Talks for the conference.

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.
	Foldalignº
	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: