CCBPP
Computational Approaches to RNA Structure and Function

Organizers:

E. Rivas (Harvard University), E. Westhof (University of Strasbourg)

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
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

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

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

Tuesday, July 30

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

Wednesday, July 31

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

Thursday, August 01

10:30-11:00 Coffee
11:00-13:00 RNA motifs
Chair: Vladimir Reinharz
17:30-19:30 RNA visualization
Chair: Anton Petrov

Friday, August 02

11:00-13:00 Synthetic biology, design aspects
Chair: Michael Wolfinger
18:00-20:00 RNA annotation II
Chair: Bertrand Marchand