Centro de Ciencias de Benasque Pedro Pascual

Centro de Ciencias de Benasque Pedro Pascual

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RNA

2012, Jul 22 -- Aug 03

Organizers:
E. Rivas (Janelia Farm Research Campus, HHMI)
E. Westhof (University of Strasbourg)

Monday, July 23
  • 11:00h
  • Hunting RNA motifs
     P. Gardner

    Tuesday, July 24
    • 11:00h
    • RNA Motifs
       E. Westhof, C. Zirbel, Jakob, L. Barquist and M. Lladser

    • Comparative identification of novel human structural RNA families
       J. S. Pedersen
        Homology vs Analogy via Motifs
       M. Lladser
        Discovering bacterial transcription termination motifs
       L. Barquist

    • 18:00h
    • Structure probing, HTS
       I. Hofacker

      Wednesday, July 25
      • 11:00h
      • RNA Evolution
         F. Major and J. Waldispuhl

      • Efficient Algorithms to Explore the RNA Mutational Landscape
         J. Waldispuhl
          TBA
         N. Jarewsky
          TBA
         F. Major
          TBA
         R. Bundschuh
          TBA
         D. Barash

      • 18:00h
      • Algorithms I
         E. Rivas and R. Giegerich

      • TBA
         K. Sato
          Predicting functional RNA structures beyond the one-sequence-one-structure dogma
         I. Meyer
          TBA
         Y. Frid
          TBA
         R. Backofen

        Thursday, July 26
        • 11:00h
        • Visualization, Tools & Software
           Y. Ponty

        • R-chie: a visualization tool for RNA structures
           I. Meyer
            The UEA sRNA Workbench
           M. Stocks
            JmolTools.js: An embeddable tool for 3D structure visualization
           B. Sweeney
            Human-computing framework for genetic data analysis
           J. WaldispŁhl
            R2R: Faster drawing of RNA aesthetic secondary structure diagrams
           Z. Weinberg
            RILogo: Visualising RNA-RNA interactions
           S. Seemann
            Current challenges in RNA structure visualization
           Y. Ponty
            The sRNA Workbench
           M. Stocks

        • 18:00h
        • Session on 'Annotating transcripts / dark matter'
           Heads: Pedersen / Gautheret

        • About the birth of regulatory RNA
           D. Gautheret
            Expression and conservation of human ncRNAs
           J. Skou Pedersen
            Aligning RNAseq profiles
           J. Gorodkin
            Computational analysis of mapping patterns of RNA-seq short reads in small non-coding RNA genes
           Y. Sakakibara
            Assaying ncRNAs using high-throughput transposon mutagenesis in Salmonella
           L. Barquist


          Friday, July 27
          • 11:00h
          • Beyond Mfold
             D. Pervouchine

          • RNA pseudoknotted secondary structure prediction using integer programming
             Y. Kato
              Folding space analysis: abstraction and filtering
             B. Voss
              Thermodynamic RNA secondary structure prediction with a kinetic twist
             I. Meyer
              Fast detection of conserved complementary motifs using gapped-seed associative arrays
             D. Pervouchine

          • 18:00h
          • RNA-RNA
             R. Bundschuh

          • A Needle in a Haystack or Systematic Search for lncRNA Targets
             D. Pervouchine
              RNA-RNA interaction prediction using integer programming
             Y. Kato
              A partition function algorithm for RNA-RNA interaction
             H. Chitsaz
              Some more things you can calculate from the RIP partition functions
             P. Stadler
              Conservation in RNA-RNA interaction
             R. Backofen
              RNA-DNA interactions
             S. Bernhardt

            Monday, July 30
            • 11:00h
            • RNA-proteins
               N. Rajewski and J. Bujnicki

            • Incorporating RNA-Protein Interactions into RNA Secondary Structure Prediction
               R. Bundschuh

            • 18:00h
            • Databases
               S. Griffiths-Jones, P. Gardner and R. Knight

            • RNAcentral
               S. Griffiths-Jones
                RNASTAR, greengenes and an environmental seq database
               R. Knight
                miRBase
               A. Kozomara
                Modomics and RNA processing
               J. Bujnicki
                Rfam
               S. Burge


              Tuesday, July 31
              • 11:00h
              • RNA mutagenesis
                 A. Laederach and M. Zuker

              • SHAPE as a way to evaluate our ability to predict the effects of SNPs on RNA
                 A. Laederach
                  Finding locally altered RNA structure inferred by SNPs using RNAsnp
                 J. Gorodkin

              • 18:00h
              • Gene finding
                 Z. Weinberg

              • Hide and Seek: The Complete Transcriptome
                 R. D. Dowell
                  Two freakish RNAs, and the search for more
                 Z. Weinberg
                  A phylogenetic structure application to ncRNA gene predictions
                 T. Gesell
                  Families of ribosomal regulatory elements
                 M. Meyer
                  Genome-wide RNA structure screen
                 S. Seeman

                Wednesday, August 01
                • 11:00h
                • Covariance Models
                   E. Nawrocki

                • Covariance models and Infernal 1.1
                   E. Nawrocki
                    Multiple Consensus Structures for Infernal Style Covariance Models
                   S. Janssen

                • 18:00h
                • Beyond 2D
                   P. Stadler and R. Backofen

                • A Combinatorial Framework for Designing 2D+e RNA Algorithms
                   Y. Ponty
                    Pseudoknot Folding and Topology
                   P. F. Stadler
                    Motified RNA structure prediction
                   B. Voss
                    Folding with G-quadruplexes
                   S. Bernhart
                    Predicting internal loop 3D structure from sequence
                   C. L. Zirbel
                    RNAwolf: folding with non-standard base pairs
                   C. Hoener

                  Thursday, August 02
                  • 11:00h
                  • RNA 3D
                     E. Westhof and J. Bujnicki

                  • Progress in RNA 3D Modelling
                     E. Westhof
                  • 18:00h
                  • Algorithms II
                     E. Rivas and R. Giegerich

                  • Beyond Mfold with probabilistic models
                     E. Rivas
                      Impact of the energy model on the complexity of RNA folding with psedoknots
                     Y. Ponty
                      Signifince of motif frequencies in non-Markovian models of genome sequences
                     M. Lladser
                      Enjoy dynamic programming in Bellman's GAP
                     R. Giegerich

                    This session has received financial support from the following institutions:

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

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