Time

Sunday, 11 Feb 2024 - Friday, 16 Feb 2024

Topics

"Computational Biology, Computational Mathematics, Theoretical Biology, Bioinformatics, Biological Networks"

Registration Fee

300,- € (double room) / 400,- € (single room)

Available AV equipment

black board, overhead projector, beamer, laptop (linux) network, internet access via Wlan

Participants

• Institute of Theoretical Chemistry (University of Vienna)
• Department of Bioinformatics (University of Leipzig)
• Chair of Bioinformatics (University of Freiburg)
• Center for non-coding RNA in Technology and Health (RTH) (University of Copenhagen)
• RNA Bioinformatics and High-Throughput Analysis Group (Friedrich Schiller University Jena)
• and guests (by invitation only).

Location(s)

View Larger Map

Program

• Sun 0
• Mon 15
• Tue 16
• Wed 15
• Thu 16
• Fri 1
• All 63

Arrival and Get Together at the Villa 11 Feb 20245pmVilla Plemlj

Computational Biology / Bioinformatics 12 Feb 20243pmHotel Astoria

Session Chair: Stephan Bernhart
Slides	Speaker	Talk Title
	Tushar Patel	Regulatory aging clock
	Isabell Kraus	Using single-cell sequencing to investigate the epigenetic role in early embryonic development
	Pierre Hardouin	Design and High-throughput Screening of artificial SAM-I Aptamer by using SHAPE chemical probing method
	Jannes Uwe Spangenberg	RNA modifications: traces in the ONT signal
	Vincent Messow	Bayesian Inference of Chromosome Structures at Multiple Scales from Single-Cell Hi-C Data
	Gabor Balogh	Automated analysis of epigenetic and transcriptomic biomarkers from public data to assist individualised treatment success prediction
	Sarah Krautwurst	Multi-genome mapping: Are short-read mapping tools influenced by the order of reference sequences?
	Tycho Kirchner	Global transcriptional shutdown in RNA-seq data
	Alexander Cherkasov	About single cell multiome of LZTR-1 depleted mice
	Alena van Bömmel	Nonlinear DNA methylation trajectories in aging mice

Graph Theory / Networks 12 Feb 20248pmHotel Astoria

Session Chair: Josef Leydold
Slides	Speaker	Talk Title
	Marc Hellmuth	Clustering Systems of Phylogenetic Networks
	Guillaume Scholz	Arboreal Networks: What and Why?
	Juri Kolčák	Parameterless Identification of Microbial Interactions
	Nicola Vassena	Stoichiometric mechanisms for oscillations and multistability in reaction networks
	Tomaž Pisanski	Polycirculant unit-distance graphs

RNA structure 13 Feb 20243pmHotel Astoria

Session Chair: Sebastian Will
Slides	Speaker	Talk Title
	Yann Ponty	Automated design of dynamic programming schemes for RNA folding with pseudoknots
	Hua-Ting Yao	Something about probing
	Thomas Spicher	Free energy calculation of modified nucleotides by molecular dynamics simulations
	Yuliia Varenyk	The effect of modified nucleotides on RNA structure
	Nan Pan	Structure modelling of RNA virus genomes
	Leonhard Sidl	Designing RNase-resistant Riboswitches
	Stefan Badelt	The commit & delay model for exact coarse grained dynamics of RNA folding
	Théo Boury	Searching for exact solutions for the inverse folding problem using graphs and parameterization
	Casper Asbjørn	Sampling RNA Secondary Structures with Pseudoknots using Analytic Combinatorics

Cheminformatics 13 Feb 20248pmHotel Astoria

Session Chair: Thomas Gatter
Slides	Speaker	Talk Title
	Maria Waldl	Matomics Intro
	Rupert Tscheliessnig	Unlocking Network Scalability in Communities
	Nora Beier	Converting KEGG RCLASS data into DPO graph rewriting rules
	Richard Golnik	Modelling isotope labeling in atom transition networks
	Tieu Long Phan + Klaus Weinbauer	Synthesis Rebalancing Framework
	Mikkel Poselt	Quantum Mechanics and Chemical Graph Transformation
	Jonas Stisen	Categories for Chemically Inspired Graph Transformation

Cheminformatics / Graph Theory 14 Feb 20243pmHotel Astoria

Session Chair: Christoph Flamm
Slides	Speaker	Talk Title
	Peter Stadler	Electron Pushing Diagrams and Atom-Atom Maps
	Anne-Susann Abel	Natural carbon assimilation and synthetic pathways: Exploring the chemical space of carbon fixation
	Manuel Uhlir	Challenges in Mass Spectral Prediction
	Maximilian Faissner	Enzyme Promiscuous Activity: Substrate Prediction based on 3-Dimensional Structure
	Sissel Banke	Realisability of Chemical Pathways
	Yitao Cai	Exploring Chemical Reaction Space with Intrinsically Motivated Agent
	Yingjie Pan	Stoichiometric Conversion of Cellulosic Biomass by in Vitro Synthetic Enzymatic Biosystems
	Thomas Gatter	Simulating the Unknown

*Omics 14 Feb 20248pmHotel Astoria

Session Chair: Cristian A. Velandia
Slides	Speaker	Talk Title
	Christopher Klapproth	Synthetic structured RNAs - playing with Genetic algorithms
	Alan Azede	Deciphering the RNA structurome in the pathogenic bacterium Staphylococcus aureus
	Amos Onn	Single Cell Lineage Reconstruction using Short Tandem Repeats
	Karl Kaether	Annotation-Free Synteny Computation
	Muriel Ritsch	Endogenous Viral Elements in the Shadows: Challenges in Data Availability and Accessibility
	Daria Meyer	Identifying tumor biomarkers based on Nanopore sequencing DNA methylation data
	Kanstantsin Siniuk	Convergent promoters: collision or cooperation?

Graph Theory 15 Feb 20243pmHotel Astoria

Session Chair: Marc Hellmuth
Slides	Speaker	Talk Title
	Annachiara Korchmaros	The Xenology Graph Completion Problem
	Bruno Schmidt	Sorting by TDRL and iTDRL
	Kasper Beider	Learning Graph Canonicalisation and Rule Inference
	Akbar Davoodi + Daniel Merkle	Maximum Common Subgraph Finding and Dynamic Programming for Mechanistic Explanation in Mass Spectrometry
	Erika Herrera Machado	A Sensitivity Analysis for Rule-based Systems Chemistry
	Marcos Laffitte	Progressive Graph Alignment: ambiguous edges, mutants and heuristics
	Alexander Blokhuis	Some structural aspects of CRNS in theory and experiment
	Nino Lauber	Expansion and Exploration of Prebiotic Chemical Reaction Spaces through Rule Based Modeling
	Nino Bašić	Nut graphs with a given automorphism group

Bioinformatics 15 Feb 20248pmHotel Astoria

Session Chair: Helene Kretzmer
Slides	Speaker	Talk Title
	Jan Gorodkin	CRISPR/Cas9 gRNA design for base editing
	Atakan Ayden	Differential histone marks between Clca3a1 high and low stem cells
	Ioanna Sami	Unveilling sex-differences: Exploring Methylation and Gene Expression in Multiple Sclerosis
	Mara Steiger	Live brain tumor classification from sparse epigenomic data using Naïve Bayesian modeling
	Maria Schreiber	Not everything gets bad when we get old
	Zhihan Zhu	Differentially methylated region identification for multi-groups
	Pablo Andres Perez Mesa	Evolution of plant specialized metabolism in Solanaceae from a multi-omics perspective

16 Feb 202411amHotel Astoria

Slides	Speaker	Talk Title
	Ronny Lorenz	Closing Remarks

Photos

Further Information

Find detailed information here.

Registered Participants