Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA
Hua-Ting Yao
,
Jérôme Waldispühl
,
Yann Ponty
,
Sebastian Will
RECOMB 2021 - 25th international conference on research in computational molecular biology , Apr 2021, Padova, France
Conference papers
hal-02987566v2
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SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.
Yang Zhang
,
Yann Ponty
,
Mathieu Blanchette
,
Eric Lecuyer
,
Jérôme Waldispühl
et al.
Nucleic Acids Research , 2013, Web Server Issue, 41 (Web Server issue), pp.W480-5.
⟨10.1093/nar/gkt461⟩
Journal articles
hal-00819017v1
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A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences
Vladimir Reinharz
,
Yann Ponty
,
Jérôme Waldispühl
RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013 , Apr 2013, Beijing, China
Conference papers
hal-00766781v1
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Proceedings of the 1st workshop on Computational Methods for Structural RNAs
Fabrice Jossinet
,
Yann Ponty
,
Jérôme Waldispühl
Books
hal-01071417v1
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An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.
Jérôme Waldispühl
,
Yann Ponty
Journal articles
hal-00681928v1
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Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates
Mohamed Raef Smaoui
,
Frédéric Poitevin
,
Marc Delarue
,
Patrice Koehl
,
Henri Orland
et al.
Journal articles
pasteur-02174650v1
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IncaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs
Matan Drory Retwitzer
,
Vladimir Reinharz
,
Alexander Churkin
,
Yann Ponty
,
Jérôme Waldispühl
et al.
Journal articles
hal-02423237v1
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Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families
Vladimir Reinharz
,
Antoine Soulé
,
Eric Westhof
,
Jérôme Waldispühl
,
Alain Denise
et al.
Nucleic Acids Research , 2018
Journal articles
hal-01745345v1
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Ten simple rules to create a serious game, illustrated with examples from structural biology
Marc Baaden
,
Olivier Delalande
,
Nicolas Ferey
,
Samuela Pasquali
,
Jérôme Waldispühl
et al.
Journal articles
hal-01744190v1
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Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs.
Vladimir Reinharz
,
Yann Ponty
,
Jérôme Waldispühl
Journal articles
hal-00828062v1
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Design of RNAs: comparing programs for inverse RNA folding.
Alexander Churkin
,
Matan Drory Retwitzer
,
Vladimir Reinharz
,
Yann Ponty
,
Jérôme Waldispühl
et al.
Journal articles
hal-01392958v1
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Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes
Mohamed Raef Smaoui
,
Henri Orland
,
Jérôme Waldispühl
Journal articles
cea-02926922v1
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A global sampling approach to designing and reengineering RNA secondary structures.
Alex Levin
,
Mieszko Lis
,
Yann Ponty
,
Charles W O'Donnell
,
Srinivas Devadas
et al.
Journal articles
hal-00733924v1
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An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure
Jérôme Waldispühl
,
Yann Ponty
RECOMB - 15th Annual International Conference on Research in Computational Molecular Biology - 2011 , Mar 2011, Vancouver, Canada. pp.501-515,
⟨10.1007/978-3-642-20036-6_45⟩
Conference papers
hal-00546847v1
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Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs
Antoine Soulé
,
Vladimir Reinharz
,
Roman Sarrazin-Gendron
,
Alain Denise
,
Jérôme Waldispühl
et al.
Journal articles
hal-03381570v1
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Preface.
Fabrice Jossinet
,
Yann Ponty
,
Jérôme Waldispühl
Computational methods for Structural RNAs (CMSR'14) , 22 (3),
Mary Ann Liebert , pp.189, 2015, Journal of Computational Biology
Book sections
hal-01136745v1
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Flexible RNA design under structure and sequence constraints using formal languages
Yu Zhou
,
Yann Ponty
,
Stéphane Vialette
,
Jérôme Waldispühl
,
Yi Zhang
et al.
ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013 , Sep 2013, Bethesda, Washigton DC, United States
Conference papers
hal-00823279v2
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Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces
Vladimir Reinharz
,
Yann Ponty
,
Jérôme Waldispühl
Journal articles
hal-01291754v1
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OptiMol : Optimization of Binding Affinities in Chemical Space for Drug Discovery
Jacques Boitreaud
,
Vincent Mallet
,
Carlos Oliver
,
Jérôme Waldispühl
Journal articles
hal-03122149v1
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A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution
Vladimir Reinharz
,
Yann Ponty
,
Jérôme Waldispühl
ISMB/ECCB - 21st Annual international conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology - 2013 , Jul 2013, Berlin, Germany
Conference papers
hal-00811607v1
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incaRNAfbinv : a web server for the fragment-based design of RNA sequences
Matan Drory retwitzer
,
Vladimir Reinharz
,
Yann Ponty
,
Jérôme Waldispühl
,
Danny Barash
et al.
Journal articles
hal-01319682v1
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A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.
Vladimir Reinharz
,
Yann Ponty
,
Jérôme Waldispühl
Journal articles
hal-00840260v1
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Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules Identification
Roman Sarrazin-Gendron
,
Hua-Ting Yao
,
Vladimir Reinharz
,
Carlos G Oliver
,
Yann Ponty
et al.
RECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology , May 2020, Padova, Italy
Conference papers
hal-02354733v1
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Augmented base pairing networks encode RNA-small molecule binding preferences
Carlos Oliver
,
Vincent Mallet
,
Roman Sarrazin Gendron
,
Vladimir Reinharz
,
William l Hamilton
et al.
Journal articles
hal-03122151v1
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