 

We are a national consortium composed of clinicians, researchers and industrial partners interested in improving epilepsy surgical prognosis using large–scale brain modelling based on individual epileptic patient data. A prospective, randomized multicenter trial will be conducted with subjects suffering from drug-resistant epilepsy. The clinical trial will systematically evaluate the added value of personalized brain modelling in the surgical decision making.

 

 Terms of salary and employment

 

Salary will depend on the diploma and previous experience. Operating languages in the consortium are both French and English.

 

 Applications including a cover letter, curriculum vitae and the names of two referees should be sent by October 31st 2017 to: Dr. Irene Yujnovsky at

 


 

Post-doctoral position in the Theoretical Neuroscience Group

Summary

The Theoretical Neuroscience Group (Head: Viktor Jirsa) is seeking to fill a post-doctoral position in the context of the project EPINOV to work on statistical & dynamical modeling of seizure propagation using personalized brain modeling and neuroinformatics approaches on a cohort of hundreds of epilepsy patients. EPINOV is one of 10 large-scale projects selected in the 3rd round of French scientific excellence program «RHU» managed by the National Research Agency (ANR). The aim of the EPINOV project is to significantly improve presurgical interpretation, guide surgical strategies and translate computational tools into clinical routine of personalized medicine. We use individual MRI scans to reconstruct brain anatomy and connectivity, which are combined with a neural mass model and fit using the Bayesian modeling software Stan to individuals’ intracranial electrophysiology data (stereotactic EEG), validated by clinical data from other modalities, such as MEG, fMRI, and semiology.

 

Responsibilities

• Scale up statistical models “vertically” to handle more data and higher resolution anatomy, using model comparison techniques to evaluate the advantage of different model structures

• Scale out models “horizontally”, performing coherent, reliable inference across a large cohort of patients using dedicated, on-site HPC resources

• Develop routines to evaluate and visualize inference results, making them amenable to clinical interpretation

• Integrate developed code into existing code bases and pipelines

 

Qualification 

• Highly motivated to work on an interdisciplinary project and collaborate with the various members of the consortium. 

• PhD degree in computational neuroscience, mathematical or statistical modeling, machine learning or equivalent level of knowledge. 

• Significant, demonstrable experience in data fitting (Bayesian modeling, Dynamical Causal Modeling (DCM), Monte Carlo, etc) will be highly appreciated. 

• Experience with working in a Linux/HPC environment

• Programming in a numerically oriented language (R, Python, MATLAB) 

• Familiarity with Git, unit testing, Docker/VMs is a plus

 

The Theoretical Neuroscience group 

We are a multi-national team interested in understanding the mechanisms underlying the spatiotemporal organization of large-scale brain networks. Our work comprises mathematical and computational modeling of large-scale network dynamics and human brain imaging data, the development of neuroinformatics tools for studying large-scale brain networks applied to concrete functions, dysfunctions (epilepsy, dementia) and aging.

 

Terms of salary and employment 

A 12-month renewable contract will be established. Salary will depend on the diploma and experience. Operating language in the laboratory is English. Applications including a cover letter, curriculum vitae and the names of two referees should be sent by September 30th 2017 to: Dr. Irene Yujnovsky at  

 

More information about the INS and the Theoretical Neurosciences Group can be found at: http://ins.univ-amu.fr


 

Two PhD positions in Neuroscience

PhysioNet Team, Institute of System Neuroscience (INS), UMR1106 AMU-Inserm, Marseille, FRANCE

Two 3-year PhD positions are offered at INS in the field of epilepsy, starting before the end of 2017.
They are part of the M-GATE ITN project 765549, which is financed by EU and offers high level salary. Students will be able to travel to M-GATE EU partners and learn complemetary techniques, exposing them to a beyond the state of the art multi- and trans-disciplinary project

Position 1. Disruption of memory circuit function in epilepsy.
Supervisor: ChristopheBernard, in collaboration with SISSA, INMED, UCL.

Temporal Lobe Epilepsy is associated with cognitive deficits. The underlying mechanisms remain unknown. We are now routinely performing simultaneous recordings with high-density silicon probes in the nucleus reuniens, hippocampus and medium prefrontal cortex to study working memory in freely moving control rats. We will use the same approach in a TLE rat model. We will also record the entorhinal cortexhippocampus-prefrontal cortex circuit. We will focus on neural codes and global dynamics. Specifically, we will use three key measures: sequence activation, inter-area coherence, and ability to plan future actions. We predict that a failure to encode/retrieve and/or build maps may explain cognitive deficits. SISSA will model the limited lesion of the hippocampus we make experimentally and make predictions regarding alterations in neuronal dynamics. Predictions will be tested experimentally, via a constant feedback between experimental and theoretical approaches.

Relevant team publications: Chauviere et al., J Neurosc, 2009; Ann Neurol, 2012; Marguet at al,Nature Med 2015.

Position 2. Neural, Metabolic and biochemical mechanisms of epileptic seizure genesis and propagation.
Supervisor Christophe Bernard with Viktor Jirsa, in collaboration with UCL, RU, and ATLAS.

We have proposed a comprehensive mathematical framework that includes cellular and synaptic network variables to explain seizure dynamics. The model predicts that a state variable evolving slowly in time is required to explain seizure onset, time course and offset. Preliminary data show that molecular events such as those related to metabolism and energy supply, which evolve slowly in time, are integral components of this state variable. Alterations in molecular processes may also underlie cognitive deficits. We will combine molecular sensors and high-density electrophysiological recordings to obtain a complete electro-molecular picture of the events that may explain altered neuronal coding/retrieval, using computational frameworks such as reinforcement learning (in collaboration with UCL, DEEPMIND), and data analytical techniques for detecting molecular/neural patterns and sequences (in collaboration with RU), in particular for seizure prediction.

Relevant team publications: Khogagholy et al., Nature Comm, 2013; Jirsa et al., Brain 2014.

 

Good knowledge of MATLAB or similar computing software is required. Prior experience in in vivo intracellular electrophysiology is a plus. Candidates should apply by sending a CV, a brief outline of current research, scientific interests and career goals, as well as the name and contact details of at least two academic references to Dr. Christophe Bernard (christophe.bernard@univ-amu.fr).

 


 

Post-doc in Neuroscience

PhysioNet Team, Institute of System Neuroscience (INS), UMR1106 AMU-Inserm, Marseille, FRANCE

One postdoc position (at least one year) is offered at INS in the Physionet team in the field of Alzheimer, starting end of 2017 – beginning of 2018.

Caffeine exposure in utero as a risk factor for the development of Alzheimer’s disease

We have previously shown that in utero caffeine exposure through the dam (equivalent of 2-3 espressos in humans) delays the insertion of some GABA neuron populations in the hippocampus and
cortex, with deleterious consequences (enhanced sensitivity to epilepsy and cognitive deficits) in offspring (Silva et al., Science Trans Med, 2013; Fazeli et al., Exp Neurol, 2017). Building on this we wish to determine whether caffeine exposure in utero speeds up Alzheimer’s disease in a genetic KI mouse model. To address this issue, we will combine in vivo and in vitro electrophysiology, functional morphology and behavioral studies.
Prior experience in in vitro patch clamp electrophysiology is required. Experience in functional morphology is a plus. Candidates should apply by sending a CV, a brief outline of current research, scientific interests and career goals, as well as the name and contact details of at least two academic references to Dr. Christophe Bernard (christophe.bernard@univ-amu.fr).

More information about the the PhysioNet Group can be found HERE