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