How To Teach An Rna Bioinformatics Course In Copenhagen

Transcription

1 Copenhagen Summer School on RNA bioinformatics 2014 June 23 to June 28 ===================================================================================== Content: * RNA folding and structure prediction * RNA-RNA interactions; RNA-protein interactions * Annotation of structured RNA * sirna design * RNA databases * RNA systems biology * RNA 3D strucuture Teachers: Rolf Backofen (RB) Evdoxia Karadoulama (EK) Christian Garde (CG) Jan Gorodkin (JG) Jakob Hull Havgaard (JHH) Ivo L Hofacker (ILH) Lars Juhl Jensen (LJJ) Anders Krogh (AK) Sebastien Muller (SM) Henrik Nielsen (HN) Jakob Skou Pedersen (JSP) Mireya Plass (MP) Simon H Rasmussen (SR) Sudhakar Sahoo (SS) Peter F. Stadler (PFS) Jeppe Vinther (JV) Christopher Workman (CW) 1

2 Programme: ======== June 23rd Monday: 8:30-9:15 Registration 9:15-9:30 Introduction to the summer school (JG+AK) 9:30-10:15 Lecture (HN): Introduction to RNA biology by Henrik Nielsen 10:15-10:35 Coffee break 10:35-12:30 Introduction to RNA bioinformatics 10:35-11:15 Lecture (JG): The Nussinov algorithm for RNA 2D folding (reflectory questions during the lecture) 11:15-11:30 Lecture (JG): Mutual information from multiple alignments 11:30-11:45 Lecture (JSP): Introduction to ncrna databases 11:45-12:30 Lecture (JSP): Homology search for structured RNAs and concepts of RNA gene finding 12:30-13:30 Lunch 13:30-17:00 Energy directed RNA folding / folding kinetics 13:30-14:15 Lecture (ILH): Energy directed RNA folding 14:15-15:15 Exercise (ILH/PFS): Energy directed RNA folding 15:15-15:30 Coffee break 15:30-16:15 Lecture (ILH): RNA folding kinetcs and energy landscapes 16:15-17:00 Exercise (ILH/PFS): RNA folding kinetics 18:30-20:30 Summer school dinner at Restaurant Cortigiano, Smallegade 20B, 2000 Frederiksberg 21:00-22:00 Sct. Hans, the Danish bonfire night at Frederiksberg have June 24th Tuesday: 9:00-12:00 Folding multiple RNA sequences 9:00-9:30 Lecture (IHL/PFS): Folding aligned RNA sequence 9:30-10:00 Exercise (IHL/PFS): Exercise on RNAz 10:00-10:15 Lecture (PFS): Searching for Class specific RNAs (an overview) 10:15-10:30 Coffee Break 2

3 10:30-11:00 Lecture (JHH): Structural alignment of RNA sequences 11:00-11:30 Exercise (JHH/JG): The WAR server for structural alignments 11:30-12:00 Lecture (JSP): Introduction to Stochastic Context-Free Grammars 12:00-13:00 Lunch 13:00-15:00 Probabilistic directed RNA folding 13:00-13:45 Lecture (JSP): Probabilistic integration of phylogenetic data and probing data. 13:45-14:40 Exercise (JSP/SH): Probabilistic and integrative structure prediction methods 14:40-15:00 Lecture (JG): Local structural alignments by SCFGs (CMfinder) 15:30-17:15 Experimental RNA structure probing (SHAPE, FraqSeq) 15:30-16:15 Lecture (JV): Experimental probing of RNA structure 16:15-17:15 Exercise (JV): Understanding the transcriptome through RNA structure 17:15 - [Dinner on your own] June 25 th Wednesday 8:45 9:15: Morning coffee 9:15-12:00 RNA-RNA interactions 9:15-10:00 Lecture (RB/PFS): Principles for RNA-RNA interactions 10:00-10:45 Lecture (RB/PFS): Overview of methodologies 10:45-12:00 Exercise (RB/PFS): RNA-RNA interaction by comparative genomics) 12:00-13:00 Lunch 13:15-16:00 sirna, oligo design and mirna target prediction 13:15-14:00 Lecture (ILH): sirna and oligo design 14:00-14:30 Exercise (ILH): sirna and oligo design 14:30-14:45 Coffee break 14:45-15:20 Lecture (JG): Introduction and overview of mirna target prediction 15:20-16:00 Exercise (JG): Predicting mirna targets by online resources 16:30-17:00 Break 17:00-18:00 Lecture (LJJ): Making gene networks through data integration 3

4 June 26th Thursday: 9:00-17:15 RNA-protein interactions 9:00-09:30 Lecture (CW): Introduction to RNA-binding proteins 9:30-10:15 Lecture (SM): Experimental techniques for measuring RNA-protein interactions 10:15-10:45 Coffee Break 10:45-11:30 Lecture (CG): Strategies for predicting RNA-protein interactions 11:30-12:00 Lecture (AK): CLIP Bioinformatics 12:00-13:00 Lunch Break 13:00-13:30 Lecture (MP): Case study: DGCR8 HITS-CLIP analysis 13:30-14:00 Lecture (SR): cwords, a method for motif discovery in post-transcriptional regulation 14:00-14:15 Coffee Break 14:15-16:15 Exercise (SR, EV, MP): Motif Discovery in CLIP data 16:15-16:30 Coffee Break 16:30-17:15 Lecture (RB): GraphProt: modeling binding preferences of RNA-binding proteins 17:15 - [Dinner on your own] June 27th Friday: Symposium on non-coding RNA 9:15-9:20 Welcome by Anders Krogh / Jan Gorodkin 9:20-10:05 RNA Heterogeneity in the Eukaryotic Cell by Roderic Guigo 10:05-10:50 Regulatory RNAs by Nikolaus Rajewsky 10:50-11:15 Coffee Break 11:15-12:00 (nc)rnas from active enhancers and promoters enable a body-wide regulatory atlas by Albin Sandelin 12:00-14:00 Lunch and poster session in room A :00-14:45 Circular RNA - function and biogenesis by Jørgen Kjems 14:45-15:10 Coffee Break 15:10-15:55 Predicting RNA-protein interactions: motifs and binding sites by Quaid Morris 15:55-16:40 Revisiting the coding potential of the E. coli genome by Renee Schroeder 4

5 16:40-17:00 Poster Award and closing remarks by Anders Krogh / Jan Gorodkin June 28th Saturday: Advanced topic within RNA Bioinformatics 9:45-10:15 Coffee 10:15-13:00 Advanced session 10:15-11:00 Lecture (PFS): Computational RNA design 11:00-11:45 Lecture (RB): Advanced topic within RNA Bioinformatics 11:45-12:30 Lecture (IHL): Beyond secondary structure 12:30-12:45 Closing remarks of the summer school by Jan Gorodkin ================================================================================ 5