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
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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.
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 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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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.
Journal articles
hal-00637202v1
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Models and algorithms for genome rearrangement with positional constraints
Krister M. Swenson
,
Pijus Simonaitis
,
Mathieu Blanchette
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
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
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
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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
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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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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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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.
Journal articles
hal-01907734v1
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