Computational Approaches to RNA Structure and Function
2018, Jul 15 -- Jul 27
Organizers:
E. Rivas (Harvard University), E. Westhof (University of Strasbourg)
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SCIENTIFIC ACTIVITY
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Monday, July 16
Tuesday, July 17
Wednesday, July 18
Thursday, July 19
Friday, July 20
Monday, July 23
Tuesday, July 24
Wednesday, July 25
Thursday, July 26
| Registration | |
| How to identify conserved RNA structures. HOTAIR a negative case study | |
| E. Rivas | |
| Organizational Session | |
| All participants |
Tuesday, July 17
| Morning session: RNA Modifications | |
| Chair: Stadler - Westhof | |
| Control over Translation: The Third Genetic code | |
| E. Westhof | |
| N6 - methylation of adenine in box C/D snoRNA : regulation of RNP assembly | |
| Lin Huang | |
| Patterns of tRNA Modifications | |
| P. Stadler | |
| Afternoon session: RNA Design | |
| Chair: Ponty | |
| Fixed-parameter tractable sampling for RNA design with multiple target structures | |
| Sebastian Will | |
| RNA designability | |
| Grzegorz Lach & Tomasz Wirecki | |
| Designing an alanyl suppressor tRNA | |
| Marco Matthies | |
| Computational Riboswitch detection and RNA Design | |
| Matan Drory Retwitzer |
Wednesday, July 18
| Statistics | |
| Hoener | |
| Morning session: RNA protein interactions | |
| Chair: Backofen | |
| Determing Functions of ncRNAs via RNA-protein Interactions | |
| R. Backofen | |
| On the practical use of enhanced crosslinking and immunoprecipitation (eCLIP) assay data (short talk) | |
| D. Pervouchine | |
| RNA-protein interaction and associations by RAIN (short talk) | |
| J. Gorodkin | |
| Predicting the RNA structural determinants in RNA-protein interactions | |
| F. Major | |
| Improving ribosome position assignments in RIBO-Seq by modeling nuclease-ribosome-RNA interactions (short talk) | |
| R. Bundschuh | |
| RNA-/DNA- binding sites prediction on protein | |
| Z. Miao | |
| Afternoon session: Experimental methods (chemical probing) | |
| Chair: Dmitri Pervouchine | |
| What does chemical probing 'reactivity' really mean? | |
| J. B. Lucks | |
| Transforming our view of RNA structure | |
| J. Thangappan | |
| Mining substructures in probing data | |
| S. Aviran | |
| Chemical probing approaches to enable RNA-targeted drug development | |
| L. Barrera | |
| Strategies in RNA X-ray crystallography | |
| L. Huang |
Thursday, July 19
| Morning session: RNA Viruses | |
| Chair: Marz | |
| RNA viruses | |
| Marz | |
| Explaining Flavivirus Congenital Neurotropism with Thermodynamics | |
| M. T. Wolfinger | |
| Numerical Methods for Solving the Multiscale Model of Hepatitis C Virus | |
| D. Barash | |
| Afeternoon session: RNA puzzles | |
| RNA-Puzzles advances and perspectives | |
| Z. Miao | |
| Afternonn session: RNA landscapes | |
| Chair: Heitsch | |
| Capturing the Landscapes of RNA 2D Structures by Decomposition of Partition Functions | |
| K. Asai |
Friday, July 20
| Morning session: Covariations | |
| Chair: Cocco | |
| Protein-RNA co-evolution sites are close in 3D space | |
| Z. Miao | |
| Visualization of RNA and Protein family models and their comparisons | |
| F. Eggenhofer | |
| Learning protein constitutive motifs from sequence data with restricted Boltzmann machines | |
| R. Monasson | |
| Plan of the session on RNA Sequence Covariation | |
| S. Cocco | |
| Afternoon session: RNA organizing the cell | |
| Chair: Brenner | |
| Afternoon session: Databases | |
| Chair: Anton Petrov | |
| CaRNAval: a database and a web resource for studying recurrent interaction networks in RNA structures | |
| A. Denise | |
| BGSU-NDB Collaboration: RNA Databases Update | |
| N. Leontis | |
| Improving and extending the annotation of Bacillus subtilis by curation and TSS data | |
| A. Geissler | |
| What's new in RNAcentral and Rfam | |
| A. Petrov |
Monday, July 23
| Morning session: RNA 2D/3D | |
| Chair: Hofaker | |
| Computational discovery of novel classes of bacterial non-coding RNAs | |
| Z. Weinberg | |
| RNA pseudoknotted Secondary Structure Prediction | |
| H. Jabbari | |
| RNA 2D/3D structure in RNApolis. There and Back Again | |
| M. Szachniuk, M. Antczak and T. Zok | |
| Algorithm to capture local sequential- and 2D structural- RNA motifs | |
| Hiroshi Miyake | |
| How directable are 2D predictions? | |
| Christine Heitsch | |
| Afternoon session: Hardcore Algorithms | |
| Afternoon session: RNA 3D | |
| Chair: Sulc | |
| Coarse-grained modeling of RNA for biology and nanotechnology | |
| Petr Sulc | |
| Coarse-grained nucleic acids physical modeling: basic principles and perspectives | |
| Samuela Pasquali | |
| Automated and Customizable Sequence-Based Identification of 3D Structural Modules | |
| Roman Sarrazin-Gendron | |
| RNA 3D Structure Prediction Using Multiple Sequence Alignment Information | |
| Marcin Magnus |
Tuesday, July 24
| Morning session: RNA folding kinetics and co-transcriptional folding | |
| Chair: Lorenz | |
| Co-transcriptional Folding Kinetics and Riboswitch Modeling | |
| I. Hofacker | |
| Reconstructing RNA folding pathways from cotranscriptional SHAPE-Seq data | |
| A. Yu | |
| Computational studies of co-transcriptional folding - what we learned so far | |
| I. Meyer | |
| Efficient approximations of RNA kinetics landscape using non-redundant sampling | |
| J. Michalik | |
| Sampling RNA Secondary Structure Landscapes for Kinetics Simulations | |
| R. Lorenz | |
| Afternoon session: Integrative modeling | |
| Chair: Pasquali | |
| Afternoon session: RNA Variations | |
| Chair: Brenner | |
| Motivation for analyzing RNA sequence variants in natural populations & diagnostic human genomes | |
| S. Brenner | |
| Opportunities and challenges | |
| R. Backofen | |
| Transcriptome profiling at nucleotide resolution | |
| D. Gautheret | |
| Mutually Exclusive Exons, RNA structure, and genome duplication | |
| D. Pervouchine | |
| RNA structures in fungal introns | |
| K. Hooks |
Wednesday, July 25
| Morning session: Applications of RNA design | |
| Chair: Will - Gorodkin | |
| From sequence to nanostructure - The kink turn as a building block in nano-engineering | |
| L. Huang | |
| Enhancing off-target prediction of CRISPR-Cas9 by a nucleotide duplex model | |
| J. Gorodkin | |
| Feature reductions in CRISPR-Cas9 on-target efficiency predictions | |
| G. Corsi | |
| A Nested 2-Level Cross-validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae | |
| A. Soule | |
| On the emergence of structural complexity in self-replicating RNA populations | |
| J. Waldispuehl | |
| Rfam: building your own families and other new developments | |
| Chair: Anton Petrov | |
| Afternoon session: Comparative analysis | |
| Chair: Nawrocki | |
| Discovery of Archaeal group I introns using Infernal | |
| E. Nawrocki | |
| Genome-wide screens for RNA G-quadraplexes | |
| A. Tanger | |
| Benchmarking pipelines for the detection of genome-wide structural conservation in long non-coding RNAs | |
| S. Fernandez Valverde | |
| Comparative modeling and the elusive perfect benchmark | |
| Y. Ponty |
Thursday, July 26
| Morning session: RNA regultaion + processing | |
| Chair: Pervouchine - Lang | |
| Spliceosomal introns in 'primitive' unicellular flagellates | |
| B. Franz Lang | |
| Conservation of splice sites in plant lncRNAs | |
| J. A. Corona | |
| Transcriptome wide A-to-I editing in the fruit fly and its role in RNA structure-mediated alternative splicing | |
| I. Meyer | |
| Secondary structure elements that are responsible for splicing in archaea (BHB elements) | |
| S. Berkemer | |
| Networks of regulation by splicing and nonsense-mediated mRNA decay. | |
| S. Brenner | |
| Identification of novel auto-regulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay | |
| D. Pervouchine | |
| Afternoon session: RNP + 3D modeling | |
| Chair: Bujnicki | |
| Exploring the genetic robustness of ncRNA and protein | |
| P. Gardner |
This session has received financial support from the following institutions:
