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<!DOCTYPE html>
<html lang="en-US">
<head>
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<title>BNeDiction Research Project</title>
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<header id="header">
<a href="./">
<div id="logo" style="background-image: url(./img/bnediction_logo_264.png)"></div>
<div id="title">
<h1>BNeDiction Research Project</h1>
</div>
</a>
<div id="nav">
<ul>
<li class="icon">
<a href="#" aria-label="Menu"><i class="fas fa-bars fa-2x" aria-hidden="true"></i></a>
</li>
<li><a href="mailto:[email protected]">Contact</a></li>
<li><a href="#code">Code</a></li>
<li><a href="#publications">Publications</a></li>
<li><a href="#people">Members</a></li>
</ul>
</div>
</header>
<section id="about">
<p><img src="./img/Logo-ANR-bleu-RVB.png#sponsor" alt=""></p>
<h2 id="predictive-boolean-network-ensembles">Predictive Boolean Network Ensembles</h2>
<p>Research project funded by <a href="http://www.agence-nationale-recherche.fr">ANR</a> (French National Research Agency; grant <a href="https://anr.fr/Project-ANR-20-CE45-0001">ANR-20-CE45-0001</a>).</p>
<p>Bridging the gap between dynamical systems and their partial observation, computational models of biological processes aim at uncovering key mechanisms driving cellular dynamics, and ultimately predict their behaviour under unobserved conditions.
The BNeDiction project aims at providing a general methodology for making predictions from data on systems structure and dynamics by the means of ensembles of Boolean networks, an unexplored direction.
Based on recent advances on the symbolic and implicit formal characterization of the compatible models using logic programming, the key challenges relate to the sampling of ensemble of diverse models, and the evaluation and maximization of its predictive power.
Overall, the project aspires at delivering a convincing methodology for assessing the adequacy of automated logical modelling from experimental data, a key and recurring question at the intersection of artificial intelligence and life sciences.</p>
<p><em>Principal investigator: <a href="https://loicpauleve.name">Loïc Paulevé</a> (CNRS, <a href="https://www.labri.fr">LaBRI</a>, Bordeaux, France)</em></p>
<!--
<h1 id="jobs">Jobs</h1>
<p>If you are candidate for a research internship, PhD, or post-doc and interested
in at least one of the following topic, <a
href="mailto:[email protected]">contact me</a>!
</p>
<ul>
<li>Logical modeling of biologcal processes</li>
<li>Machine learning for symbolic models, feature engineering and selection</li>
<li>Logic programming and ASP/SAT/QBF solving</li>
<li>Theoretical aspects of Boolean networks and related dynamical systems</li>
</ul>
<p lang="fr">
Si vous cherchez un stage de recherche, un sujet de thèse, ou un projet de
post-doc, et que vous êtes intéressé par un des sujets suivants,
<a href="mailto:[email protected]">contactez moi</a>!
</p>
<ul lang="fr">
<li>Modélisation logique des processus biologiques</li>
<li>Apprentissage pour des modèles symboliques, inginérie et sélection de charactéristiques</li>
<li>Programmation logique et résolution ASP/SAT/QBF</li>
<li>Théorie des réseaux booléens</li>
</ul>
<p lang="fr">
Voici quelques exemples de sujets qui peuvent se décliner en stages de Master
(voire L3), thèse de doctorat, ou projet de post-doctorat :
</p>
<p><a href="https://loicpauleve.name/md/s/sujet-stage-BNeDiction-ml#">Stage - Synthèse et apprentissage de réseaux booléens prédictifs pour la différenciation cellulaire</a>
<br>#MachineLearning #BioInformatics #LogicProgramming #Python</p>
<p><a href="https://loicpauleve.name/md/s/cK06oV754">Stage - Synthèse de réseaux booléens par résolution de problèmes de satisfiabilité avec quantificateurs</a>
<br>#SAT #QBF #Logic #DynamicalSystems</p>
<p><a href="https://loicpauleve.name/md/s/sujet-stage-simulation-MPBN#">Stage - Implémentation en Julia d’un simulateur de réseaux booléens</a>
<br>#Programming #Simulations #HighPerformance</p>
</section>
-->
<section id="code">
<h1>Code</h1>
<ul class="project-list">
<li class="project-item">
<a href="https://bnediction.github.io/bonesis">BoNesis</a>: Synthesis of Boolean networks from static and dynamical properties
</li>
<li class="project-item">
<a href="https://github.com/bnediction/mpbn">mpbn</a>: Analysis and simulation of Most Permissive Boolean networks
</li>
<li class="project-item">
<a href="https://github.com/bnediction/scBoolSeq">scBoolSeq</a>: scRNA-Seq data binarisation and synthetic generation from Boolean dynamics
</li>
</ul>
</section>
<section id="publications">
<h1>Publications</h1>
<p><a href="https://hal-anr.archives-ouvertes.fr/search/index/?q=%2A&anrProjectReference_s=ANR-20-CE45-0001&sort=producedDate_tdate+desc"
>List of publications</a></p>
</section>
<section id="people">
<h1>Members</h1>
<ul>
<li>
<a href="https://loicpauleve.name">Loïc Paulevé</a>, Principal investigator
</li>
<li>
<a href="https://gmagannadevelop.github.io/">Gustavo Magaña López</a>, PhD student
</li>
<li>
<a href="https://www.linkedin.com/in/th%C3%A9o-roncalli-63225a127">Théo Roncalli</a>, PhD student
</li>
<li>
<a href="https://www-dyliss.irisa.fr/kerian-thuillier/">Kerian
Thuillier</a>, PhD student @ IRISA, Rennes (co-supervised with <a href="https://www-dyliss.irisa.fr/anne-siegel/">Anne Siegel</a>)
</li>
</ul>
<h4>Alumni</h4>
<ul>
<li>
<a href="https://www.i3s.unice.fr/~riva/">Sara Riva</a> (was: Post-doc)
</li>
<li>
<a href="https://www.lri.fr/~schevalier/">Stéphanie Chevalier</a> (was: PhD student)
</li>
<li>
Hélène Siboulet (was: internship)
</li>
<li>
<a href="https://fr.linkedin.com/in/victor-levallois-8239311a3">Victor Levallois</a> (was: internship)
</li>
<li>
<a href="https://mhmini.com/">Mohamed Hmini</a> (was: internship)
</li>
<li>
<a href="https://www.linkedin.com/in/alan-adamiak-767aa9252">Alan Adamiak</a> (was: internship)
</li>
</ul>
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<div class="footer-left">
Copyright © Loïc Paulevé
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