Organizers:
E. Rivas (Harvard University), E. Westhof (University of Strasbourg)
Computational Approaches to RNA Structure and Function
(Benasque Science Center, Jul 21 - Aug 03, 2024)
Monday, July 22
| 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 |
Tuesday, July 23
| 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 |
Wednesday, July 24
| 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 |
Thursday, July 25
| 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 |
| 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 |
Friday, July 26
| 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 |
Monday, July 29
| 11:00-13:00 | Chemical modifications and RNA Probing Chair: Christine Heitsch |
| RNA structure determination via chemical probing Christine Heitsch | |
| RNA structure-function insights via hairpin-centric NNTM-free structurome probing data analysis Sharon Aviran | |
| Dynamics of plant telomerase RNA structure revealed by chemical probing Jiri Fajkus | |
| PaRNAssus: More insights into RNA probing data Yao Hua-Ting | |
| Improving uniformity in large-scale chemical probing experiments Hamish Blair | |
| Viral RNA secondary structure prediction Nan Pan | |
| Secondary Structures with Led-Seq Peter Stadler | |
| 18:00-20:00 | RNA 2D/3D prediction (singular) with experimental data Chair: Janusz Bujnicki |
| Conservation as Soft Constraint Peter F. Stadler | |
| RNA-MobiSeq: Deep mutational scanning and mobility-based selection for RNA 2D and 3D structure inference Yaoqi Zhou |
Tuesday, July 30
| 11:00-13:00 | Analysis of base pairs Chair: Bohdan Schneider |
| About Basepairs, mostly in RNA Eric Westhof | |
| Identification of Basepairs in 3D structures Bohdan Schneider | |
| 18:00-20:00 | RNA 2D prediction Chair: Yaoqi Zhou |
| Revisiting the base pair maximization approach for RNA secondary structure prediction with SQUARNA Eugene Baulin | |
| Sparsified MFE algorithms for RNA secondary structures Mateo Gray | |
| Efficient partition function computation for pseudoknotted RNAs Sebastian Will | |
| SPOT-RNA: Base-pair prediction on unseen RNAs Yaoqi Zhou |
Wednesday, July 31
| 11:00-13:00 | RNA puzzles / CASP Chair: Eric Westhof |
| RNA-Puzzles Round V Eric Westhof | |
| RNA-Puzzles website and automation Chichau Miao | |
| Now that we found base pairs, what are we gonna do with them? Francois Major | |
| 17:30-19:30 | RNA evolution Chair: Anton S. Petrov |
| RNAbialign: Incongruent Evolution of RNA Sequence and Structure Maria Waldl | |
| RNase P has also evolved by accretion Anton S. Petrov | |
| Searching the dark matter in 202 Cyanobacteria for conserved RNA structures Jan Gorodkin | |
| Decoding the determinants of stop codon readthrough in insects Nadya Makarova | |
| Evolution of mitogenome-encoded RNAs: everything goes Franz Lang | |
| Evolution of mitochondrial ribosomal RNAs Gertraud Burger |
Thursday, August 01
| 11:00-13:00 | RNA motifs Chair: Vladimir Reinharz |
| Navigating the RNA Landscape: Secondary Structure Prediction and SARS-CoV-2 Frameshift Dynamics Hosna Jabbari | |
| Discovery of novel cis-regulatory RNA motifs in plant organelles Dolly Mehta | |
| Exploring isosteric RNA 3D motifs with ARTEM Eugene Baulin | |
| All basepairs interactions RNA 3D modules, variants, and prediction Vladimir Reinharz | |
| Integrated prediction of multiple RNA 3D motifs via probabilistic modelling framed by evolutionary information Elena Rivas | |
| 17:30-19:30 | RNA visualization Chair: Anton Petrov |
| Pseudoknot visualization and some statistics on pk Otagaki Takumi | |
| VARNAjs: a javascript library for RNA visualization Yao Hua-Ting | |
| RNA interaction inspection with PyMOL/rna-tools [short demo] Marcin Magnus | |
| RNA basepair modules and their 3D occurrences in carnaval.cbe.uqam.ca Vladimir Reinharz | |
| RiboVision2: A Web Server for Advanced Visualization of Ribosomal RNAs Anton S Petrov | |
| Visualising RNA secondary structure using R2DT Anton I. Petrov |
Friday, August 02
| 11:00-13:00 | Synthetic biology, design aspects Chair: Michael Wolfinger |
| Towards xrRNA riboswitches Michael T. Wolfinger | |
| What can geometric combinatorics say about RNA design? Christine Heitsch | |
| 18:00-20:00 | RNA annotation II Chair: Bertrand Marchand |
| Annotation and validation of nucleic acid structures. Increasing quality and interoperability of the data Bohdan Schneider | |
| Annotate the Annotations using 1D2DSimScore Naeim Moafinejad | |
| A tool for systematic retrieval of structural RNAs in a broad evolutionary context - GERONIMO Agata Kilar | |
| Formulation of Pseudoknotted Covariance Models Bertrand Marchand | |
| Mammalian SRA lncRNA Encodes a Protein Serafina Nieves |
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