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Structure: Internal structure identifier : 222004
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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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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

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Annabelle A. Haudry , Adrian Platts , Emilio Vello , Douglas Hoen , Mickael Leclercq et al.
Nature Genetics, 2013, 45 (8), pp.891 - 898. ⟨10.1038/ng.2684⟩
Journal articles hal-01907704v1
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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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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
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Gene tree correction guided by orthology

Manuel Lafond , Magali Semeria , Krister M. Swenson , Eric Tannier , Nadia El-Mabrouk et al.
BMC Bioinformatics, 2013, 14 (Suppl 15), pp.S5
Journal articles hal-00873235v1
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Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish.

Emmanuel Mongin , Thomas O Auer , Franck Bourrat , Franziska Gruhl , Ken Dewar et al.
PLoS ONE, 2011, 6 (5), pp.e19747. ⟨10.1371/journal.pone.0019747⟩
Journal articles hal-00637202v1
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Models and algorithms for genome rearrangement with positional constraints

Krister M. Swenson , Pijus Simonaitis , Mathieu Blanchette
Algorithms for Molecular Biology, 2016, 11 (1), pp.13-24. ⟨10.1186/s13015-016-0065-9⟩
Journal articles lirmm-01348502v1
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Gene Maps Linearization using Genomic Rearrangement Distances

Guillaume Blin , Eric Blais , Danny Hermelin , Pierre Guillon , Mathieu Blanchette et al.
Journal of Computational Biology, 2007, 14 (4), pp.394-407
Journal articles hal-00619755v1
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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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Large-scale mammalian genome rearrangements coincide with chromatin interactions

Krister M. Swenson , Mathieu Blanchette
Bioinformatics, 2019, 35 (14), pp.i117-i126. ⟨10.1093/bioinformatics/btz343⟩
Journal articles lirmm-02410438v1
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Exponentially few RNA structures are designable

Hua-Ting Yao , Cedric Chauve , Mireille Regnier , Yann Ponty
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⟩
Conference papers hal-02141853v2
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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
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Inferring Gene Orders from Gene Maps using the Breakpoint Distance

Guillaume Blin , Eric Blais , Pierre Guillon , Mathieu Blanchette , Nadia El-Mabrouk et al.
4th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'06), Sep 2006, Montréal, Canada. pp.99-112
Conference papers hal-00620364v1

Reprogramming of the tumour microenvironment by stromal PTEN-regulated miR-320

Agnieszka Bronisz , Jakub Godlewski , Julie Wallace , Anand S. Merchant , Michal O. Nowicki et al.
Nature Cell Biology, 2011
Journal articles hal-00921623v1
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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

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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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

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

Robert Williamson , Emily Josephs , Adrian Platts , Khaled Hazzouri , Annabelle A. Haudry et al.
PLoS Genetics, 2014, 10 (9), ⟨10.1371/journal.pgen.1004622⟩
Journal articles hal-01907734v1