Charlotte HERICE

Experience

Since November 2019

Research and Teaching Assistant in BioInformatics

Institut Chimie et Biologie des Membranes et des Nano-objets (CBMN)
University of Bordeaux, Bordeaux, France
Referent: Pr. Jean-Christophe Taveau

July 2017 - July 2019

Associate Researcher

Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS)
University of Strathclyde, Glasgow, Sctoland, UK

Reseach: I was a part of Dr. Shuzo Sakata's team. Our goal was to understand state-dependent information processing in the brain at the level of neural circuits. Taking multidisciplinary approaches, we were aiming to elucidate the function of sub-second brain waves and underlying neural ensemble dynamics during REM sleep in rodents. My project particularly concerned REM sleep and the implementation of a computational model of the brain structures involved in the REM sleep genesis. We also wanted to study the implication of the cholinergic neurons in the REM sleep mechanisms in the mouse.
Referent : Dr. Shuzo Sakata
Languages/Softwares: Python, R, Bash, ImageJ, Illustrator, LaTeX.

Feb. - June 2017

Guest Researcher

Laboratoire Bordelais de Recherche en Informatique (LaBRI), Bordeaux, France

Research: Customization of a web application previously developped in the lab.
Referent: Dr. Marie Beurton-Aimar

2013-2017

PhD in Computational Neurosciences

Team Mnemosyne INRIA, Institut des Maladies Neurodénégératives (IMN), CNRS UMR 5293, Bordeaux, France
Doctoral School of Life and Health Sciences (ED SVS), University of Bordeaux

PhD Topic: Action selection and decision-making mechanisms in basal ganglia with a connexionist model.
Supervisor: Dr. André GARENNE
Keywords: computational neurosciences, connectionism, basal ganglia, decision-making, closed loop, spiking neurons.
Abstract : I worked in the Mnemosyne team from the Institute of Neurodegenerative Diseases (IMN) of Bordeaux, in collaboration with the National Institute for Research in Informatics and Automatics (INRIA) of Talence. The research work of this team is based on integrative and computational neurosciences. Its objective is to model the brain as a system of active memories in synergy and in interaction with the internal and external world and to simulate it as a whole and in situation. During my thesis in this team, I focused on the exploration of the dynamics of information's flow in the basal ganglia circuit through a connectionist computational model with their impact on learning. The model was submitted to a simple tasks of decision-making (applicable to both animal models and human subjects) in order to develop a generic model in an incremental way (constant consistency with the experimental data).

2013

Master 2 Intern (6 months)

Institut Interdisciplinaire de NeuroSciences (IINS), Team Mulle (Physiology of glutamatergic synapses), CNRS UMR 5297, Bordeaux, France

Topic: Computer modelisation of the mossy fibre synapse functioning (CA3 cell of the hippocampus). Implementation of a stochastic model in order to reproduce the variability of the synaptic responses observed in basal conditions recording.
Supervisors: Dr. Christophe BLANCHET and Dr. André GARENNE
Languages/Softwares: Python (3.7 and 3.1), softwares MCell and Blender, Gimp, LaTeX.

2012

Master 1 Intern (3 months)

Laboratoire Chimie et Biologie des Membranes et Nanoobjets (CBMN), CNRS UMR 5248, Bordeaux, France

Pick_EM Project: Development of a plug-in for the software ImageJ to select the particles observed by cryo-electron microscopy.
Supervisor: Pr. Jean-Christophe TAVEAU
Languages/Softwares: Java, ImageJ macros, LaTeX.

Education

Schools and Workshops

- "European Institute for Theoritical Neuroscience Spring School". Paris, France. (2018). Understanding and designing neural models at multiple scales, ranging from cellular and circuit models to large-scale brain networks. (Link to the web page).
- "European Neuroscience Conference for Doctoral Students (ENCODS)". Helsingor, Danemark (2016).
- "Emergent: Neural Network Simulation System". Collaboration with the team of Dr. Randall O'Reilly. Department of Psychology and Neuroscience of the University of Colorado Boulder - Boulder, Colorado, États-Unis (2015).

2013-2017

PhD in Computational Neurosciences

Team Mnemosyne INRIA, Institut des Maladies Neurodénégératives (IMN), CNRS UMR 5293, Bordeaux, France
Doctoral School of Life and Health Sciences (ED SVS), University of Bordeaux

Link to the manuscript (written in french).

2011-2013

Master of Science in BioInformatics

University of Bordeaux, Bordeaux, France

Programming, Softwares conception, Algorithmic applied to Biology, Data Mining, Modeling, Imaging, Data proseccing, Statistics.
Supervisor: Dr. Marie BEURTON-AIMAR

2008-2011

Bachelor's Degree in Cell Biology and Physiology

University of Bordeaux, Bordeaux, France

Neurosciences, Cell, Plant and Micro Biology, Biochemistry, Statistics, Immunology, Genetics, Chemistry, Physiology.

Publications

PhD Thesis

- C. Héricé. "Mécanismes de la sélection de l'action et de la prise de décision dans les ganglions de la base: approche par un modèle connexionniste". Thèse de l'Université de Bordeaux (2016). Link to the manuscript (written in French).

Articles and reviews

- C. Héricé and S. Sakata. "Developping a computational model of the sleep/wake cycle". In press for Frontiers in Neuroscience.
- M. Carlu*, O. Chehab*, L. Dalla Porta*, D. Depannemaecker*, C. Héricé*, M. Jedynak*, E. Köksal Ersöz*, P. Muratore*, S. Souihel*, C. Capone*, Y. Zerlaut*, A. Destexhe & M. Di Volo. "A mean-field approach to the dynamics of networks of complex neurons, from nonlinear Integrate-and-Fire to Hodgkin-Huxley models". In press for Journal of Neurophysiology.
- C. Héricé*, A. Patel* and S. Sakata. "Circuit mechanisms and computational models of REM sleep". Neuroscience Research (2019). Link.
- C. Héricé, R. Khalil, M. Moftah, T. Boraud, M. Guthrie and A. Garenne. "Decision-making under uncertainty in a spiking neural network model of the basal ganglia". Journal of Integrative Neuroscience (2016). Link.

Posters and Conferences

- C. Héricé and S. Sakata. "A Computational Model of the Sleep/Wake cycle". Scottish Neuroscience Group Meeting - Dundee, UK (2018).
- C. Héricé and S. Sakata. "Developping a Computational Model of Rapid Eye Movement Sleep". Eleventh FENS (Federation of European Neuroscience Societies) Forum of Neuroscience - Berlin, Germany (2018).
- C. Héricé, R. Khalil, M. Moftah, T. Boraud, M. Guthrie and A. Garenne. "Decision-making in a neural network model of the basal ganglia". Sixth International Symposium on Biology of Decision Making (SBDM 2016) - Paris, France (2016) Link (PDF).
- C. Héricé, R. Khalil, M. Moftah, T. Boraud, M. Guthrie and A. Garenne. "Decision making mechanisms in a connectionist model of the basal ganglia (updated)". Multi-Disciplinary Conference on Reinforcement Learning and Decision Making (RLDM 2015) - Edmonton, Alberta, Canada (2015) Link (PDF).
- C. Héricé, M. Bonnet-Save, A. Garenne, J-M. Cabelguen and T. Boraud. "Setting a behavioral task for assessing decision-making in Urodele amphibian". Fifth International Symposium on Biology of Decision Making (SBDM 2015) - Paris, France (2015) Link (PDF).
- M. Guthrie, C. Héricé, R. Khalil, M. Moftah, T. Boraud and A. Garenne. "Decision making mechanisms in a connectionist model of the basal ganglia". Fourth International Symposium on Biology of Decision Making (SBDM 2014) - Paris, France (2014) Link (PDF).

Talks

- C. Héricé. "Computational Neurosciences: Introduction to Artificial Neural Networks". Jagiellonian University Medical College - Cracovie, Pologne (2019).
- C. Héricé. "Highliting decision-making and action-selection processes with a computer". Scientific Day of the Doctoral School - Arcachon, France (2016). Selected talk.

Computer Skills

Programming Languages

Python, Java, Bash, C/C++, Javascript, Perl

ANN

Brian Simulator, NEURON

Object Oriented Programming

Design Pattern, UML

Data Bases

PostgreSQL

Web

HTML, CSS, PHP, WebGL

Imaging

ImageJ, Illustrator, GIMP

Modelling

MCell, Blender 3D, Matlab

Data Analysis

R, bio-statistics, dada mining

Systems

Linux, Mac OS, Windows

IDE

NetBeans, Eclispe

Open Source

WordPress

Office

LaTeX, Mac Office, Microsoft Office, Open Office

Languages

French

Native speaker

English

Fluent speaker

German

Basic knowledge

Spanish

Basic knowledge

Scientific mediation

Talk - "Printemps de la mixité INRIA"

May 2015/2016 - Bordeaux, France

"Informatique cognitive : Du cerveau à la machine"

C. Héricé et I. Chraibi-Kaadoud

Explanation of the research work in cognitive informatics to high-school students.

Workshop - INRIA Science Party

October 2014/2015 - Bordeaux, France

"Sciences manuelles du numérique : Déconstruire l'informatique pour mieux la comprendre"

Explanation of the computer science whitout a computer to high-school students.

Poster - Meeting INRIA and Industries

October 2015 - Bordeaux, France

"Modélisation bio-inspirée dans le numérique et la santé"

C. Héricé, I. Chraibi-Kaadoud et F. Alexandre

Presentation of topics and the work of the Mnemosyne team.

Animation - "Salon Aquitec"

February 2014/2015 - Bordeaux, France

INRIA Stand for the research fields and university opportunities.

Présentation of the work done at the INRIA Bordeaux - Sud-Ouest.

Teaching activity

2019-2020

Structural BioInformatics and Modelling

Master Students - University of Bordeaux

Biological processes simulations and programming with MCell and Blender.

2017

How to use the Python programming language?

University of Strathclyde, UK

3 full days workshop to introduce the Python programming language to Dr. Sakata's group (simple and complex scripts, functions, figures and graphs, writting and reading data files).

2015-2016

Informatics applied to Biology: Imaging and modeling

Master 1 students - University of Bordeaux

How to use the modeling softwares MCell and Blender to answer a biological question.

2013-2016

Statistic tests and scripts in Biology with the software R

Master 1 students - University of Bordeaux

Reviewing of the main statistic tests to answer a scientific question, getting familiar with R (console and scripts).

2014-2016

Data Bases and SQL programming language

Master 1 students - University of Bordeaux

Introduction to the concept of the data bases and to the SQL programming language, preparing and correcting group projects and final exams.

2013-2014

Introduction to modeling and imaging in Biology

Master 1 students - University of Bordeaux

Reviewing of neurology and electrophysiology basics, getting familiar with Python programming for neural networks and vPython.

Other

Association

Secretaty a PhD Students association ("Association des Doctorants et Docteurs en Biologie de Bordeaux" - 2D2B) during all the PhD duration

Setting up and managing a website and social networking profiles, involvement in the organization of the Scientific Day of the Doctoral School (registrations, schedule and events of the day.

University Councils

PhD Students Representative

IMN Laboratory Council from 2014 to 2016

Scientific Council of the Sciences of Life and Health Doctoral School of the University of Bordeaux in 2015 and 2016