Centro de Ciencias de Benasque Pedro Pascual

Centro de Ciencias de Benasque Pedro Pascual

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Computational methods for RNA analysis

2009, Jul 26 -- Aug 08

Organizers:
E. Rivas (HHMI)
E. Westhof (U. Louis Pasteur, Strasbourg)

Monday, July 27
  • 11:00h
  • Semantics of family model grammars
     Robert Giegerich.
  • 17:00h
  • Organizational meeting
     

    Tuesday, July 28
    • 11:00h
    • Splicing, editing, RNA expression
       Gertraud Burger, Robin Dowell, Dimitri Pervouchine, Zasha Weinberg.

    • RNA pocessing: which signals we would like to understand?
       Gertraud Burger.
        Expression analysis to find non coding transcripts
       Robin Dowell.
        There is plenty more RNAs in the sea
       Zasha Weinberg.
        Modulation of alternative splicing by RNA structures
       Dimitri Pervouchine.

    • 18:00h
    • De novo RNA searching. coord.: Robert Giergenich
       Daniel Gautheret, Peter Stadler, Jan Gorodkin, Yasu Sakakibara, Yukata Saito, Stephan Washiete.

    • Overview non coding RNAs in the ENCODE project
       Jan Gorodkin.
        Bacterial ncRNA predictions using unusual signals: phylogenetic profiling
       Daniel Gautteret.
        Genome - wide detection of ncRNAs on genomes using kernel functions
       Yasu Sakakibara.
        Improving ncRNA detection: improving backgrounds models and protein coding models
       Stefan Washietl.

      Wednesday, July 29
      • 11:00h
      • Partition Function, Combinatorics, Random Matrix coord.: François Major.
         Jerome Waldispuhl, Peter Stadler, Yann Ponty, Tony Zee, Peter Clote.

      • Partition Function
         Peter Stadler.
          Saturated secundary structures and parametric models
         Peter Clote.
          Algorithmics and combinatorics of RNA Sampling
         Yann Ponty.
          Algorithms for exploring the RNA combinatorial landscape
         Jerome Waldispuhl.
          RNA secundary structure design is NP-hard
         Michael Schnall-levin.
          Selex experiments for triptofan-binding RNAs
         Jens Reeder.
          Folding RNAs: a confluence of biology, mathematics, and physics
         Tony Zee.

      • 18:00h
      • ZD state of the art prediction. coord.: David Mathews.
         Kiyoshi Asai, Yuki kato, Kengo Sato, Michael Zuker.

      • Overview of 2R RNA folding
         David Mathews.
          www.ncRNA.org
         Kiyoshi Asai.
          Centroid Fold for predicting RNA structures
         Kengo Sato.
          Integer programming for pseudoknots
         Yuri Kato.
          Pseudo-recursive pseudoknots
         Rune Lynso.
          The entropy of the botzman distribution of RNA folding
         Michael Zuker.

        Thursday, July 30
        • 11:00h
        • Databases and practical tools for RNA. coord.: Kiyoshi Asai.
           James Brown, Paul Gardner, Sam Griffiths-Jones, Eric Nawrocki.

        • RNA databases, what is the point?
           Jin Brown.
            The Rfan database
           Paul Gardner.
            miRBase.org
           San Griffith-Jones.
            Practical covariance model methos for Rfan
           Eric Nawrocki.
            WAR: a webserver of aligning structural RNAs
           Stirus Lindgreen.

        • 18:00h
        • Homology I. coord.: Jan Gorodkin.
           Chonjian Chen, Diana Kolbe, Liming Cai, Sebastian Will.

        • Intro: what does homology mean
           Sean Eddy.
            Homology search for pseudoknots and beyond
           Limming Cai.
            Local aligment for structural RNA fragments
           Diane Kolbe.
            Match probabilities for sankoff-style aligments
           Sebastian Will.
            Exploring ncRNA elements using single-genome analysis
           Chong-jian Chen.

          Friday, July 31
          • 11:00h
          • Homology II. coord.: Sean Eddy.
             Rob Knigth, Dimitri Pervouchine, Stephan Janssen.

          • rRNA and the evolution of the human microbiota
             Rob Knigth.
              Use of hash tables for RNA structure detection
             Dimitri Pervouchine.
              Role of structure on Rfam
             Stefan Janssen.
              On aligments and 2D structure of RNA sequences
             Kiyoshi Asai.
              A general effect on selection
             Rune Lyngso.
              Comparism of RNAs based on exact common substructures
             Steffen Heyne.

          • 18:00h
          • 3D, validation and casp?. coord.: Michael Zuker.
             Eric Westhof, Francois Major, Jess Fellsen.

          • Modeling RNA structure using chemical probing, sequence alignments, and computer manipulations
             Eric Westhof.
              Modelling 3D: MCfold | MCSim
             François Major.
              Method for comparing a structure prediction to a reference structure
             Jose Cruz.
              A probabilistic approach to modelling RNA comfornational space
             Jess Frellsen.
              Predicting RNA tertiary structure
             David Mathews.

            Monday, August 03
            • 11:00h
            • High throughput sequencing coord.: Ivo Hofacker.
               Vincent Moulton, Peter Stadler, Jens Reeder.

            • Fast Flowgram chistering
               Jens Reeder.
                High throughput sequencing of small RNAs
               Simon Moxon.
                Analysis of short-read sequencing data
               Peter Stadler.
                IncRNAS in oncogenic pathways and processes
               Jorg Hackermüller.
                Looking at RNA structures in high throughput way
               Alain Laederach.

            • 18:00h
            • Visualization tools. coord.: Neoclis Leontis.
               Jesse Stonbaugh, San Griffith-Jones, Yann Ponti, Zasha Weinberg.

            • Boulder ALE
               Jesse Stombaugh.
                Perspectives on issues of RNA aligments and visualizations
               Sam Griffith - Jones.
                VARNA: RNA secondary structure visualization (mostly) for webservers
               Yann Ponty.
                R2R: behind the scenes of there is plenty more RNAs in the sea
               Zasha Weinberg.

              Tuesday, August 04
              • 11:00h
              • RNA ontology.
                 
              • What is the RNA ontology consortium?
                 Neocles Leontis.
                  Ontology of RNA notifs and base-phosphate interactions
                 Craig Zirbel.
                  Frequency and isostericity of basepairs
                 Jesse Stombaugh.
                  Aubmaled motif extraction and classification of RNA structure
                 Mahassine Djelloul.
                  Eric Westhof.
                 
              • 18:00h
              • Improvements on alignments of real RNAs. coor.: Eric Nesthof.
                 Franz Lang, Alain Denise, Kiyushi Asai, Gaurav Sharma, JH Havgaard.

              • Aligning long intron RNAs with patchy conservation-and-finding them in genomes
                 Franz Lang.
                  An initation to benchmarking secondary structure comparism software
                 Alain Denise.
                  Sequence-structure alignment: Reliabilities
                 Rolf Backofen.
                  Foldalignş
                 Jakob Haavgaard.

                Wednesday, August 05
                • 11:00h
                • RNA interactions. coord.: Alain Denise.
                   Rolf Backofen, Yuki Kato, Ye Ding, Stephan Bernhart.

                • RNA-RNA Interactions
                   Alain Denise, coord.nator
                    Prediction of RNA-RNA interactions
                   Rolf Backofen.
                    Prediction of interacting RNA secondary structures including binding sites.
                   Yuki Kato.
                    Impact of target secondary structure on function of small RNAs.
                   Ye Ding.
                    Computing accessibilities in cubic time.
                   Stephan Bernhardt.

                • 18:00h
                • RNA folding kinetics, landscapes. coord.: Dimitri Pervouchine.
                   Ivo Hofacker, Eric Westhof.

                • RNA kinetics
                   coord. D. Pervouvhine
                    Using chemical probing to monitor time resolved RNA folding
                   Alain Laederach.
                    Some real examples where kinetics is in control
                   Eric Westhof.
                    Time-dependent energy landscapes for RNA
                   Ivo Hofacker.

                  Thursday, August 06
                  • 11:00h
                  • RNA - system biology
                     Open discussion.

                  • Abstract Shape Analysis
                     Robert Giegerich.
                      An alternative mechanism for translation initiation in bacteria
                     Liam Childs.
                      Computational identification & characterization of mammalian structural RNAs
                     Jakob Pedersen.
                      The algorithmic complexity of RNA 2D structure alignment
                     Alain Denise.
                      Random generation of realistic RNA 2D structures.
                     Yann Ponty.
                      FR3D annotations
                     Craig Zirbel.

                  • 18:00h
                  • RNA Systems Biology
                     Alain Laederach, coord.nator.

                  • Towards sRNA Systems Biology
                     Vincent Moulton.

                    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
                    • Fundación BBVA

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