Organizers:
E. Rivas (Harvard University), E. Westhof (University of Strasbourg)
Computational Approaches to RNA Structure and Function
(Benasque Science Center, Jul 05 - Jul 17, 2026)
Monday, July 06
| 09:00-10:30 | Registration |
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Morning Session |
| RNA structure 3D prediction and cryo-EM structures Rachael Kretsch | |
| 17:30-18:30 | Afternoon Session |
| A Bottom-up Approach to RNA Architecture: Dinucleotide Conformers and Base Pairs Bohdan Schneider | |
| 18:30-19:30 | Organizational meeting |
Tuesday, July 07
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA Interactions I Chaired by: Ralf Bundschuh |
| Nucleotide-nucleotide interaction networks Vladimir Reinharz | |
| RNA binding pockets characterization, prediction, and dynamics samuela pasquali | |
| Ligand-based methods for the discovery of small-molecule RNA binders Filip Stefaniak | |
| Computational modeling of RNA-protein binding interactions under an external force Ralf Bundschuh | |
| R3BIND: Decoding Protein-Nucleic Acid Recognition through 3D Structural Templates Kunal Shewani | |
| 17:30-19:30 | Session: RNA 2D structure Chaired by: Ronny Lorenz |
| Exact algorithms for the RNA energy barrier Théo Boury | |
| Combinatorial inverse folding ...when helix size matters, but energy models maybe safely simplified?! Yann Ponty | |
| RNA 2D Structure Prediction: Integrating Shape/DMS-Mapseq and AI Rolf Backofen | |
| Predicting RNA 2D and 3D structures with SQUARNA and R3FOLD Eugene Baulin | |
| 20:00-22:00 | Welcome reception |
Wednesday, July 08
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA 3D (I) Chaired by: Elise White |
| Coupled tertiary interactions drive self-assembly of the glmS ribozyme Elise White | |
| Structural assemblies for an RNA world Lin Huang | |
| Thermodynamically consistent single-interaction site model to simulate long RNA molecules Naoto Hori | |
| RNA Puzzles Zhichao Miao | |
| RNApdbee 3.0: A unified web server for comprehensive secondary structure annotation from 3D coordinates Jan Pielesiak | |
| OpenRNAFold: an end-to-end approach for RNA 3D structure prediction Marcin Marcin Magnus | |
| 16:00-17:00 | Conformational Space of RNA: What Experimentalists See Yun-Xing Wang |
| 18:00-20:00 | RNA 2.5D + pseudoknots + modifications Chaired by: Hosna Habbari |
| High-throughput experimental approaches mapping RNA structure to function Leonard Scharfen | |
| Predicting pseudoknot probabilities proficiently-efficiently encompassing KHPs and 4Cs Sebastian Will | |
| Zooming out to see clearer Hosna Jabbari | |
| Finding templates for template-free modelling Tomasz Zok |
Thursday, July 09
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA AI/ML (I) Chaired by: Jerome Waldispuhl |
| Minimal-AI: unsupervised learning of the rules of RNA base pairing Elena Rivas | |
| Disentangling RNA Evolution and Thermodynamics in Genomic Language Models Yuchen Xu | |
| Towards generalisable deep learning models for RNA structure prediction Marcell Szikszai | |
| How Good Are Current RNA 3D Quality Assessment Methods? A Cross-Training Comparison Bartosz Adamczyk | |
| RGCN for binding site/affinity prediction Jerome Waldispuhl | |
| 16:00-18:00 | Session: Demo Section, databases and software (show up with your computer) Chaired by: Samuela Pasquali |
| 18:00-20:00 | Session: RNA evolution Chaired by: Dmitri Pervouchine |
| Miniaturized tRNAs in nematode and arachnid mitochondria Peter Stadler | |
| Benchmark of R-scape for various phylogenetic trees Stefan Seemann | |
| Computational identification of conserved structural RNAs in Nematoda Agata Kilar | |
| How non-coding RNA structures adapt to abiotic factors across taxonomic boundaries Maria Schreiber | |
| RNA structures regulating alternative splicing in paralogs Dmitri Pervouchine |
Friday, July 10
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA Modification Chaired by: Ivo Hofacker |
| Predicting m6A sites: from human to viral transcript Ivan Lecce | |
| Computational estimation of energy parameters for modified nucleotides - A tRNA use case Thomas Spicher | |
| SimRNA is aware of modified nucleotides Seyed Naeim Moafinejad | |
| Experimental mapping of tRNA modification evolution in archaea and bacteria Todd Lowe | |
| 16:00-17:30 | RNA 3D Motifs Chaired by: Bohdan Schenider |
| Identifying RNA 3D motifs with ARTEM Eugene Baulin | |
| 18:00-20:00 | Session: RNA viruses Chaired by: Manja Marz |
| Noncoding RNA at the phage-host interface Liana Merk | |
| AnchoRNA: Multiple sequence alignments for secondary structure prediction using anchors in coding regions Tom Eulenfeld | |
| A double-pseudoknotted motif in tick-borne flaviviruses confers exonuclease resistance during infection Conner Langeberg | |
| Computational Studies of HDV RNA Regulation Danny Barash | |
| Rational design of exoribonuclease-resistant RNAs Leonhard Paul Sidl |
Monday, July 13
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA Interactions Chaired by: Vlad Reinharz |
| Interacting Interval Pair Constraints in RNA Secondary Structure Prediction Ronny Lorenz | |
| BlockBuster 2D: chimera reads clustering Hua-Ting Yao | |
| RIsearch and RIOT, an integrated, high-performance framework for RNA–RNA interaction and siRNA off-target prediction Lorenzo Favaro | |
| Understanding the rules of RNA repeat droplet formation Mostafa Elraies | |
| ClaPNAC: a Classifier of Protein – Nucleic Acid Contacts Grigory Nikolaev | |
| 16:00-17:30 | EuRNAFold: Extensible Unified RNAFold Chaired by: Maria Waldl and Magnus Marcin |
| 18:00-20:00 | Session: RNA Design Chaired by: Kiyoshi Asai |
| Differentiation in RNA sequence Design Revisited Kiyoshi Asai | |
| RNA design landscapes and homotopy RNA design Grzegorz Grzegorz Lach | |
| PKProbDesign: RNA inverse folding including pseudoknots by optimizing thermodynamic folding probability Takumi Otagaki | |
| mRNA design with deep generative models Kengo Sato | |
| Understanding the protein products of structure/codon-optimised mRNA therapeutics Max Walk |
Tuesday, July 14
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA 3D Chaired by: Jiri Cerny |
| Modeling of RNA 3d structure using CryoEM map Sunandan Mukherjee | |
| Evaluating and Advancing RNA Structure Prediction: Lessons from Benchmarks and Community Challenges Nithin Chandran | |
| How to recognize native-like structure in a set of 3D RNA predictions Maciej Antczak | |
| Analysis and refinement of 3D RNA structures with RNAmoley Mikolaj Mlynarczyk | |
| RNArefine: structure prediction and refinement Sho Tsukiyama | |
| DNATCO 5.0 et al Jiri Cerny | |
| 17:00-19:00 | Session: RNA Kinetis and Ensembles Chaired by: Stefan Badelt |
| RNA binding proteins conformationally capture targets from RNA secondary structure ensembles Aisha Haley Bianchi | |
| Applied stochastic RNA folding: flexible move types, new parameters, and a modern framework Stefan Badelt | |
| Conformational ensembles encode molecular recognition Francois Major | |
| Alexander von Humboldt's way in the RNA world Huong Vu | |
| 19:30-20:30 | Divulgative Talk (in spanish): Como el RNA dirige nuestras vidas Elena Rivas |
Wednesday, July 15
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA AI/ML (II) Chaired by: Yann Ponty |
| Features of Function for Machine Learning Daniela Schiavinato | |
| Efficient parameterized learning DCA models of RNA evolution Samuel Gardelle | |
| Controlling thermostability in RNA families Jacopo Boccato | |
| gRNA efficiency prediction Jan Gorodkin | |
| Generative modeling of aptamers from Directed Evolution experiments Stefano Crotti | |
| 16:00-17:30 | Session: Bioinformatics of Riboswitches Chaired by: Danny Barash and Marta S zachniuk |
| Modeling the 3D structure of a riboswitch: a case study Marta Szachniuk | |
| Extending the covariation motif for riboswitch aptamers Laura Hertz | |
| Riboswitch 3D prediction Zhichao Miao | |
| 18:00-20:00 | Session: tRNAs and long RNAs Chaired by: Tood Lowe |
| Modification landscape in the translational apparatus Eric Westhof | |
| Recognition of wobble base pairs by tRNA modifications Xumin Ou | |
| Epigenetics and Evolution of Human tRNA Genes Todd Lowe | |
| DIGtRNA: Discriminative element Identification via GNN for tRNAs Roma Nagle | |
| Divergent self-splicing introns in Patescibacteria Kate Shulgina and Connor Langeberg | |
| 20:00-22:00 | Reception |
Thursday, July 16
| 10:30-11:00 | Coffee |
| 11:00-13:00 | Session: RNA evolutions + 3D Chaired by: Laura Hertz |
| Discovery of conserved RNA structures in plants Dolly Mehta | |
| Found in Translation: Evolution (of Structural RNAs) in 3D Anton S Petrov | |
| Expanding covariation analysis for riboswitches and gene editing RNA-protein systems Laura Hertz | |
| Incongruent RNA sequence and structure evolution Maria Waldl | |
| An RNA Deaminase with Broad Substrate Specificity Gertraud Burger | |
| RNA-ligand pose ranking using graph neural networks Xareni Reyes Soto | |
| 16:00-17:30 | Session: MD Simulations of RNA Chaired by: Elise White |
| Coarse-graining the finer structure of RNA interactions at the interface with macromolecular assemblies Horacio Andres VARGAS GUZMAN | |
| 17:30-19:30 | Session: ncRNAs with Infernal + lessons from Claude Chaired by: Eric Nawrocki |
| Infernal development Eric Nawrocki | |
| HMM-based inference of gene models for ncRNA identification B Franz Lang | |
| Conservation and folding of intrastrand DNA triplexes Christopher King | |
| Avoided Base Pairs: Covariation Signals of Negative Design in RFAM Alignments Ivo Hofacker |
Friday, July 17
| 09:00 | Return Bus |
Sponsors
Contact Information
- info@benasque.org
- (+34) 974551475
- Av. Francia 17
Benasque - 22440, Huesca (Spain)