CURRICULUM VITAE
Experience and Education
Research associate, Heinrich Heine University Düsseldorf (Düsseldorf, Germany)
Jan. 2023 - Present
Lab: Faculty of Mathematics and Natural Sciences, Institute of Computational Cell Biology.
Training:
• EPCP Summer school 2023 (Paris, France - 2023): Economic principles in cell biology.
Jan. 2023 - Present
Lab: Faculty of Mathematics and Natural Sciences, Institute of Computational Cell Biology.
Training:
• EPCP Summer school 2023 (Paris, France - 2023): Economic principles in cell biology.
Postdoctoral research fellow, University of Helsinki (Helsinki, Finland)
Sept. 2021 - Dec. 2022
Lab: Organismal and Evolutionary Biology Research Program (OEB), Prof. Frédéric Guillaume's group.
Training:
• DrosEU/ESEB STN Summer school (Prague, Czech Republic - 2022): Integrating -omics approaches for eco-evolutionary research.
• PRACE Autumn School (Kajaani, Finland - 2021): Introduction to deep-learning and GPU computing.
Sept. 2021 - Dec. 2022
Lab: Organismal and Evolutionary Biology Research Program (OEB), Prof. Frédéric Guillaume's group.
Training:
• DrosEU/ESEB STN Summer school (Prague, Czech Republic - 2022): Integrating -omics approaches for eco-evolutionary research.
• PRACE Autumn School (Kajaani, Finland - 2021): Introduction to deep-learning and GPU computing.
Postdoctoral research fellow, Hungarian Academy of Sciences (Szeged, Hungary)
May 2018 - Aug. 2021
Lab: Dr. Balazs Papp laboratory.
May 2018 - Aug. 2021
Lab: Dr. Balazs Papp laboratory.
Postdoctoral research fellow, INRIA (Lyon, France)
May 2019 - Aug. 2020
Lab: Project-team INRIA-Beagle.
May 2019 - Aug. 2020
Lab: Project-team INRIA-Beagle.
Ph. D. Computational and mathematical modeling of bacterial evolution, INSA-Lyon (Lyon, France)
Nov. 2013 - Nov. 2017 (defended on 17th Nov., 2017)
Lab: Project-team INRIA-Beagle.
Subject: Studying the evolution of bacterial micro-organisms by modeling and numerical simulation approaches.
Supervisors: Prof. Guillaume Beslon, Prof. Carole Knibbe.
Training: Berder-Villers School 2015: Sex and Gender: from Biology to Sociology.
Nov. 2013 - Nov. 2017 (defended on 17th Nov., 2017)
Lab: Project-team INRIA-Beagle.
Subject: Studying the evolution of bacterial micro-organisms by modeling and numerical simulation approaches.
Supervisors: Prof. Guillaume Beslon, Prof. Carole Knibbe.
Training: Berder-Villers School 2015: Sex and Gender: from Biology to Sociology.
M. Sc. Computational and mathematical biology, Université de Lyon (Lyon, France)
2011 - 2013
Internships:
• 2012-2013: Indirect selection of variability in fluctuating environment. Supervisor: Prof. Guillaume Beslon.
• 2011-2012: Modeling the evolution of stochasticity of gene expression. Supervisor: Prof. Guillaume Beslon.
• 2011: Application of graph theory to metabolic stories. Supervisor: Prof. Vincent Lacroix.
2011 - 2013
Internships:
• 2012-2013: Indirect selection of variability in fluctuating environment. Supervisor: Prof. Guillaume Beslon.
• 2011-2012: Modeling the evolution of stochasticity of gene expression. Supervisor: Prof. Guillaume Beslon.
• 2011: Application of graph theory to metabolic stories. Supervisor: Prof. Vincent Lacroix.
B. Sc. Computational and mathematical biology, Université de Lyon (Lyon, France)
2008 - 2011
Internships:
• 2010-2011: Inferring chromatine states by modeling genetic expression. Supervisor: Dr. Olivier Gandrillon.
• 2009: Lab internship (cellular and molecular biology). Supervisor: Dr. Olivier Gandrillon.
2008 - 2011
Internships:
• 2010-2011: Inferring chromatine states by modeling genetic expression. Supervisor: Dr. Olivier Gandrillon.
• 2009: Lab internship (cellular and molecular biology). Supervisor: Dr. Olivier Gandrillon.
Teaching experience
Lecturer, undergraduate department, Heinrich Heine Düsseldorf Universität (Düsseldorf, Germany)
2023-Now
• In charge of the unit "Introduction to Metabolic Networks Modeling" (Linear algebra, linear/quadratic/logical programming, constraint-based modeling, ODEs, Python).
2023-Now
• In charge of the unit "Introduction to Metabolic Networks Modeling" (Linear algebra, linear/quadratic/logical programming, constraint-based modeling, ODEs, Python).
Teaching assistant, graduate department, University of Helsinki (Helsinki, Finland)
2021-2022
• Introduction to R,
• Population genetics tutorial with R,
• Population structure tutorial with R.
2021-2022
• Introduction to R,
• Population genetics tutorial with R,
• Population structure tutorial with R.
Teaching assistant, graduate department, INSA-de-Lyon (Lyon, France)
2014-2016
• Genetic algorithms and project management.
2014-2016
• Genetic algorithms and project management.
Teaching assistant, undergraduate department, INSA-de-Lyon (Lyon, France)
2014-2016
• C/C++ programming.
2014-2016
• C/C++ programming.
Supervision of students
Supervisor of Furkan Mert, Bachelor thesis, Henrich-Heine Universität Düsseldorf (Germany)
2024
• Evolutionary algorithms for growth balance analysis.
2024
• Evolutionary algorithms for growth balance analysis.
Supervisor of Aymeric Bonnamour, Master 1, Université de Lyon (Lyon, France)
2019
• Combining landscape genetics and numerical simulation to understand how humans disperse invasive species on a landscape scale.
2019
• Combining landscape genetics and numerical simulation to understand how humans disperse invasive species on a landscape scale.
Grants
- 2019-2020: INRIA@SiliconValley postdoctoral grant (1.5 year funding).
- 2015: Grant (€5,000) from the Institute of Complex Systems (Lyon, France) to develop MoRIS.
- 2013-2017: INRIA PhD fellowship funded by the European project EvoEvo (www.evoevo.eu).
- 2011-2013: Merit scholarship (€200/month), granted by CROUS, Lyon, France.
- 2011: Merit scholarship (€2,000), granted by Université de Lyon, France.
Implication in the Research Community
- 2024: Reviewer for Science Advances.
- 2022-2024: Reviewer for Peer Community In Evolutionary Biology (PCI EvolBiol).
- 2021: Reviewer for Frontiers in Ecology & Evolution international journal.
- 2021: Reviewer for Genome Biology and Evolution (GBE) international journal.
- 2017: Reviewer for BioSystems international journal.
- Sept. 2017: Organizing committee of the 14th European Conference on Artificial Life, Lyon, France.
- 2013-2016: Development and management of the website of the European project EvoEvo (www.evoevo.eu, EVLIT call of the FP7 program).
Computer skills
- Programming languages: C/C++, Python, Bash, R.
- Developing tools: Project management (Github Actions/Projects/Copilot, Slack, Jira, Trello), VCS (svn, git), Build and Packaging (autotools, Cmake, Pypi), Debug (gdb, Valgrind), Profiling and Code Optimization (Intel-Advisor, OSX-Instruments), Documentation (Doxygen, LaTeX, Github, Markdown, R-Knit), HPC and GPU-computing (TBB, OAR, Slurm, regular user of the computer clusters IN2P3 and CSC).
- Scientific computing: R, GSL, numpy, scipy, mpmath, tidyverse.
- Bioinformatics/Omics: samtools, vcftools, picard, Plink, GATK, Beagle, Gemma, Lep-MAP3, edgeR, Limma, Rsubread, WGCNA.
- Constraint-based modeling and ODE solving: COBRApy, optlang, SBML, COPASI, libroadrunner, Tellurium.
- Machine learning and deep-learning: pygmo, cma, Tensorflow, Keras, Keras tuner, Ray tune.
- Visualization: matplotlib, ggplot, Jupyter Notebook, Google Collab.
- Web: HTML, CSS, SQL, Hugo, WordPress, Bootstrap.
© 2020-2024 Charles Rocabert. All rights reserved. Powered by Hugo and Github Pages. Drawings: © Manuela Michel Dikongué.