Curriculum Vitae

Louis Becquey

Personal details

(+33)6 44 12 96 78
louisbecquey (at) hotmail.fr
LinkedIn : /in/louis-becquey/
GitHub : persalteas

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Intro : Louis is a Ph.D. in bioinformatics, with theoretical knowledge in various areas of biology, biotechnology, and biomathematics, and practical skills in several fields of computer science, including data analysis and machine learning.

Louis’ thesis was pursued within the team « Algorithmique, Recherche Opérationnelle, Bioinformatique et Apprentissage Statistique (AROBAS) », IBISC lab, Université Paris-Saclay. He worked on non-coding RNA in-silico 3D structure prediction, using hybrid physics-based and data-based methods.

Now part of Capgemini as a computational biologist (in a branch which formerly was known as Tessella), Louis helps the team of data-scientists to model living systems and build intelligent tools which use data to improve our mastery of the industrial processes.

Beyond bioinformatics, Louis is curious about the latest tech methods, and happy to work on various engineering projects.

Education

PhD in Computer Sc.: Multicriteria algorithms to predict RNA Structures [2018 – 2021 ]
Directed by Dr. Fariza Tahi and Dr. Eric Angel, AROBAS team, IBISC lab, Université Paris-Saclay (Evry, France)
Multiobjective optimization • RNA structural bioinformatics • Deep Learning • Software development

Bioinformatics & Modelling engineering degree [2015 – 2018]
National Institute of Applied Sciences (INSA Lyon)
Biochemistry • Molecular Biology • Statistics • Programming • Differential Equations • Data Mining • Computational Biology • Drug Design

Foundation courses in Science and Biology [2013 – 2015]
La Martinière Duchère (Lyon)
Preparation for national competitive entrance exams to leading French agronomic, biotech and veterinary ”grandes écoles”. Staff promo at all agronomic, biotech & veterinary 2015 exams (TB exam bank).

1st core year for health studies [2011 – 2013]
Joseph Fourier University (Grenoble)

Technical baccalaureate in lab sciences [2009 – 2011]
Lycée Louis Armand (Chambéry)
Biochemistry & Molecular Biology. With mention (TB).

Professional Experience

Data Science Consultant [2021 – … ]
Altran Lab (part of Capgemini), in a division formerly known as Tessella
Working on CALIPSO, a project funded by the french BPI to reach national autonomy in biomedicine production, using Sanofi’s bioproduction lines.
Systems Biology • Data Analysis • CI/CD practices

Teaching [2015 – 2021 ]
Private lessons, and at University of Evry Val d’Essonne
Tutoring in various scientific disciplines for college, CPGE and bachelor students.
Modules at university in 2019 : Introduction to C programming (Semester 2, bachelor level) and Introduction to statistics and probability (Semester 7, master level).

Molecular Modelling & Design [2018, 6 months]
Galapagos (GLPG)
Internship, development of computational methods to predict kinase inhibitors selectivity issues.
Pipeline Pilot • Schrödinger Maestro • Machine learning • Statistical analysis

Consultant for the INSA’s ”Junior Entreprise” [2017, 2 months]
ETIC INSA Technologies, for Inoviem Scientific
Design of a mass-spectrometry database for Inoviem Scientific.
PHP • MySQL• Web • Relational Model

Algorithmic differentiation of C++ force-fields [2017, 4 months]
INRIA Sophia Antipolis
Internship in the ”Algorithms for Structural Biology” research team (dir. F. Cazals).
Algorithmic differenciation • C++ development • Molecular mechanics • Geometry

DNA/RNA Molecular Modelling [2015 – 2016]
INSA Lyon iGEM Team 2016
DNA de-novo3D structure prediction. Scripting in Python. Gold medal & scientific award at iGEM. Published in PLoS Blog.

Web Redactor & Moderator [2011 – 2015]
TI-Planet.org
International community about graphing calculators.
Website administration • Tutorials writing • Video making • Low-level Programming

Computer-science skills

  • Software development in Python (multiprocessing, TensorFlow 2.x), Go, C++, OpenMP, databases with MySQL
  • Scripting in Python, R, bash
  • Mastered software : Knime • Pipeline Pilot • MatLab • MOE • Schrödinger Maestro • COPASI
  • Mastered OSes : Windows, Debian/Ubuntu, Fedora, ArchLinux • Desktop & Server
  • Communication : Office • LATEX • Audio and Video edition • Image Processing (2D)
  • Web administration & basic dev • Apache/LAMP/WAMP • Nginx • PHP, HTML5 & CSS3

Languages

  • French, mother tongue
  • Very good English, spoken in public [TOEIC score 950/990]
  • Unpracticed German, read, written, understood orally

Public engagement

  • INSA DNA Concept Club [2015/18], Promoting synthetic biology
  • Student Unions [2013/18], as secretary & Communication manager
  • Union Promoting Scientific Courses and Careers [2014/…], helping students and teachers with ITC for education
  • Administration boards [2014/…] Lycée la Martinière Duchère, Biosciences Dpt of INSA, IBISC Lab
  • Open-science enthusiast and proud Wikipedia contributor

Other Jobs/Internships

2015, Worker, Chemical stripping, sandblasting (Alp’décap)
2013, Worker, Ski resort markets (Chez Lino&Bere)
2012, Vintager, Beaujolais (Domaine de la Terrière)
2009,Trainee, Medical analysis laboratory (Biomédica Montmélian)

Academic Publications

Academic thesis (in french)

Ph.D. Thesis : Louis Becquey. Algorithmes multi-critères pour la prédiction de structures d’ARN. Bio-informatique [q-bio.QM]. Université Paris-Saclay; Université d’Evry, 2021. Français. ⟨NNT : 2021UPASG065⟩⟨tel-03440181⟩

Master internship reports :
2018, Exploration of kinase inhibitors selectivity and development of in-silico methods to predict their cross-pharmacology. (confidential)
2017, Algorithmic differentiation of C/C++ force-fields used in biophysics. (available upon demand)

Peer-reviewed journals, as first author

L. Becquey, E. Angel, and F. Tahi, « RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures », Bioinformatics, vol. 37, Issue 9, pp. 1218–1224, Nov. 2020 https://doi.org/10.1093/bioinformatics/btaa944

L. Becquey, E. Angel, and F. Tahi, “BiORSEO: A bi-objective method to predict RNA secondary structures with pseudoknots using RNA 3D modules”, Bioinformatics, vol. 36, no. 8, pp. 2451–2457, Jan. 2020. https://doi.org/10.1093/bioinformatics/btz962

Peer reviewed, as co-author

Orlans et al., iGEM REPORT: Gotta Detect ‘Em All: a multi-STI sensor based on aptamers, PLoS Blog, 05/2017

Presentations at scientific events


RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures”, ELIXIR’s 3D Bioinfo Annual Workshop, 18 Nov 2020

A dataset for machine learning of RNA molecules’ 3D structure”, EUGLOH Annual Student Research Conference, 30 Sept 2020

Modeling RNA structures : An introduction & state of the art”, visit at GLPG, 12 Jan 2020

A review of different ways to insert known RNA modules into RNA secondary structures”, JOBIM 2019, 4 Juil 2019