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

2022, Aug 07 -- Aug 20

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

Monday, August 08
  • 11:00-11:15
  • Open remarks
  • 11:15-12:15
  • Talk by Kate Shulgina
  • 12:30-13:30
  • Talk by Quaid Morris
  • 18:00-19:00
  • Organizational meeting

    Tuesday, August 09
    • 11:00-13:00
    • Session I: Machine learning methods for RNA structure
       Chair: Marcel Szikzsai

    • Unsupervised generative models for in vitro selection experiments
       R. Monasson
    • Experiments in Deep Learning for RNA Secondary Structure Prediction
       I. L. Hofacker

    • 18:00-20:00
    • Session II: RNA puzzles
       Chair: Marta Szachniuk

    • RNA Puzzles
       E. Westhof
       C. Fidelis
        Evaluation of predictions. The geometry of RNA 3D models
       M. Szachniuk
        Finding entanglements of RNA structural elements
       T. Zok
        RNA-Tools A swiss army knife for RNA 3d structure modeling workflow
       M. Magnus

      Wednesday, August 10
      • 11:00-13:00
      • Session III: Elixir
         Chair: B. Schneider

      • ELIXIR and its communities
         B. Schneider
          Rfam and RNACentral
         B. Sweeny
          Annotation of nucleic acid structures at dnatco.datmos.org
         B. Schneider
          Annotation and validation of nucleic acid structures
         J. Cerny
          Platicity of base pairing observed in the A-form 18-mer DNA structures
         J. Svoboda

      • 17:00-19:00
      • Session IV: RNA-protein interactions
         Chair: R. Backofen

      • Interpretable sequence-structure RBP motif finding using PRIESSTESS
         Q. Morris
          Prediction of RNA-protein Interactions with AlphaFold-derived Protein Representations
         Long Yat Tam
          What can we do with RNA-protein interaction predictions?
         R. Backofen
          Dancing to Silence
         F. Major
          Uncovering regulatory elements transcriptome-wide using subcellular in situ RNA sequencing
         D. Fürth

        Thursday, August 11
        • 11:00-13:00
        • Session V: RNA design, CRISPR
           Chair: Y. Ponty

        • CRISPR/Cas9 gRNA design
           J. Gorodkin
            Eukaryotic riboswitch detection using inverse RNA folding
           D. Barash
            Declarative design using Infrared/RNAPond
           S. Will
            Fitness functions for RNA design algorithms
           M. Ward
            An evolutionary algorithm for pseudoknotted RNA design inspired by Lévy Flights
           Nono Saha Cyrille Merleau
            Generative models for riboswitch design
           J. Fernández de Cossio Diaz
            Differentiable RNA design
           M. Matthies

        • 16:00-18:00
        • Session VI: Alphafold insipired RNA 3D structure prediction. Can it work? can not? If so, what next?
           Chair: C. Zirbel
        • 18:00-20:00
        • Session VII: evol of RNA, remote homology
           Chair: E. Rivas

        • Natural catalytic RNAs: strange structural variants in mysterious organisms
           Z. Weinberg
            Bacillaceae-1 RNA motifs and rapid sequence divergence of conserved RNA structures
           S. Seemann
            Incongruent Evolution of RNA Sequence and Structure
           M. Waldl
            Forbidden motifs and the cardinality of secondary structure space
           Hua-Ting Yao
            Exploring RNA folds and remote evolutionary relationships with an improved structurally similarity search methods
           E. Baulin
            Using positive and negative evolutionary information for RNA structure prediction
           E. Rivas

          Friday, August 12
          • 11:00-13:00
          • Session VIII: viral RNA
             Chair: M. Marz

          • RNA structuredness of viral genomes
             M. T. Wolfinger
              Reference-based viral sequence validation and annotation using VADR
             E. Nawrocki
              Shapify: Pathways to SARS-CoV-2 frameshifting pseudoknot
             L. Trinity
              Analysis and evolution of immunogenic dinucleotide motifs in SARS-CoV-2
             A. Di Gioacchino
          • 18:00-20:00
          • Session IX: non-coding RNAs
             P. Gardner

          • Any conserved RNA structure?
             E. Rivas
              Genomic landscape of conserved RNA secondary structure signatures and their homologs
             V. Gaonach-Lovejoy
              Identification of ncRNAs in 'ancestral' free-living eukaryotes: the jakobids and malawimonads
             S. Prince
              Features of functional human genes
             P. Gardner
              Immunostimulatory viral-like features in genomic repeats
             S. Cocco

            Monday, August 15
            • 11:00-13:00
            • Session X: RNA Kinetics
               Chair: S. Will

            • Cotranscriptional RNA Kinetics with Dr Transformer
               I. Hofacker
                An RNA kinetics ansatz derived from an efficient prediction of RNA pathways
               Nono Saha
                Long-range RNA structure dynamically controls alternative splicing
               D. Pervouchine
                RNA dynamics within the spliceosome
               M. Magnus

            • 18:00-20:00
            • Session XI: RNA in vivo
               Chair: M. Meyer

            • Uncovering Regulatory Elements Transcriptome-Wide using subcellular in situ RNA sequencing
               D. Fürth
                Circular stable intronic RNAs in early-stage bladder cancer
               A. Mannstaedt Rasmussen
                Assessing RNA structure and function via fitness landscape
               M. Meyer
                A systemics view of puras cellular rna-binding function from omics data gives insights into pura related diseases
               M. Klostermann

              Tuesday, August 16
              • 11:00-13:00
              • Session XII: RNA structure from alignments
                 Chair: F. Major

              • Aligning and modeling a few thousand unknown ncRNAs in “primitive” unicellular eukaryotes
                 F. Lang
                  Rfam 3D and R-scape updates
                 N. Ontiveros
                  High-quality customizable algorithms for RNA 3D structure alignment
                 M. Antczak
                  Dynamic programming from an input helical pattern
                 B. Marchand
                  An integer programming framework for simultaneous prediction of RNA structure with pseudoknots and insertion of local 3D motifs
                 G. Loyer

              • 15:00-17:00
              • Session XIII: RNA annotation using NtC classes
                 Chair: I. Bohdan Schneider

              • Use of NtC knowledge for nucleic acid structure refinement
                 J. Svoboda

              • 18:00-20:00
              • Session XIV: RNA processing and regulation
                 Chair: B. Yoseph

              • Transcriptome sequencing suggests lariat polyadenylation
                 M. Vlasenok
                  Regulation of gene expression via unproductive splicing
                 D. Pervouchine
                  Fantastic rG4s: What they do and where to find them?
                 Y. Barash
                  What happens to the CRISPR-Cas extra repeat?
                 Z. Weinberg
                  Net Oligo Binding Free Energies
                 D. Aalberts

                Wednesday, August 17
                • 11:00-13:00
                • Session XIV: Translation, mRNA vaccines, antibiotics
                   Chair: D. Aalberts

                • Interactions between Gs and Us in Translation
                   E. Westhof
                    Design of modified aptamers against the Beta-Secretase 1 involved in Alzheimer’s disease
                   T. Yacoub
                    Structural studies into ribosome-binding natural product antibiotics
                   O. Kalinina
                    Optimizing coding sequences
                   D. Aalberts

                • 17:00-19:00
                • Session XV: RNA-RNA interactions
                   Chair: D. Pervouchine

                • Introduction
                   D. Pervouchine
                    Long range RNA-RNA interactions inferred from RNA in situ conformational sequencing
                   S. Margasyuk
                    RNA Palindromic sequences matter
                   Á. Cantero Camacho
                    Predicting the kinetics of RNA-RNA interactions
                   S. Will
                    Modeling RNA-RNA interaction formation on direct paths
                   M. Waldl

                  Thursday, August 18
                  • 11:00-13:00
                  • Session XVI: RNA 3D structure modeling with experimental data
                     Chair: J. M. Bujnicki

                  • Modeling of RNA 3D structure based on medium- and low-resolution maps from cryo-electron microscopy and macromolecular crystallography
                     J. Bujnicki
                      A cryo-EM map as the target - how to evaluate predictions
                     M. Antczak
                      Refinement of RNA crystal structures with NtCs
                     J. Cerny
                      Getting Darwin into SHAPE
                     I. Meyer
                      NACDDB: Nucleic Acid Circular Dichroism DataBase, a new computational resource for experimental data on RNA 3D structure
                     A. Cappannini

                  • 18:00-20:00
                  • Session XVII: RNA modules
                     Chair: C. Zirbel

                  • A few memories of Neocles, non-Watson-Crick pairs and RNA modules
                     E. Westhof
                      My time with Neocles Leontis and updates on our work
                     C. Zirbel
                      The Overrepresented RNA Blocks
                     F. Major
                      Craig wants me to talk about G4s
                     M. Szachniuk
                      Arbitrarily large RNA structural modules
                     V. Reinharz
                      Yet another definition of a long-range RNA tertiary motif
                     E. Baulin

                    Friday, August 19
                    • 11:00-12:00
                    • Session XVIII: RNA visualization
                       Chair: A. Petrov

                    • Visualization of quadruplex structures
                       T. Zok
                        Visualization of nucleic acid conformations
                       J. Cerny
                        Detailed circular basepair diagrams
                       C. Zirbel
                        Visualizing structural models for long(er) RNAs
                       Y. Ponty
                        R2DT: Visualizing RNA secondary structure using templates
                       A. Petrov

                    • 18:00-20:00
                    • Session XIX: RNA modifications, nanopore
                       Chair: V. Reinharz

                    • Direct RNA sequencing with modifications
                       J. Spangenberg
                        nanoShape: Nanopore based sequence and structure detection on novel RNA
                       J. White Bear
                        Newest features in MODOMICS a database of RNA modification pathways
                       A. Cappannin
                        Evolution of the RNA editing sites in filamin genes
                       A. Tanzer
                        Tracing tRNA Modifications with Deep Sequencing
                       P. Stadler
                        Something interesting about RNA modifications
                       E. Westhof

                      The CCBPP has received financial support for the organization of scientific meetings from the following institutions:

                      • Ministerio de ciencia, innovación y universidades
                      • Gobierno de Aragón
                      • logo CSIC
                      • DPH
                      • Universidad de Zaragoza
                      • Ayuntamiento de Benasque


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