Talks for the conference.

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. Waldispühl
	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