CENTRO DE CIENCIAS DE BENASQUE
RNA-2006
2006, July 16-28
Monday, July 17
-
10:30h
| Welcome |
| Lecture room.
|
-
11:00h
| Peter STADLER |
| Lecture room
|
-
18:00h
| Organizational meeting. |
| Lecture room
|
Tuesday, July 18
-
11:00h
| RNA Structure Prediction, abstract shapes, representative structures, complete shapes probabiliies |
| Robert Giegerich (coordinator)
|
| Structure clustering with centroids |
| Ye Ding
|
| Locally optimal structures |
| Peter Clote
|
| Structure prediction with force |
| Ralf Bundschuh
|
| Classified dynamic programming |
| Robert Giegerich
|
-
18:00h
| microRNA target precition |
| Ye Ding (coordinator)
|
| RNAhybrid |
| Robert Giegerich
|
| Thermodynamic structure of RNA hybrids |
| Stephen Bernhart
|
| miRNA target prediction |
| Erik van Nimwegen and Mihaela Zavolan
|
| FASTH: application to microRNA target prediction |
| Michael Zuker
|
| Ponent role of target structure on microRNA function |
| Ye Ding
|
Wednesday, July 19
-
11:00h
| Special models for RNA secondary structure |
| Dimitri Perchouvine (coordinator)
|
| Algorithms for RNA-RNA matching |
| Dimitri Perchouvine
|
| Folding RNA with pseudoknots |
| Jens Redder
|
| Asymtotic behaviour of equilibrium free energy per nucleotide for randomly generated sequences |
| Peter Clote
|
| k-point mutants and k-superoptimal secondary structures |
| Jerome Waldispuhl
|
-
18:00h
| RNA processing |
| Steven Brenner (coordinator)
|
| NAG NAG and small exon variation |
| Mihaela Zavolan
|
| Insertional RNA editing |
| Ralf Bundschuh
|
| Ultraconserved nonsense |
| Steven Brenner
|
Thursday, July 20
-
09:00h
| RNA ontology - motifs |
| Neocles Leontis, Steven Brenner, Francois Major
|
-
11:00h
| Generic structural RNA genefinders |
| Stefan Washietl, Jakob Pedersen (coordinators)
|
| Methods based on energy directed consensus folding |
| Stefan Washietl
|
| phylo-SCFG based structural RNA identification |
| Jakob Pedersen
|
| Conserved strucutres in non-conserved sequences |
| Elfar Torarinsson
|
| noncoding RNA detection using mfe (dynalign) |
| Andrew Usilov
|
| Kernel function for RNA sequence analysis |
| Yasubumi Sakakibara
|
| C elegans and noncoding RNAs |
| Sean Eddy
|
-
18:00h
| Specific RNA genefinders |
| Daniel Gautheret (coordinator)
|
| miRNA prediction using SVM classification. snoRNA prediction |
| Jana Hertel
|
| What's and what's not a miRNA precursor? |
| Daniel Gautheret
|
| Viral miRNA gene search |
| Ye Ding
|
| A generic tool for specific genefinding |
| Robert Giegerich
|
| viral miRNAs |
| Mihaela Zavolan
|
Friday, July 21
-
11:00h
| RNA alignments I (applications of the Sankoff algorithm) |
| Rolf Backofen (coordinator)
|
| Local and global sequence/structure alignment and the Sankoff algorithm |
| Rolf Backofen
|
| FOLDALIGN (a version of the Sankoff algorithm) |
| Jan Gorodkin
|
| DYNALIGN |
| Dave Mathews
|
| Simulfold: efficient co-estimation of phylogeny, alignment and common RNA structure including pseudoknots |
| Irmtraud Meyer
|
-
16:00h
| Systematic dynamic programming (unauthorized talk) |
| Robert Giegerich
|
-
18:00h
| RNA phylogeny and evolution |
| Ian Holmes (coordinator)
|
| Conserved RNAs in mammals |
| Mike Pheasent
|
| Environmental sequencing and phylogeny |
| Rob Knight
|
| Phylo-grammars and PFOLD |
| Bjarne Knudsen
|
| RNA decoder |
| Irmi Meyer
|
| Tree transducers and Xrate |
| Ian Holmes
|
| Jukes-Cantor with gaps |
| Elena Rivas
|
Monday, July 24
-
11:00h
| Three dimensional structure |
| Eric Westhof (coordinator)
|
| Alignments |
| Karine St-Onge
|
| 3D search of motifs |
| Craig Zirbel
|
-
18:00h
| RNA folding kinetics and energy landscapes |
| Ivo Hofacker (coordinator)
|
| Sequences, structures, shapes and conformations |
| Peter Schuster
|
| Barrier trees and dynamic landscapes |
| Ivo Hofacker
|
| RNA kinetics: a webserver for RNA folding |
| Dimitri Pervouchine
|
| Clusters and energy wells of suboptimals |
| Ye Ding
|
| Translocation through nanopores |
| Ralf Bundschuh
|
| Conformational change pathways |
| Dave Mathews
|
Tuesday, July 25
-
11:00h
| RNA ontology |
| Neocles Leontis (coordinator)
|
| Why do we need an ontology for RNA? |
| Neocles Leontis
|
| Ontology and multiple sequence alignments |
| Eric Westhof
|
| Automating motif recognition alignment |
| Craig Zirbel
|
-
17:00h
| RNA alignments II |
| Jan Gorodkin (coordinator)
|
| Complexity of RNA editing and alignment |
| Alain Denise
|
| Different ways of locality |
| Rolf Backhofen
|
| RNACAST |
| Jens Reeder
|
| STRAL and Bralibase |
| Gerhard Steger
|
| Folding profiles |
| Rune Lyngso
|
| CONSAN: the sankoff algorithm with alignment constraints |
| Robin Dowell
|
Wednesday, July 26
-
11:00h
| RNA homology |
| Paul Gardner (coordinator)
|
| Introduction to profile HMMs and CMs |
| Sean Eddy
|
| Speedups for CMs |
| Eric Nawrocki
|
| Heuristics for faster annotation of noncoding RNA families |
| Zasha Weinberg
|
| Benchmarking RNA homology search tools |
| Paul Gardner
|
| RNA secondary structural alignment with conditional random fields |
| Kengo Sato
|
| Hardware accelerated BLAST/Smith-Waterman |
| Bjarne Knudsen
|
-
15:00h
| RNA ontolgy - alignment |
| Neocles Leontis, Eric Westhof
|
-
18:00h
| RNA design |
| Anne Condon (coordinator)
|
| Nucleic acid design: motivation, design criteria, and computational complexity |
| Anne Condon
|
| SimilRNA - what does it mean for RNA designs to be similar? |
| Amanda Birmingham
|
| Designing multistable RNA sequences |
| Ivo Hofacker
|
| Design by evolution |
| Peter Schuster
|
| Rational design of mRNA-targeting nucleases |
| Ye Ding
|
Thursday, July 27
-
11:00h
| RNA databases |
| Sam Griffith-Jones (coordinator)
|
| What can and can't they do for us? |
| Sam Griffiths-Jones
|
| (And panel discussants respond:) |
| Jakob P, Robin D, Paul G, Jens R, Eric W, Jan G
|
-
16:00h
| Stochastic multiple context-free grammar for RNA pseudoknot modeling (ad hoc talk) |
| Yuki Kato
|
-
18:00h
| Pragmatic tools for RNA analysis |
| Bjarne Knudsen (coordinator)
|
| Software used for Rfam |
| Sam Griffiths-Jones
|
| SARSE: Semi-Automated RNA Sequence Editor |
| Jan Gorodkin & Bjarne Knudsen
|
| GenRGenS: Generalizing random sequences and structures |
| Alain Denise
|
| Deep sequencing of Arabidopsis siRNAs and miRNAs |
| Vincent Moulton
|
| MC-web |
| Francois Major
|
| Should there be a contest for RNA 2D structure prediction (a la CASP)? |
| Eric Westhof
|
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