Amibio (LIX, Ecole Polytechnique) is a research group in computational biology with a primary interest on the molecular levels of organization in the cell, and a strong focus on RNAs. Starting from the genomic sequences and NGS data, we currently concentrate our efforts on structures, interactions, evolution and design, trying to meet the growing needs for a rational synthetic biology. Towards that goal, we develop methodological approaches, based on abstract models that are computationally tractable and biologically relevant. A common toolkit of computational methods is developed, relying on our strong background in discrete mathematics, algorithmic design and analysis. Our ultimate goal is to provide software tools and platform elements, to formulate and test hypotheses for the sequence/structure/function relationship in molecular biology.
Research
Our team addresses central questions in bioninformatics, related to the molecular levels of organization in the cells. The biological function of macromolecules such as proteins and nucleic acids relies on their dynamic structural nature and their ability to interact with many different partners. Therefore, folding and docking are still major issues in modern structural biology and we currently concentrate our efforts on structure and interactions and aim at a contribution to RNA design. With the recent development of computational methods aiming to integrate different levels of information, protein and nucleic acid assemblies studies should provide a better understanding on the molecular processes and machinery occurring in the cell and our research extends to several related issues in comparative genomics.
On the one hand, we study and develop methodological approaches for dealing with macromolecular structures and annotation: the challenge is to develop abstract models that are computationally tractable and biologically relevant. Our approach puts a strong emphasis on the modeling of biological objects using classic formalisms in computer science (languages, trees, graphs…), occasionally decorated and/or weighted to capture features of interest. To that purpose, we rely on the wide array of skills present in our team in the fields of combinatorics, formal languages and discrete mathematics. The resulting models are usually designed to be amenable to a probabilistic analysis, which can be used to assess the relevance of models, or test general hypotheses.
On the other hand, once suitable models are established we apply these computational approaches to several particular problems arising in fundamental molecular biology. One typically aims at designing new specialized algorithms and methods to efficiently compute properties of real biological objects. Tools of choice include exact optimization, relying heavily on dynamic programming, simulations, machine learning and discrete mathematics. As a whole, a common toolkit of computational methods is developed within the group.The trade-off between the biological accuracy of the model and the computational tractability or efficiency is to be addressed in a close partnership with experimental biology groups. One outcome is to provide software or platform elements to predict structural models and functional hypotheses.
Members
Faculty members
CNRS Researcher (DR)
Full Prof. at Ecole Polytechnique
Asst Prof. at Ecole Polytechnique
Full Prof. (aemeritus) at Ecole Polytechnique
Administrative Assistant
Karem Witt Martínez
PhD Students
Taher Yacoub
Fragment-based docking for ssRNA-protein complexes
Co-supervised with Fabrice Leclerc (I2BC@Univ. Paris Saclay)
Alan Azede
RNA structurome dynamics in staphylococcus aureus
Co-supervised with Philippe Bouloc (I2BC@Univ. Paris Saclay)
Théo Boury
Parameterized complexity for RNA design and kinetics
Co-supervised with Laurent Bulteau (LIGM@Univ. Gustave Eiffel)
Nan Pan
Algorithms for the Integrative Modeling
of Viral RNA Architectures
Alumni
Former faculty members and staff
Inria Research Director (DR) – AMIBio founder and former lead (2009/16)
Now director of Inria Lille Nord-Europe research center
Prof. at Ecole Polytechnique
Evelyne Rayssac
Former AMIBio administrator
Ecole Polytechnique
Julie Bernauer – Former Inria Researcher (CR) – Now at nVidia, USA
Former postdoctoral fellows
- Olga Berillo – Research associate@ Lady Davis Institute, Canada
- Rasmus Fonseca – R&D developper@zoox.com
- Loic Paulevé – CNRS Researcher@LABRI, Bordeaux
- Balaji Raman – Associate professor@IIIT Sri City, India
- Christelle Rovetta – Data Scientist@Fujitsu France
- Saad Sheikh – Tech lead@Facebook, USA
Former PhD candidates
Exact parameterized algorithmics for structural RNA bioinformatics
Now postdoc at Univ. Sherbrooke, Canada
Hua-Ting Yao – PhD 2021 (X+McGill)
Local Decomposition in RNA Structural Design
Now postdoc at Univ. of Vienna, Austria
Ha Ngoc Nguyen – PhD 2020
Now Lecturer at Thuy Loi University, Vietnam
Jorgelindo Da Veiga Moreira – PhD 2019
Now postdoc at Polytechnique Montreal, Canada
Juraj Michalik – PhD 2019
Non-redundant sampling in RNA Bioinformatics
Now postdoc at Czech Academy of Sciences, Czech Republic
Afaf Saaidi – Phd 2018
Multi-dimensional probing for RNA secondary structure(s) prediction
Now consultant at Capgemini Engineering, France
Wei Wang – PhD 2017
Practical structure-sequence alignment of pseudoknotted RNAs
Now R&D researcher at Merck Shanghai, China
Alice Héliou – PhD 2017
Analyse des séquences génomiques : identification des ARNs circulaires et calcul de l’information négative
Now data scientist at Thalès, France
Amélie Héliou – PhD 2017
Molecular conformations and game theory
Now senior ML engineer at Google Paris, France
Vladimir Reinharz – PhD 2016
Algorithmic properties of evolved structured RNAs
Now Associate Prof at UQAM, Montreal, Canada
- Ievgeniia Furletova – Lecturer@IMPB, Russia
- Adrien Guilhot-Gaudeffroy – R&D@Thales
- Daria Iakovishina – CEO/founder@Ksivalue.com, Russia
- Vincent Le Gallic – R&D engineer@Telecom Paris Tech
- Pauline/Maria Pommeret
- Antoine Soulé – Postdoc@University McGill, Canada
Former visiting Scientists
- Cédric Chauve – Simon Fraser University, Canada
- Peter Clote – Boston College, USA
- Robert Giegerich – Univ. Bielefeld, Germany
- Vsevolod Makeev – Vavilov Institute of General Genetics, Russian Academy of Science
- Laurent Mouchard – University of Rouen
- Laurent Schwarz – APHP
Amibio (LIX, Ecole Polytechnique) is a research group in computational biology with a primary interest on the molecular levels of organization in the cell, and a strong focus on RNAs. Starting from the genomic sequences and NGS data, we currently concentrate our efforts on structures, interactions, evolution and design, trying to meet the growing needs for a rational synthetic biology. Towards that goal, we develop methodological approaches, based on abstract models that are computationally tractable and biologically relevant. A common toolkit of computational methods is developed, relying on our strong background in discrete mathematics, algorithmic design and analysis. Our ultimate goal is to provide software tools and platform elements, to formulate and test hypotheses for the sequence/structure/function relationship in molecular biology.