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authFullName_s : Jérôme Waldispühl
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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

Proceedings of the 1st workshop on Computational Methods for Structural RNAs

Fabrice Jossinet , Yann Ponty , Jérôme Waldispühl
Jossinet, Fabrice; Ponty, Yann; Waldispühl, Jérôme. McGill University, pp.76, 2014, 978-2-9550187-0-5. ⟨10.15455/CMSR.2014.0000⟩
Books hal-01071417v1

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.

Jérôme Waldispühl , Yann Ponty
Journal of Computational Biology, 2011, 18 (11), pp.1465-79. ⟨10.1089/cmb.2011.0181⟩
Journal articles hal-00681928v1

Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates

Mohamed Raef Smaoui , Frédéric Poitevin , Marc Delarue , Patrice Koehl , Henri Orland et al.
Biophysical Journal, 2013, 104 (3), pp.683-693. ⟨10.1016/j.bpj.2012.12.037⟩
Journal articles pasteur-02174650v1

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.
Bioinformatics, 2020, 36 (9), pp.2910--2922. ⟨10.1093/bioinformatics/btaa039⟩
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.
PLoS Computational Biology, 2018, 14 (3), pp.e1005955. ⟨10.1371/journal.pcbi.1005955⟩
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 of Computational Biology, 2013, 20 (11), pp.905-19. ⟨10.1089/cmb.2013.0085⟩
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.
Briefings in Bioinformatics, 2018, 19 (2), pp.350--358. ⟨10.1093/bib/bbw120⟩
Journal articles hal-01392958v1

Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes

Mohamed Raef Smaoui , Henri Orland , Jérôme Waldispühl
Bioinformatics, 2015, 31 (14), pp.2294-2302. ⟨10.1093/bioinformatics/btv143⟩
Journal articles cea-02926922v1

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.
Nucleic Acids Research, 2012, 40 (20), pp.10041-10052. ⟨10.1093/nar/gks768⟩
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.
PLoS Computational Biology, 2021, 17 (5), pp.e1008990. ⟨10.1371/journal.pcbi.1008990⟩
Journal articles hal-03381570v1

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
Nucleic Acids Research, 2016, 44 (11), pp.e104 - e104. ⟨10.1093/nar/gkw217⟩
Journal articles hal-01291754v1

OptiMol : Optimization of Binding Affinities in Chemical Space for Drug Discovery

Jacques Boitreaud , Vincent Mallet , Carlos Oliver , Jérôme Waldispühl
Journal of Chemical Information and Modeling, 2020, 60 (12), pp.5658-5666. ⟨10.1021/acs.jcim.0c00833⟩
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.
Nucleic Acids Research, 2016, 44 (W1), pp.W308 - W314. ⟨10.1093/nar/gkw440⟩
Journal articles hal-01319682v1

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl
Bioinformatics, 2013, 29 (13), pp.i308-15. ⟨10.1093/bioinformatics/btt217⟩
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.
Nucleic Acids Research, 2020, 48 (14), pp.7690-7699. ⟨10.1093/nar/gkaa583⟩
Journal articles hal-03122151v1