Théo Boury

About me

Position: PhD Student in AMIBio team

Institution: Laboratoire d’informatique de l’École Polytechnique (LIX)

OrcID: 0009-0004-0553-4789

Office: 2013, Bâtiment Alan Turing, 1 rue Estienne d’Orves, 91120 Palaiseau, France

Topics of interests

RNA and DNA bioinformatics
Discrete algorithms
Complexity
Machine Learning

Conferences (full paper)

2025

Old dog, new tricks: Exact seeding strategy improves RNA design performances
Théo Boury; Leonhard Sidl; Ivo L. Hofacker; Yann Ponty; Hua-Ting Yao
In Research in Computational Molecular Biology (RECOMB), April 2025 (coming soon!), Seoul, South Korea
paper - code - slides

2024

RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs
Théo Boury; Laurent Bulteau; Yann Ponty
In 24rd International Workshop on Algorithms in Bioinformatics (WABI 2024), Sep 2024, London, United Kingdom
paper - code - doi

2023

Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique
Théo Boury; Yann Ponty; Vladimir Reinharz
In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 20:1-20:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Sep 2023, Houston, United States
paper - code - doi - slides

Presentations (selected from abstract)

2024

RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs
Théo Boury; Laurent Bulteau; Yann Ponty
Sequences in Bioinformatics, Computer Science and Mathematics (SeqBIM, CNRS GdR), November 2024, Rennes, France
abstract - slides

Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique
Théo Boury; Yann Ponty; Vladimir Reinharz
Talk at the Journées Ouvertes en Biologie, Informatique, et Mathématiques 2024 (JOBIM 2024), Jun 2024, Toulouse, France Talk at the Junior Conference on Data Science and Engineering , Paris-Saclay
abstract

2023

Simulation of Ancient DNA Sequences Using Transformer-based Techniques
Théo Boury; Jazeps Medina-Tretmanis; Maria Avila-Arcos; Emilia Huerta-Sanchez; Burak Yelmen; Flora Jay
Talk at the Junior Conference on Data Science and Engineering , Sep 2024, Paris-Saclay, France
abstract - slides

Talks

2024

RNA Design in linear time and space! (most of the time)
Théo Boury; Laurent Bulteau; Yann Ponty
20th Fall Seminar of Bioinformatics, October 2024, Doubice, Czech Republic
slides

RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs
Théo Boury; Laurent Bulteau; Yann Ponty
Computational Approaches to RNA Structure and Function, July 2024, Benasque, Spain

Searching for exact solutions for the inverse folding problem using graphs and parameterization
Théo Boury; Laurent Bulteau; Yann Ponty
40th TBI Winterseminar, February 2024, Bled, Slovenia
slides

Preprints

Independent set reconfiguration: general and RNA-focused parameterized algorithms
Théo Boury; Laurent Bulteau; Bertrand Marchand; Yann Ponty
Preprint on HAL
paper

Research experience

Interdisciplinary Laboratory of Digital Sciences (LISN), Gif-sur-Yvette, France
Internship in Population Genetics – Supervisors: Flora Jay, Burak Yelmen
March 2023- August 2023

Combinatorial and Mathematical Computer Science Laboratory (LaCIM), Montréal, Canada
Internship in Structural Bioinformatics – Supervisor: Vladimir Reinharz
October 2022- February 2023

Laboratoire d’Informatique de l’École polytechnique (LIX), Palaiseau, France
Internship in Algorithmic Bioinformatics – Supervisors: Yann Ponty, Laurent Bulteau, Bertrand Marchand
March 2022- August 2022

Research Institute in Computer Science (IRIT), Toulouse, France
Internship in Network – Supervisors: Daniel Hagimont, Brice Ekane
April 2021- August 2021

Lille Research Center in Computer Science, Signal and Automatics (CRIStAL), Lille, France
Internship in Sequence Bioinformatics – Supervisor: Hélène Touzet
June 2020- July 2020

Education

École Normale Supérieure de Lyon
MSc in Computer Science, end of BSc and school diploma.
2019-2023

Lycée Henri Poincaré de Nancy
Classe Préparatoire Maths and Physics. BSc 1 and 2.
2016-2019