{"id":13700,"date":"2025-09-25T14:05:32","date_gmt":"2025-09-25T12:05:32","guid":{"rendered":"https:\/\/www.ibisc.univ-evry.fr\/clement-bernard-soutient-sa-these-de-doctorat-le-lundi-6-octobre-2025-computational-methods-based-on-deep-learning-for-the-prediction-of-rna-3d-structures\/"},"modified":"2025-10-26T17:53:24","modified_gmt":"2025-10-26T16:53:24","slug":"clement-bernard-will-defend-his-doctoral-thesis-on-monday-october-6-2025-computational-methods-based-on-deep-learning-for-the-prediction-of-rna-3d-structures","status":"publish","type":"post","link":"https:\/\/www.ibisc.univ-evry.fr\/en\/clement-bernard-will-defend-his-doctoral-thesis-on-monday-october-6-2025-computational-methods-based-on-deep-learning-for-the-prediction-of-rna-3d-structures\/","title":{"rendered":"Cl\u00e9ment BERNARD will defend his doctoral thesis on Monday, October 6, 2025: \u201cComputational methods based on deep learning for the prediction of RNA 3D structures.\u201d"},"content":{"rendered":"
\n\t\t\t\t\t
\n\t\t\t\t\t\t

Cl\u00e9ment BERNARD defends his doctoral thesis on Monday October 6th, 2025 at 2 pm, “petit amphith\u00e9\u00e2tre” of the IBGBI building, \u00c9vry Paris-Saclay University.<\/p>\n

The session is also available online, via the link: https:\/\/univ-evry-fr.zoom.us\/j\/94635690967?pwd=rgl9Mq5ftJEexjj|ViXj7xsa1VT5j6.1<\/strong><\/span><\/a> .<\/p>\n

Title: Computational methods based on deep learning for the prediction of RNA 3D structures<\/h2>\n

Abstract<\/strong>:<\/h2>\n
\n
RNAs are, like proteins, biological molecules that play essential roles at various stages in the life of an organism and are involved in various diseases. Determining their structure, especially 3D, is essential to understand their function better. Recently, Google DeepMind proposed a method called AlphaFold, for the prediction of the 3D structure of proteins based on deep learning, which revolutionized the field by showing a high outperformance compared to the state-of-art. However, RNA and protein molecules differ significantly in structure and dynamics, making it non-trivial to apply protein- based methods directly to RNA. AlphaFold, AlphaFold 2, as well as AlphaFold 3, its new version that also predicts RNA 3D structure, rely heavily on multiple sequence alignments (MSAs) as input, which are expensive to compute and not always available, especially for RNAs.
\nIn this thesis, we aim to get ride of the MSA information for the prediction of RNA 3D structures. We seek to develop methods to predict RNA 3D structures from sequence information only. For this, we leverage deep learning methods and particularly language-based models
\nto map sequences to structure features. By using language-based models pretrained on a large set of RNA sequences, we can learn RNA structural features and then predict the 3D structure.<\/div>\n
The work in this thesis is separated into three main contributions. The first, called RNAdvisor, is a tool that wraps the state-of-the-art RNA 3D structure assessment tools to comprehensively evaluate RNA 3D structures, both with and without experimental references. The second contribution, State-of-the-RNArt, is a benchmark of the state-of-the-art RNA 3D structure prediction methods, highlighting current methods\u2019 limitations and challenges. It is followed by a more detailed analysis of the limitations of AlphaFold 3. The third contribution, RNA-TorsionBERT, is a deep learning method that predicts the torsion angles of RNA 3D structures from the sequence, which are an important feature of RNA 3D structures. It leverages a language-based model to map sequences to structure features. It is extended to a new scoring function, TorsionBERT-MCQ, that can assess the quality of RNA 3D structures in torsional space. This work is a step towards the development of deep learning methods for RNA 3D structure prediction, using only sequence information and not relying on costly multiple-sequence alignments.<\/div>\n<\/div>\n<\/div>

Composition du jury de th\u00e8se\/Composition of the doctoral thesis jury<\/span><\/h3>\n<\/div>\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Membre du jury<\/th>\nTitre<\/th>\nLieu d’exercice<\/th>\nFonction dans le jury<\/th>\n<\/tr>\n<\/thead>\n
Fr\u00e9d\u00e9ric CAZALS<\/td>\nDirecteur de Recherche<\/td>\nCentre Inria d\u2019Universit\u00e9 C\u00f4te d\u2019Azur<\/td>\nRapporteur<\/td>\n<\/tr>\n
Florence D\u2019ALCHE-BUC<\/td>\nProfesseure<\/td>\nInstitut Polytechnique de Paris, Telecom Paris<\/td>\nExaminatrice<\/td>\n<\/tr>\n
Alain DENISE<\/td>\nProfesseur des Universit\u00e9s<\/td>\nUniversit\u00e9 Paris-Saclay, LISN<\/td>\nExaminateur<\/td>\n<\/tr>\n
Pierre GEURTS<\/td>\nFull professor<\/td>\nUniversit\u00e9 de Li\u00e8ge<\/td>\nRapporteur<\/td>\n<\/tr>\n
Sahar GHANNAY<\/td>\nMa\u00eetre de conf\u00e9rences<\/td>\nUniversit\u00e9 Paris-Saclay, LISN<\/td>\nCo-encadrante<\/td>\n<\/tr>\n
Sebastian KMIECIK<\/td>\nFull professor<\/td>\nUniversity of Warsaw<\/td>\nRapporteur<\/td>\n<\/tr>\n
Guillaume POSTIC<\/td>\nMa\u00eetre de Conf\u00e9rences<\/td>\nUniversit\u00e9 Evry Paris-Saclay<\/td>\nCo-encadrant<\/td>\n<\/tr>\n
Elena RIVAS<\/td>\nSenior Research Fellow<\/td>\nHarvard University<\/td>\nExaminatrice<\/td>\n<\/tr>\n
Marta SZACHNIUK<\/td>\nFull professor<\/td>\nPoznan University of Technology<\/td>\nMembre invit\u00e9e<\/td>\n<\/tr>\n
Fariza TAHI<\/td>\nProfesseure des Universit\u00e9s<\/td>\nUniversit\u00e9 Evry Paris-Saclay<\/td>\nDirectrice de th\u00e8se<\/td>\n<\/tr>\n
Tomasz ZOK<\/td>\nAssociate professor<\/td>\nPoznan University of Technology<\/td>\nExaminateur<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
<\/div>
<\/div>
    \n
  • Date: Monday, October 6, 2025, 2:00 p.m.<\/li>\n
  • Location: Small Amphitheater in the IBGBI building, \u00c9vry Paris-Saclay University. The session will also be broadcast online via the following link:<\/li>\n
  • PhD student: Cl\u00e9ment BERNARD, University of \u00c9vry Paris-Saclay, IBISC AROBAS team<\/li>\n
  • Thesis supervisors: Fariza TAHI (Professor, University of \u00c9vry, IBISC AROBAS team, thesis supervisor), Guillaume POSTIC (Assistant Professor, University of \u00c9vry, IBISC AROBAS team, thesis co-supervisor), Sahar GHANNAY (Assistant Professor, University of Paris-Saclay, LISN, thesis co-supervisor)<\/li>\n<\/ul>\n<\/div>
    <\/div>\n\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":12,"featured_media":1364,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"categories":[41,41,53,53,162,162,182,9,182,83,83,52,52,169,169],"tags":[],"class_list":{"0":"post-13700","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","6":"hentry","7":"category-in-the-headlines","9":"category-arobas-team","11":"category-events","13":"category-evry-rna-platform","14":"category-uncategorized","16":"category-platforms","18":"category-research","20":"category-phd-thesis-defense"},"acf":[],"_links":{"self":[{"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/posts\/13700"}],"collection":[{"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/comments?post=13700"}],"version-history":[{"count":5,"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/posts\/13700\/revisions"}],"predecessor-version":[{"id":13705,"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/posts\/13700\/revisions\/13705"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/media\/1364"}],"wp:attachment":[{"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/media?parent=13700"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/categories?post=13700"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ibisc.univ-evry.fr\/en\/wp-json\/wp\/v2\/tags?post=13700"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}