Talks for the conference.

Computational Approaches to RNA Structure and Function

2022, Aug 07 -- Aug 20

Organizers:
E. Rivas (Harvard University)
E. Westhof (University of Strasbourg)

Monday, August 08

11:00-11:15	Open remarks

11:15-12:15	Talk by Kate Shulgina

12:30-13:30	Talk by Quaid Morris

18:00-19:00	Organizational meeting

Tuesday, August 09

11:00-13:00	Session I: Machine learning methods for RNA structure
	Chair: Marcel Szikzsai
	Unsupervised generative models for in vitro selection experiments
	R. Monasson
	Experiments in Deep Learning for RNA Secondary Structure Prediction
	I. L. Hofacker
18:00-20:00	Session II: RNA puzzles
	Chair: Marta Szachniuk
	RNA Puzzles
	E. Westhof
	CASP-RNA
	C. Fidelis
	Evaluation of predictions. The geometry of RNA 3D models
	M. Szachniuk
	Finding entanglements of RNA structural elements
	T. Zok
	RNA-Tools A swiss army knife for RNA 3d structure modeling workflow
	M. Magnus

Wednesday, August 10

11:00-13:00	Session III: Elixir
	Chair: B. Schneider
	ELIXIR and its communities
	B. Schneider
	Rfam and RNACentral
	B. Sweeny
	Annotation of nucleic acid structures at dnatco.datmos.org
	B. Schneider
	Annotation and validation of nucleic acid structures
	J. Cerny
	Platicity of base pairing observed in the A-form 18-mer DNA structures
	J. Svoboda
17:00-19:00	Session IV: RNA-protein interactions
	Chair: R. Backofen
	Interpretable sequence-structure RBP motif finding using PRIESSTESS
	Q. Morris
	Prediction of RNA-protein Interactions with AlphaFold-derived Protein Representations
	Long Yat Tam
	What can we do with RNA-protein interaction predictions?
	R. Backofen
	Dancing to Silence
	F. Major
	Uncovering regulatory elements transcriptome-wide using subcellular in situ RNA sequencing
	D. Fürth

Thursday, August 11

11:00-13:00	Session V: RNA design, CRISPR
	Chair: Y. Ponty
	CRISPR/Cas9 gRNA design
	J. Gorodkin
	Eukaryotic riboswitch detection using inverse RNA folding
	D. Barash
	Declarative design using Infrared/RNAPond
	S. Will
	Fitness functions for RNA design algorithms
	M. Ward
	An evolutionary algorithm for pseudoknotted RNA design inspired by Lévy Flights
	Nono Saha Cyrille Merleau
	Generative models for riboswitch design
	J. Fernández de Cossio Diaz
	Differentiable RNA design
	M. Matthies
16:00-18:00	Session VI: Alphafold insipired RNA 3D structure prediction. Can it work? can not? If so, what next?
	Chair: C. Zirbel
18:00-20:00	Session VII: evol of RNA, remote homology
	Chair: E. Rivas
	Natural catalytic RNAs: strange structural variants in mysterious organisms
	Z. Weinberg
	Bacillaceae-1 RNA motifs and rapid sequence divergence of conserved RNA structures
	S. Seemann
	Incongruent Evolution of RNA Sequence and Structure
	M. Waldl
	Forbidden motifs and the cardinality of secondary structure space
	Hua-Ting Yao
	Exploring RNA folds and remote evolutionary relationships with an improved structurally similarity search methods
	E. Baulin
	Using positive and negative evolutionary information for RNA structure prediction
	E. Rivas

Friday, August 12

11:00-13:00	Session VIII: viral RNA
	Chair: M. Marz
	RNA structuredness of viral genomes
	M. T. Wolfinger
	Reference-based viral sequence validation and annotation using VADR
	E. Nawrocki
	Shapify: Pathways to SARS-CoV-2 frameshifting pseudoknot
	L. Trinity
	Analysis and evolution of immunogenic dinucleotide motifs in SARS-CoV-2
	A. Di Gioacchino
18:00-20:00	Session IX: non-coding RNAs
	P. Gardner
	Any conserved RNA structure?
	E. Rivas
	Genomic landscape of conserved RNA secondary structure signatures and their homologs
	V. Gaonach-Lovejoy
	Identification of ncRNAs in 'ancestral' free-living eukaryotes: the jakobids and malawimonads
	S. Prince
	Features of functional human genes
	P. Gardner
	Immunostimulatory viral-like features in genomic repeats
	S. Cocco

Monday, August 15

11:00-13:00	Session X: RNA Kinetics
	Chair: S. Will
	Cotranscriptional RNA Kinetics with Dr Transformer
	I. Hofacker
	An RNA kinetics ansatz derived from an efficient prediction of RNA pathways
	Nono Saha
	Long-range RNA structure dynamically controls alternative splicing
	D. Pervouchine
	RNA dynamics within the spliceosome
	M. Magnus
18:00-20:00	Session XI: RNA in vivo
	Chair: M. Meyer
	Uncovering Regulatory Elements Transcriptome-Wide using subcellular in situ RNA sequencing
	D. Fürth
	Circular stable intronic RNAs in early-stage bladder cancer
	A. Mannstaedt Rasmussen
	Assessing RNA structure and function via fitness landscape
	M. Meyer
	A systemics view of puras cellular rna-binding function from omics data gives insights into pura related diseases
	M. Klostermann

Tuesday, August 16

11:00-13:00	Session XII: RNA structure from alignments
	Chair: F. Major
	Aligning and modeling a few thousand unknown ncRNAs in “primitive” unicellular eukaryotes
	F. Lang
	Rfam 3D and R-scape updates
	N. Ontiveros
	High-quality customizable algorithms for RNA 3D structure alignment
	M. Antczak
	Dynamic programming from an input helical pattern
	B. Marchand
	An integer programming framework for simultaneous prediction of RNA structure with pseudoknots and insertion of local 3D motifs
	G. Loyer
15:00-17:00	Session XIII: RNA annotation using NtC classes
	Chair: I. Bohdan Schneider
	Use of NtC knowledge for nucleic acid structure refinement
	J. Svoboda
18:00-20:00	Session XIV: RNA processing and regulation
	Chair: B. Yoseph
	Transcriptome sequencing suggests lariat polyadenylation
	M. Vlasenok
	Regulation of gene expression via unproductive splicing
	D. Pervouchine
	Fantastic rG4s: What they do and where to find them?
	Y. Barash
	What happens to the CRISPR-Cas extra repeat?
	Z. Weinberg
	Net Oligo Binding Free Energies
	D. Aalberts

Wednesday, August 17

11:00-13:00	Session XIV: Translation, mRNA vaccines, antibiotics
	Chair: D. Aalberts
	Interactions between Gs and Us in Translation
	E. Westhof
	Design of modified aptamers against the Beta-Secretase 1 involved in Alzheimer’s disease
	T. Yacoub
	Structural studies into ribosome-binding natural product antibiotics
	O. Kalinina
	Optimizing coding sequences
	D. Aalberts
17:00-19:00	Session XV: RNA-RNA interactions
	Chair: D. Pervouchine
	Introduction
	D. Pervouchine
	Long range RNA-RNA interactions inferred from RNA in situ conformational sequencing
	S. Margasyuk
	RNA Palindromic sequences matter
	Á. Cantero Camacho
	Predicting the kinetics of RNA-RNA interactions
	S. Will
	Modeling RNA-RNA interaction formation on direct paths
	M. Waldl

Thursday, August 18

11:00-13:00	Session XVI: RNA 3D structure modeling with experimental data
	Chair: J. M. Bujnicki
	Modeling of RNA 3D structure based on medium- and low-resolution maps from cryo-electron microscopy and macromolecular crystallography
	J. Bujnicki
	A cryo-EM map as the target - how to evaluate predictions
	M. Antczak
	Refinement of RNA crystal structures with NtCs
	J. Cerny
	Getting Darwin into SHAPE
	I. Meyer
	NACDDB: Nucleic Acid Circular Dichroism DataBase, a new computational resource for experimental data on RNA 3D structure
	A. Cappannini
18:00-20:00	Session XVII: RNA modules
	Chair: C. Zirbel
	A few memories of Neocles, non-Watson-Crick pairs and RNA modules
	E. Westhof
	My time with Neocles Leontis and updates on our work
	C. Zirbel
	The Overrepresented RNA Blocks
	F. Major
	Craig wants me to talk about G4s
	M. Szachniuk
	Arbitrarily large RNA structural modules
	V. Reinharz
	Yet another definition of a long-range RNA tertiary motif
	E. Baulin

Friday, August 19

11:00-12:00	Session XVIII: RNA visualization
	Chair: A. Petrov
	Visualization of quadruplex structures
	T. Zok
	Visualization of nucleic acid conformations
	J. Cerny
	Detailed circular basepair diagrams
	C. Zirbel
	Visualizing structural models for long(er) RNAs
	Y. Ponty
	R2DT: Visualizing RNA secondary structure using templates
	A. Petrov
18:00-20:00	Session XIX: RNA modifications, nanopore
	Chair: V. Reinharz
	Direct RNA sequencing with modifications
	J. Spangenberg
	nanoShape: Nanopore based sequence and structure detection on novel RNA
	J. White Bear
	Newest features in MODOMICS a database of RNA modification pathways
	A. Cappannin
	Evolution of the RNA editing sites in filamin genes
	A. Tanzer
	Tracing tRNA Modifications with Deep Sequencing
	P. Stadler
	Something interesting about RNA modifications
	E. Westhof