CSDAI

Department of Institut Polytechnique de Paris

Group amibio

amibio (Algorithms and models for integrative biology)

LIX, Ecole Polytechnique

Themes: computer science in biology and health

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.

Contact person: Yann Ponty, https://www.lix.polytechnique.fr/~ponty

Web site: https://www.lix.polytechnique.fr/amibio/

Journal articles

2024

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Irene Beckmann, Maria Waldl, Sebastian Will, Ivo Hofacker. 3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations. RNA, 2024, 30 (2), pp.113-123. ⟨10.1261/rna.079756.123⟩. ⟨hal-04483612⟩
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https://inria.hal.science/hal-04483612/file/3D_Feasibility_of_2D_RNA-RNA_Interaction_Paths_by_.pdf BibTex
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Marie-Olive Thaury, Simon Genet, Léopold Maurice, Paola Tubaro, Sarah J Berkemer. City composition and accessibility statistics in and around Paris. Frontiers in Big Data, 2024, 7, ⟨10.3389/fdata.2024.1354007⟩. ⟨hal-04460871⟩
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https://hal.science/hal-04460871/file/frontiers.pdf BibTex
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Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty, Sebastian Will. Infrared: a declarative tree decomposition-powered framework for bioinformatics. Algorithms for Molecular Biology, 2024, ⟨10.1186/s13015-024-00258-2⟩. ⟨hal-04211173v2⟩
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https://inria.hal.science/hal-04211173/file/s13015-024-00258-2-2.pdf BibTex

2023

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Christiane Gärtner, Jörg Fallmann, Peter F Stadler, Thorsten Kaiser, Sarah J Berkemer. Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis. Journal of Personalized Medicine, 2023, 13 (6), pp.924. ⟨10.3390/jpm1010000⟩. ⟨hal-04460883⟩
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https://hal.science/hal-04460883/file/Toward_a_Systematic_Assessment_of_Sex_Differences.pdf BibTex
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Bertrand Marchand, Sebastian Will, Sarah Berkemer, Yann Ponty, Laurent Bulteau. Automated design of dynamic programming schemes for RNA folding with pseudoknots. Algorithms for Molecular Biology, 2023, 18 (1), pp.18. ⟨10.1186/s13015-023-00229-z⟩. ⟨hal-04103565⟩
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https://hal.science/hal-04103565/file/long_version_autodp.pdf BibTex

2022

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Alexander Churkin, Yann Ponty, Danny Barash. IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. BMC Bioinformatics, 2022, 23 (S8), pp.424. ⟨10.1186/s12859-022-04943-0⟩. ⟨hal-03815555⟩
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Bertrand Marchand, Yann Ponty, Laurent Bulteau. Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. Algorithms for Molecular Biology, 2022, 17 (1), pp.8. ⟨10.1186/s13015-022-00213-z⟩. ⟨hal-03608412v2⟩
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https://hal.science/hal-03608412/file/Treewidth_Reduction_AMB.pdf BibTex
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Peter F Stadler, Sebastian Will. Bi-Alignments with Affine Gaps Costs. Algorithms for Molecular Biology, 2022, ⟨10.1186/s13015-022-00219-7⟩. ⟨hal-03711809⟩
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https://hal.science/hal-03711809/file/affishift.pdf BibTex

2021

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Lorraine a K Ayad, Golnaz Badkobeh, Gabriele Fici, Alice Héliou, Solon P Pissis. Constructing Antidictionaries of Long Texts in Output-Sensitive Space. Theory of Computing Systems, 2021, 65 (5), pp.777-797. ⟨10.1007/s00224-020-10018-5⟩. ⟨hal-03498331⟩
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https://inria.hal.science/hal-03498331/file/1902.04785.pdf BibTex
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Grégoire de Bisschop, Delphine Allouche, Elisa Frezza, Benoît Masquida, Yann Ponty, et al.. Progress Toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. Non-Coding RNA, 2021, 7 (4), pp.71. ⟨10.3390/ncrna7040071⟩. ⟨hal-03413594⟩
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https://inria.hal.science/hal-03413594/file/ncrna-1422092.pdf BibTex
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Gregor Entzian, Ivo Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer. RNAxplorer: Harnessing the Power of Guiding Potentials to Sample RNA Landscapes. Bioinformatics, 2021. ⟨hal-02889448v3⟩
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https://inria.hal.science/hal-02889448/file/RNAxplorer-preprint-2020.pdf BibTex
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Ha T.N. Nguyen, Haoliang Xue, Virginie Firlej, Yann Ponty, Melina Gallopin, et al.. Reference-free transcriptome signatures for prostate cancer prognosis. BMC Cancer, 2021, 21 (1), pp.394. ⟨10.1186/s12885-021-08021-1⟩. ⟨hal-04241891⟩
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Ha Tn Nguyen, Haoliang Xue, Virginie Firlej, Yann Ponty, Mélina Gallopin, et al.. Reference-free transcriptome signatures for prostate cancer prognosis. BMC Cancer, 2021, 21 (394), ⟨10.1186/s12885-021-08021-1⟩. ⟨hal-02948844⟩
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https://inria.hal.science/hal-02948844/file/39043604_File000004_951818349-1.pdf BibTex
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Dehe Wang, Ao Jiang, Jiangpeng Feng, Guangnan Li, Dong Guo, et al.. The SARS-CoV-2 Subgenome Landscape and its Novel Regulatory Features. Molecular Cell, In press, ⟨10.1016/j.molcel.2021.02.036⟩. ⟨hal-03154155v2⟩
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https://hal.science/hal-03154155/file/main.pdf BibTex

2020

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Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen. Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. Algorithms for Molecular Biology, 2020, 15 (1), ⟨10.1186/s13015-020-00179-w⟩. ⟨hal-03131203⟩
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Teresa Müller, Milad Miladi, Frank Hutter, Ivo Hofacker, Sebastian Will, et al.. The locality dilemma of Sankoff-like RNA alignments. Bioinformatics, 2020, 36 (Supplement_1), pp.i242-i250. ⟨10.1093/bioinformatics/btaa431⟩. ⟨hal-02909014⟩
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Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, et al.. IncaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs. Bioinformatics, 2020, 36 (9), pp.2910--2922. ⟨10.1093/bioinformatics/btaa039⟩. ⟨hal-02423237⟩
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Afaf Saaidi, Delphine M Allouche, Mireille Regnier, Bruno Sargueil, Yann Ponty. IPANEMAP: Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles. Nucleic Acids Research, 2020, 48 (15), pp.8276--8289. ⟨10.1093/nar/gkaa607⟩. ⟨hal-02889041v3⟩
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https://inria.hal.science/hal-02889041/file/IPANEMAP-BioRXvix-2020.pdf BibTex
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Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl. A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae. Journal of Computational Biology, 2020, 27 (3), pp.390-402. ⟨10.1089/cmb.2019.0464⟩. ⟨hal-04466122⟩
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2019

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Cedric Chauve, Yann Ponty, Michael Wallner. Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. Journal of Mathematical Biology, 2019, 80 (5), pp.1353--1388. ⟨10.1007/s00285-019-01465-x⟩. ⟨hal-02169271⟩
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https://inria.hal.science/hal-02169271/file/Counting_DLT_Histories_notes.pdf BibTex
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Maxime Crochemore, Alice Héliou, Gregory Kucherov, Laurent Mouchard, Solon Pissis, et al.. Absent words in a sliding window with applications. Information and Computation, 2019, pp.104461. ⟨10.1016/j.ic.2019.104461⟩. ⟨hal-02414839⟩
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Stefan Hammer, Wei Wang, Sebastian Will, Yann Ponty. Fixed-parameter tractable sampling for RNA design with multiple target structures. BMC Bioinformatics, 2019, 20 (1), pp.209. ⟨10.1186/s12859-019-2784-7⟩. ⟨hal-02112888⟩
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https://inria.hal.science/hal-02112888/file/RNARedPrint.pdf BibTex
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Jordy Homing Lam, Yu Li, Lizhe Zhu, Ramzan Umarov, Hanlun Jiang, et al.. A deep learning framework to predict binding preference of RNA constituents on protein surface. Nature Communications, 2019, 10 (1), pp.4941. ⟨10.1016/j.ic.2019.104461⟩. ⟨hal-04466074⟩
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Defne Surujon, Yann Ponty, Peter Clote. Small-world networks and RNA secondary structures. Journal of Computational Biology, 2019, 26 (1), pp.16--26. ⟨10.1089/cmb.2018.0125⟩. ⟨hal-01424452v2⟩
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https://inria.hal.science/hal-01424452/file/main2018.pdf BibTex

2018

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Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, et al.. Meet-U: educating through research immersion. PLoS Computational Biology, 2018, 14 (3), pp.1-10. ⟨10.1371/journal.pcbi.1005992⟩. ⟨hal-01722019⟩
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https://inria.hal.science/hal-01722019/file/journal.pcbi.1005992.pdf BibTex
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Cedric Chauve, Julien Courtiel, Yann Ponty. Counting, generating, analyzing and sampling tree alignments. International Journal of Foundations of Computer Science, 2018, 29 (5), pp.741--767. ⟨hal-01500116⟩
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https://inria.hal.science/hal-01500116/file/main.pdf BibTex
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Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, et al.. Design of RNAs: comparing programs for inverse RNA folding.. Briefings in Bioinformatics, 2018, 19 (2), pp.350--358. ⟨10.1093/bib/bbw120⟩. ⟨hal-01392958⟩
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https://inria.hal.science/hal-01392958/file/Design_Software_Review_2016.pdf BibTex
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Hosna Jabbari, Ian Wark, Carlo Montemagno, Sebastian Will. Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. Bioinformatics, 2018, 34 (22), pp.3849-3856. ⟨10.1093/bioinformatics/bty420⟩. ⟨hal-02908990⟩
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Joong Chae Na, Hyunjoon Kim, Seunghwan Min, Heejin Park, Thierry Lecroq, et al.. FM-index of alignment with gaps. Theoretical Computer Science, 2018, 710, pp.148 - 157. ⟨10.1016/j.tcs.2017.02.020⟩. ⟨hal-01894852⟩
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Gydo van Zundert, Brandi Hudson, Saulo de Oliveira, Daniel Keedy, Rasmus Fonseca, et al.. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. Journal of Medicinal Chemistry, 2018, 61 (24), pp.11183-11198. ⟨10.1021/acs.jmedchem.8b01292⟩. ⟨hal-04466087⟩
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2017

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Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, et al.. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biology and Evolution, 2017, 9 (5), pp.1312-1319. ⟨10.1093/gbe/evx069⟩. ⟨hal-01503766v2⟩
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https://inria.hal.science/hal-01503766/file/evx069.pdf BibTex
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Björn Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, et al.. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Research, 2017, 45 (W1), pp.W560-W566. ⟨10.1093/nar/gkx409⟩. ⟨hal-04645102⟩
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Jozef Haleš, Alice Héliou, Ján Maňuch, Yann Ponty, Ladislav Stacho. Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models. Algorithmica, 2017, 79 (3), pp.835--856. ⟨10.1007/s00453-016-0196-x⟩. ⟨hal-01285499v2⟩
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https://inria.hal.science/hal-01285499/file/CombinatorialRNADesign-Hales-Manuch-Ponty-Stacho-Algorithmica-2015.pdf BibTex
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Marcel Levy Nogueira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Olivier Lafitte, et al.. Mechanical stress increases brain amyloid β, tau, and α‐synuclein concentrations in wild‐type mice. Alzheimer's & Dementia : the Journal of the Alzheimer's Association, 2017, 14 (4), pp.444-453. ⟨10.1016/j.jalz.2017.11.003⟩. ⟨hal-04466110⟩
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Benedikt Löwes, Cedric Chauve, Yann Ponty, Robert Giegerich. The BRaliBase dent - a tale of benchmark design and interpretation.. Briefings in Bioinformatics, 2017, 18 (2), pp.306--311. ⟨10.1093/bib/bbw022⟩. ⟨hal-01273406⟩
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https://inria.hal.science/hal-01273406/file/bbw022.pdf BibTex
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Laurent Schwartz, Jorgelindo da Veiga Moreira, Mario Jolicoeur. Physical forces modulate cell differentiation and proliferation processes. Journal of Cellular and Molecular Medicine, 2017, 22 (2), pp.738-745. ⟨10.1111/jcmm.13417⟩. ⟨hal-04466153⟩
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Conference papers

2024

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Kimon Boehmer, Sarah J Berkemer, Sebastian Will, Yann Ponty. RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. WABI 2024 - 24th Workshop on Algorithms in Bioinformatics, 2024, London, United Kingdom. ⟨hal-04589903v2⟩
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https://hal.science/hal-04589903/file/Algorithms_for_Folding_of_Triplet_Repeat_RNAs___Paper-9.pdf BibTex
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Théo Boury, Vladimir Reinharz, Yann Ponty. Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique. Journées Ouvertes en Biologie, Informatique, et Mathématiques 2024 (JOBIM 2024), Jun 2024, Toulouse, France. ⟨hal-04575263⟩
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https://hal.science/hal-04575263/file/PLR1Fuzzy_SubGraph_Isomorphism_using_Tree_Decomposition-3.pdf BibTex
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Théo Boury, Laurent Bulteau, Yann Ponty. RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs. WABI 2024 - 24th Workshop on Algorithms in Bioinformatics, 2024, London, United Kingdom. ⟨hal-04589901v2⟩
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https://hal.science/hal-04589901/file/Linear_BP_Design___WABI_2024-14.pdf BibTex
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Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty. Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. RECOMB 2024 - 28th International Conference of Research in Computational Molecular Biology, Apr 2024, Boston, United States. ⟨hal-03816423v3⟩
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https://hal.science/hal-03816423/file/ColorCoding_Bioinfo_2023-8.pdf BibTex

2023

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Sarah J. Berkemer, Simon Genet, Léopold Maurice, Marie-Olive Thaury, Paola Tubaro. Is Paris a good example for a X-minute city?: Modeling city composition on POI data and X-minute statistics in Paris. FRCCS 2023, May 2023, Le Havre, France. ⟨hal-04103593⟩
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https://hal.science/hal-04103593/file/FRCCS_extended_abstract_onecolumn.pdf BibTex
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Théo Boury, Yann Ponty, Vladimir Reinharz. Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique. WABI 2023 - 23rd Workshop on Algorithms in Bioinformatics, Texas A&M University, Sep 2023, Houston, United States. ⟨10.4230/LIPIcs.WABI.2023.20⟩. ⟨hal-04094288v2⟩
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https://hal.science/hal-04094288/file/PLR1Fuzzy_SubGraph_Isomorphism_using_Tree_Decomposition-2.pdf BibTex
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Matthieu Dinot, Benjamin Doerr, Ulysse Hennebelle, Sebastian Will. Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. International Joint Conference on Artificial Intelligence, IJCAI 2023, 2023, Macao SAR, Macau SAR China. pp.5549-5557, ⟨10.24963/ijcai.2023/616⟩. ⟨hal-04100997⟩
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https://hal.science/hal-04100997/file/Noisy_SEMO-58.pdf BibTex
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Mateo Gray, Sebastian Will, Hosna Jabbari. SparseRNAFolD: Sparse RNA pseudoknot-free Folding including Dangles. Workshop on Algorithms in Bioinformatics (WABI2023), Sep 2023, Houston, TX, United States. ⟨10.4230/LIPIcs.WABI.2023.19⟩. ⟨hal-04477375⟩
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https://inria.hal.science/hal-04477375/file/main.pdf BibTex

2022

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Bertrand Marchand, Sebastian Will, Sarah Berkemer, Laurent Bulteau, Yann Ponty. Automated design of dynamic programming schemes for RNA folding with pseudoknots. WABI 2022 - 22nd Workshop on Algorithms in Bioinformatics, Sep 2022, Potsdam, Germany. ⟨hal-03676377v2⟩
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https://inria.hal.science/hal-03676377/file/auto_DP.pdf BibTex

2021

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Laurent Bulteau, Bertrand Marchand, Yann Ponty. A new parametrization for independent set reconfiguration and applications to RNA kinetics. IPEC 2021 - 16th International Symposium on Parameterized and Exact Computation, Sep 2021, Lisbon, Portugal. ⟨hal-03272963v2⟩
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https://hal.science/hal-03272963/file/article.pdf BibTex
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Sammy Khalife, Yann Ponty, Laurent Bulteau. Sequence graphs realizations and ambiguity in language models. COCOON 2021 - 27th International Computing and Combinatorics Conference, Oct 2021, Tainan, Taiwan. ⟨10.1007/978-3-030-89543-3_13⟩. ⟨hal-02495333v4⟩
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https://hal.science/hal-02495333/file/_open_access__TCS22_sequence_graphs_ambiguity_language_models%20%281%29.pdf BibTex
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Bertrand Marchand, Yann Ponty, Laurent Bulteau. Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. WABI 2021 - 21st Workshop on Algorithms in Bioinformatics, 2021, Paris, France. ⟨hal-03206132⟩
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https://inria.hal.science/hal-03206132/file/main.pdf BibTex
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Hua-Ting Yao, Jérôme Waldispühl, Yann Ponty, Sebastian Will. Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA. RECOMB 2021 - 25th international conference on research in computational molecular biology, Apr 2021, Padova, France. ⟨hal-02987566v2⟩
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https://inria.hal.science/hal-02987566/file/main.pdf BibTex

2020

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Alexander Churkin, Yann Ponty, Danny Barash. IndelsRNAmute: Predicting deleterious multiple point substitutions and indels mutations. ISBRA 2020 - 16th International Symposium on Bioinformatics Research and Applications, Dec 2020, Moscow, Russia. ⟨hal-02936276⟩
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https://inria.hal.science/hal-02936276/file/RNAMute_Evolved.pdf BibTex
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Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G Oliver, Yann Ponty, et al.. Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules Identification. RECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology, May 2020, Padova, Italy. ⟨hal-02354733⟩
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https://inria.hal.science/hal-02354733/file/BayesPairing2_recomb_submitted.pdf BibTex

2019

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Maher Mallem, Alain Denise, Yann Ponty. Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity tests. SEQBIM 2019 - Séquences en Bioinformatique, Informatique et Mathématiques, Dec 2019, Marne-la-Vallée, France. ⟨hal-02403517⟩
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https://inria.hal.science/hal-02403517/file/Design_Connectivity_Maher_2019%283%29.pdf BibTex
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Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen. Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. Workshop on Algorithms in Bioinformatics (WABI 2019), Sep 2019, Niagara Falls, NY, United States. ⟨10.4230/LIPIcs.WABI.2019.14⟩. ⟨hal-04477418⟩
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https://inria.hal.science/hal-04477418/file/LIPIcs.WABI.2019.14.pdf BibTex
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Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov. Effective Rotation-invariant Point CNN with Spherical Harmonics kernels. 3DV - International Conference on 3D Vision - 2019, Sep 2019, Québec City, Canada. ⟨hal-02167454v2⟩
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https://inria.hal.science/hal-02167454/file/Spherical_harmonic_cnn_Pro_version.pdf BibTex
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Maria Waldl, Sebastian Will, Peter F. Stadler, Michael T. Wolfinger, Ivo L. Hofacker. Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. CIBB 2019 - 16th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, Sep 2019, Bergamo, Italy. pp.159-170, ⟨10.1007/978-3-030-63061-4_15⟩. ⟨hal-03131248⟩
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https://inria.hal.science/hal-03131248/file/cibb_lnbi.pdf BibTex
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Hua-Ting Yao, Cedric Chauve, Mireille Regnier, Yann Ponty. Exponentially few RNA structures are designable. ACM-BCB 2019 - 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Sep 2019, Niagara-Falls, United States. pp.289-298, ⟨10.1145/3307339.3342163⟩. ⟨hal-02141853v2⟩
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https://inria.hal.science/hal-02141853/file/CountingDesigns.pdf BibTex

2018

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Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB - 22nd Annual International Conference on Research in Computational Molecular Biology - 2018, Apr 2018, Paris, France. ⟨hal-01631277v2⟩
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https://inria.hal.science/hal-01631277/file/RNARedPrint-Bioinfo2018.pdf BibTex
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Yann Ponty, Sebastian Will, Stefan Hammer. Nucleic Acids design targeting integer-valued features: FPT counting and uniform sampling. WEPA 2018 - 2nd International Workshop on Enumeration Problems and Applications, Nov 2018, Pisa, Italy. ⟨hal-01911878⟩
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https://inria.hal.science/hal-01911878/file/WEPA_2018.pdf BibTex
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Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl. A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. RECOMB 2018 - 22nd International Conference on Research in Computational Molecular Biology, 2018, Paris, France. pp.177-193, ⟨10.1007/978-3-319-89929-9_12⟩. ⟨hal-04466141⟩
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2017

ref_biblio
Juraj Michálik, Hélène Touzet, Yann Ponty. Efficient approximations of RNA kinetics landscape using non-redundant sampling. ISMB/ECCB - 25th Annual international conference on Intelligent Systems for Molecular Biology/16th European Conference on Computational Biology - 2017, Jul 2017, Prague, Czech Republic. pp.i283 - i292, ⟨10.1093/bioinformatics/btx269⟩. ⟨hal-01500115⟩
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https://inria.hal.science/hal-01500115/file/michalik-ISMB-2017.pdf BibTex
ref_biblio
Afaf Saaidi, Yann Ponty, Mathieu Blanchette, Mireille Regnier, Bruno Sargueil. An EM algorithm for mapping short reads in multiple RNA structure probing experiments. Matbio2017, King's College London Sep 2017, London, United Kingdom. ⟨hal-01590528⟩
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2015

ref_biblio
Jozef Haleš, Ján Maňuch, Yann Ponty, Ladislav Stacho. Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. ⟨hal-01115349v2⟩
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https://inria.hal.science/hal-01115349/file/RNADesign-CPM2015-Final.pdf BibTex

Book sections

2024

ref_biblio
Delphine M Allouche, Grégoire de Bisschop, Afaf Saaidi, Pierre Hardouin, Francois-Xavier Lyonnet Du Moutier, et al.. RNA secondary structure modelling following the IPANEMAP workflow. RNA Folding - Methods and Protocols, 2726, Springer Nature; Springer US, pp.85-104, 2024, Methods in Molecular Biology, ⟨10.1007/978-1-0716-3519-3_4⟩. ⟨hal-02324783⟩
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https://inria.hal.science/hal-02324783/file/RNA_Probing_IPANEMAP12_07.pdf BibTex
ref_biblio
Hua-Ting Yao, Yann Ponty, Sebastian Will. Developing complex RNA design applications in the Infrared framework. RNA Folding - Methods and Protocols, 2726, Springer US, pp.285-313, 2024, Methods in Molecular Biology, ⟨10.1007/978-1-0716-3519-3_12⟩. ⟨hal-03711828v2⟩
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https://hal.science/hal-03711828/file/infrared-bookchapter.pdf BibTex

2022

ref_biblio
Yann Ponty, Vladimir Reinharz. RNA Folding. From text to graphs: Discrete structures and methods for Bioinformatics, ISTE, 2022. ⟨hal-03614168⟩
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https://hal.science/hal-03614168/file/Book.pdf BibTex
ref_biblio
Sebastian Will. LocARNA 2.0: versatile simultaneous alignment and folding of RNAs. RNA Folding - Methods and Protocols, In press. ⟨hal-03864352⟩
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https://hal.science/hal-03864352/file/locarna-bookchapter.pdf BibTex

2021

ref_biblio
Yann Ponty, Stefan Hammer, Hua-Ting Yao, Sebastian Will. Advanced design of structural RNAs using RNARedPrint. Ernesto Picardi. RNA Bioinformatics, 2284, pp.1--15, 2021, Methods in Molecular Biology, 978-1-0716-1306-1. ⟨10.1007/978-1-0716-1307-8_1⟩. ⟨hal-02990264⟩
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https://inria.hal.science/hal-02990264/file/RNARedPrint_Chapter_MiMB.pdf BibTex

2020

ref_biblio
Yann Ponty, Vladimir Reinharz. Repliement de l'ARN. Annie Chateau; Mikaël Salson. Du texte aux graphes : méthodes et structures discrètes pour la bioinformatique, A paraître. ⟨hal-02864246⟩
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https://inria.hal.science/hal-02864246/file/Chapitre_ISTE%283%29.pdf BibTex

Habilitation à diriger des recherches

2020

ref_biblio
Yann Ponty. Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond. Bioinformatics [q-bio.QM]. Université Paris-Saclay, 2020. ⟨tel-03219977v2⟩
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https://theses.hal.science/tel-03219977/file/HDR-Ponty.pdf BibTex

Proceedings

2024

ref_biblio
Tijana Milenković, Yann Ponty. ISMB 2024 Proceedings. ISMB - 25th Annual international conference on Intelligent Systems for Molecular Biology - 2024, Bioinformatics, 40 (Supplement_1), pp.i1-i2, 2024, ⟨10.1093/bioinformatics/btae286⟩. ⟨hal-04654725⟩
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2023

ref_biblio
Sven Findeiß, Christoph Flamm, Yann Ponty. Preface/Executive summary. Report of Dagstuhl Seminar 22381: Rational Design of RiboNucleic Acids, 12 (9), Dagstuhl publishing, pp.121-149, 2023, ⟨10.4230/DagRep.12.9.121⟩. ⟨hal-04058064⟩
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https://inria.hal.science/hal-04058064/file/dagrep_v012_i009_p121_22381.pdf BibTex
ref_biblio
Yann Ponty, Sushmita Roy. ISMB/ECCB 2023 proceedings. Bioinformatics, 39 (Supplement_1), pp.i1-i2, 2023, ⟨10.1093/bioinformatics/btad319⟩. ⟨hal-04146834⟩
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2022

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Sean O’donoghue, Jim Procter, Lucy Collinson, Andrew David Yates, Lydia Gregg, et al.. VIZBI 2021 special issue. VIZBI 2021 - 11th international meeting on visualizing biological data, Frontiers in Bioinformatics, 1, 2022, 11th international meeting on visualizing biological data (VIZBI 2021), ⟨10.3389/978-2-83250-637-0⟩. ⟨hal-03902813⟩
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Theses

2021

ref_biblio
Hua-Ting Yao. Local decomposition in RNA structural design. Bioinformatics [q-bio.QM]. Institut Polytechnique de Paris; McGill university (Montréal, Canada), 2021. English. ⟨NNT : 2021IPPAX126⟩. ⟨tel-03538576v3⟩
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https://theses.hal.science/tel-03538576/file/108219_YAO_2021_archivage.pdf BibTex

Preprints, Working Papers, ...

2023

ref_biblio
Théo Boury, Laurent Bulteau, Bertrand Marchand, Yann Ponty. Independent set reconfiguration: general and RNA-focused parameterized algorithms. 2023. ⟨hal-04094405⟩
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https://hal.science/hal-04094405/file/RNA_barriers-3.pdf BibTex
ref_biblio
Jorge Fernandez-De-Cossio-Diaz, Pierre Hardouin, Francois-Xavier Lyonnet Du Moutier, Andrea Di Gioacchino, Bertrand Marchand, et al.. Designing molecular RNA switches with Restricted Boltzmann machines. 2023. ⟨hal-04294884⟩
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https://hal.science/hal-04294884/file/Fernandez-de-Cossio-Diaz%20et%20al.%20-%202023%20-%20Designing%20molecular%20RNA%20switches%20with%20Restricted%20B.pdf BibTex