Organizers:
E. Rivas (Harvard University), E. Westhof (University of Strasbourg)
Organizers:
E. Rivas (Harvard University), E. Westhof (University of Strasbourg)
10:00-11:00 | Registration |
11:00-12:00 | Misfolded or not - that is the question… Marta Szachniuk |
17:00-18:00 | Recent advances in RNA secondary structure prediction with machine learning and deep learning Kengo Sato |
18:30-19:30 | Organizational meeting |
11:00-13:00 | RNA structure, RNA processing and regulation Chair: Dmitri Perovouchine |
Cross-species view of transcription termination in bacteria Amir Bar | |
Processing of ribosomal RNA Ralf Bundschuh | |
Multiple modes of unproductive splicing regulation Dmitri Pervouchine | |
Modeling microRNA::mRNA Interaction Networks François Major | |
Gibbs sampling for RNA duplex structure prediction: Application to RNAi by microRNAs Simon Chasles | |
17:30-19:30 | RNA modifications I Chair: Manja Marz |
RNA modification detection (different methods) Cristian Arley Velandia Huerto | |
RNA modification detection (nanopore) Manja Marz | |
RNA modifications changing secondary structures Ronny Lorenz | |
Probabilistic modeling of RNA-RNA Interactions and Complex Formation using Nanopore Direct RNA Sequencing Jay White Bear |
11:00-13:00 | RNA Design I Chair: Danny Barash |
Generative Modeling of RNA Switches Jorge Fernandez-de-Cossio-Diaz | |
Riboswitch Detection Using RNA Design Danny Barash | |
DesiRNA: Application to EteRNA benchmark, bacterial and viral structures Tomasz Wirecki | |
Generation of constrained RNA mutations as a SAT-problem Grzegorz Lach | |
CRISPR gRNA Design and Analysis Jan Gorodkin | |
18:00-20:00 | Long RNA prediction Chair: Horacio V. Guzman |
Coarse grained sampling of RNA 3D structures Ivo Hofacker | |
RNA secondary structure prediction in viruses - a full-genome multiple sequence alignment approach Sandra Triebel | |
Multi-scaling the finer structure of RNA interactions: from polymer theory to the dis/assembly of viruses Horacio V. Guzman | |
Open discussion |
11:00-13:00 | RNA interaction with other molecules Chair: Janusz Bujnicki |
Bioinformatics methods in the study of RNA interactions with small-molecule ligands Filip Stefaniak | |
Structural biology of mRNA driving drug design Irina Tuszynska | |
ClaPNAC: Classifier of Protein Nucleic Acid Contacts Grigory Nikolaev | |
Automated differential interaction analysis by Gaussian Mixture Models Manja Marz | |
18:00-20:00 | Databases and RNA annotation I Chair: Eric Nawrocki |
18:01-19:XX | RNAcentral and Rfam: Updates and some possible future plans Blake Sweeney |
RNAsolo in the RNA structure study Maciej Antczak | |
Ribocentre: Databases for functional RNAs Chichau Miao | |
Annotation of intron-containing ribosomal RNA genes Samuel Prince | |
RNA annotation in Hydractinia genomes Eric Nawrocki |
11:00-13:00 | RNA 3D Chair: Marcin Magnus |
RNA 3D structure prediction in the post-AlphaFold area Marcin Magnus | |
De novo modeling of RNA 3D structure Peng Xiong | |
Benchmarking deep learning-based methods for RNA 3D structure prediction Ivona Martinovic | |
RNA 3D Modeling: Insights into Ligand Binding Site Modeling Nithin Chandran | |
RNA in 3D: more than canonical pairs and “unpaired loops” Jiri Cerny | |
16:45-18:00 | RNA-solvent interactions Chair: Janusz Bujnicki |
The first hydration layer around biomolecules is site-specific Bohdan Schneider | |
Future insights into metal ion-RNA interaction prediction and analysis Dina Hussein | |
Simulations of RNA-solvent interactions with SimRNA-sol Janusz Bujnicki | |
The effects of cytosolic fluid forces on macromolecular stability Michael Amiss | |
18:00-20:00 | RNA design II Chair: Max Ward |
RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs Théo Boury | |
Differentiable RNA Folding with Applications Max Ward | |
Differentiation in RNA sequence Design Kyoshi Asai | |
Datasets for benchmarking RNA design algorithms Agnieszka Rybarczyk |
10:30-11:00 | Coffee |
11:00-13:00 | Chemical modifications and RNA Probing Chair: Christine Heitsch |
18:00-20:00 | RNA 2D/3D prediction (singular) with experimental data Chair: Janusz Bujnicki |
10:30-11:00 | Coffee |
11:00-13:00 | Analysis of base pairs Chair: Bohdan Schneider |
18:00-20:00 | RNA 2D prediction Chair: Yaoqi Zhou |
10:30-11:00 | Coffee |
11:00-13:00 | RNA puzzles / CASP Chair: Eric Westhof |
18:00-20:00 | RNA evolution Chair: Anton S. Petrov |
10:30-11:00 | Coffee |
11:00-13:00 | RNA motifs Chair: Vladimir Reinharz |
17:30-19:30 | RNA visualization Chair: Anton Petrov |
11:00-13:00 | Synthetic biology, design aspects Chair: Michael Wolfinger |
18:00-20:00 | RNA annotation II Chair: Bertrand Marchand |