Centro de Ciencias de Benasque Pedro Pascual

Centro de Ciencias de Benasque Pedro Pascual

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Computational Approaches to RNA Structure and Function

2018, Jul 15 -- Jul 27

E. Rivas (Harvard University), E. Westhof (University of Strasbourg)

Monday, July 16
  • 09:30:10:30h
  • Registration
  • 11:00h
  • How to identify conserved RNA structures. HOTAIR a negative case study
     E. Rivas
  • 18:00h
  • Organizational Session
     All participants

    Tuesday, July 17
    • 11:00h
    • Morning session: RNA Modifications
       Chair: Stadler - Westhof

    • Control over Translation: The Third Genetic code
       E. Westhof
        N6 - methylation of adenine in box C/D snoRNA : regulation of RNP assembly
       Lin Huang
        Patterns of tRNA Modifications
       P. Stadler

    • 18:00h
    • Afternoon session: RNA Design
       Chair: Ponty

    • Fixed-parameter tractable sampling for RNA design with multiple target structures
       Sebastian Will
        RNA designability
       Grzegorz Lach & Tomasz Wirecki
    • Designing an alanyl suppressor tRNA
       Marco Matthies
        Computational Riboswitch detection and RNA Design
       Matan Drory Retwitzer

      Wednesday, July 18
      • 10:00h
      • Statistics
      • 11:00h
      • Morning session: RNA protein interactions
         Chair: Backofen

      • Determing Functions of ncRNAs via RNA-protein Interactions
         R. Backofen
          On the practical use of enhanced crosslinking and immunoprecipitation (eCLIP) assay data (short talk)
         D. Pervouchine
          RNA-protein interaction and associations by RAIN (short talk)
         J. Gorodkin
          Predicting the RNA structural determinants in RNA-protein interactions
         F. Major
          Improving ribosome position assignments in RIBO-Seq by modeling nuclease-ribosome-RNA interactions (short talk)
         R. Bundschuh
          RNA-/DNA- binding sites prediction on protein
         Z. Miao

      • 18:00h
      • Afternoon session: Experimental methods (chemical probing)
         Chair: Dmitri Pervouchine

      • What does chemical probing 'reactivity' really mean?
         J. B. Lucks
          Transforming our view of RNA structure
         J. Thangappan
          Mining substructures in probing data
         S. Aviran
          Chemical probing approaches to enable RNA-targeted drug development
         L. Barrera
          Strategies in RNA X-ray crystallography
         L. Huang

        Thursday, July 19
        • 11:00h
        • Morning session: RNA Viruses
           Chair: Marz

        • RNA viruses
            Explaining Flavivirus Congenital Neurotropism with Thermodynamics
           M. T. Wolfinger
            Numerical Methods for Solving the Multiscale Model of Hepatitis C Virus
           D. Barash

        • 15:00h
        • Afeternoon session: RNA puzzles
        • RNA-Puzzles advances and perspectives
           Z. Miao

        • 18:00h
        • Afternonn session: RNA landscapes
           Chair: Heitsch

        • Capturing the Landscapes of RNA 2D Structures by Decomposition of Partition Functions
           K. Asai

          Friday, July 20
          • 11:00h
          • Morning session: Covariations
             Chair: Cocco

          • Protein-RNA co-evolution sites are close in 3D space
             Z. Miao
              Visualization of RNA and Protein family models and their comparisons
             F. Eggenhofer
              Learning protein constitutive motifs from sequence data with restricted Boltzmann machines
             R. Monasson
              Plan of the session on RNA Sequence Covariation
             S. Cocco

          • 15:00h
          • Afternoon session: RNA organizing the cell
             Chair: Brenner

          • 18:00h
          • Afternoon session: Databases
             Chair: Anton Petrov

          • CaRNAval: a database and a web resource for studying recurrent interaction networks in RNA structures
             A. Denise
              BGSU-NDB Collaboration: RNA Databases Update
             N. Leontis
              Improving and extending the annotation of Bacillus subtilis by curation and TSS data
             A. Geissler
              What's new in RNAcentral and Rfam
             A. Petrov

            Monday, July 23
            • 11:00h
            • Morning session: RNA 2D/3D
               Chair: Hofaker

            • Computational discovery of novel classes of bacterial non-coding RNAs
               Z. Weinberg
                RNA pseudoknotted Secondary Structure Prediction
               H. Jabbari
                RNA 2D/3D structure in RNApolis. There and Back Again
               M. Szachniuk, M. Antczak and T. Zok
            • Algorithm to capture local sequential- and 2D structural- RNA motifs
               Hiroshi Miyake
                How directable are 2D predictions?
               Christine Heitsch

            • 15:00h
            • Afternoon session: Hardcore Algorithms
            • 18:00h
            • Afternoon session: RNA 3D
               Chair: Sulc

            • Coarse-grained modeling of RNA for biology and nanotechnology
               Petr Sulc
                Coarse-grained nucleic acids physical modeling: basic principles and perspectives
               Samuela Pasquali
                Automated and Customizable Sequence-Based Identification of 3D Structural Modules
               Roman Sarrazin-Gendron
                RNA 3D Structure Prediction Using Multiple Sequence Alignment Information
               Marcin Magnus

              Tuesday, July 24
              • 11:00h
              • Morning session: RNA folding kinetics and co-transcriptional folding
                 Chair: Lorenz

              • Co-transcriptional Folding Kinetics and Riboswitch Modeling
                 I. Hofacker
                  Reconstructing RNA folding pathways from cotranscriptional SHAPE-Seq data
                 A. Yu
                  Computational studies of co-transcriptional folding - what we learned so far
                 I. Meyer
                  Efficient approximations of RNA kinetics landscape using non-redundant sampling
                 J. Michalik
                  Sampling RNA Secondary Structure Landscapes for Kinetics Simulations
                 R. Lorenz

              • 15:00h
              • Afternoon session: Integrative modeling
                 Chair: Pasquali

              • 18:00h
              • Afternoon session: RNA Variations
                 Chair: Brenner

              • Motivation for analyzing RNA sequence variants in natural populations & diagnostic human genomes
                 S. Brenner
                  Opportunities and challenges
                 R. Backofen
                  Transcriptome profiling at nucleotide resolution
                 D. Gautheret
                  Mutually Exclusive Exons, RNA structure, and genome duplication
                 D. Pervouchine
                  RNA structures in fungal introns
                 K. Hooks

                Wednesday, July 25
                • 11:00h
                • Morning session: Applications of RNA design
                   Chair: Will - Gorodkin

                • From sequence to nanostructure - The kink turn as a building block in nano-engineering
                   L. Huang
                    Enhancing off-target prediction of CRISPR-Cas9 by a nucleotide duplex model
                   J. Gorodkin
                    Feature reductions in CRISPR-Cas9 on-target efficiency predictions
                   G. Corsi
                    A Nested 2-Level Cross-validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae
                   A. Soule
                    On the emergence of structural complexity in self-replicating RNA populations
                   J. Waldispuehl

                • 15:00h
                • Rfam: building your own families and other new developments
                   Chair: Anton Petrov

                • 18:00h
                • Afternoon session: Comparative analysis
                   Chair: Nawrocki

                • Discovery of Archaeal group I introns using Infernal
                   E. Nawrocki
                    Genome-wide screens for RNA G-quadraplexes
                   A. Tanger
                    Benchmarking pipelines for the detection of genome-wide structural conservation in long non-coding RNAs
                   S. Fernandez Valverde
                    Comparative modeling and the elusive perfect benchmark
                   Y. Ponty

                  Thursday, July 26
                  • 11:00h
                  • Morning session: RNA regultaion + processing
                     Chair: Pervouchine - Lang

                  • Spliceosomal introns in 'primitive' unicellular flagellates
                     B. Franz Lang
                      Conservation of splice sites in plant lncRNAs
                     J. A. Corona
                      Transcriptome wide A-to-I editing in the fruit fly and its role in RNA structure-mediated alternative splicing
                     I. Meyer
                      Secondary structure elements that are responsible for splicing in archaea (BHB elements)
                     S. Berkemer
                      Networks of regulation by splicing and nonsense-mediated mRNA decay.
                     S. Brenner
                      Identification of novel auto-regulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay
                     D. Pervouchine

                  • 18:00h
                  • Afternoon session: RNP + 3D modeling
                     Chair: Bujnicki

                  • Exploring the genetic robustness of ncRNA and protein
                     P. Gardner

                    This session has received financial support from the following institutions:

                    • logo CSIC
                    • Gobierno de Aragón
                    • Ministerio de educación y ciencia
                    • DPH
                    • Universidad de Zaragoza
                    • Ayuntamiento de Benasque


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