Time

Sunday, 09 Feb 2025 - Friday, 14 Feb 2025

Topics

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

Registration Fee

300,- € (double room) / 425,- € (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)

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Program

• Sun 0
• Mon 14
• Tue 11
• Wed 14
• Thu 12
• Fri 3
• All 54

Arrival and Get Together at the Villa 9 Feb 20255pmVilla Plemlj

Bioinformatics I 10 Feb 20253pmHotel Astoria

Session Chair: Peter F. Stadler
Slides	Speaker	Talk Title
	David Wolpert	How Constraints Affect Evolution of Entropy - Strengthened Second Laws
	Nicola Vassena	Looking for a Bledator
	Carlos Ugarte	Horizontal transfer in small language families and isolates from Northern Peru
	Dulce Valdivia	tRNA pools as key regulators of translation in melanoma
	Karl Kaether	Improving Genome Assemblies With Syntenic Alignments
	Shahram Saghaei	VirJenDB
	Daria Meyer	DNA methylation in HNSCC samples
	Maria Schreiber	SweetSynteny - Unraveling Microsynteny Patterns

Cheminformatics 10 Feb 20258pmHotel Astoria

Session Chair: Daniel Merkle
Slides	Speaker	Talk Title
	Alex Blokhuis	Structural signatures of CRNs in reaction-monitoring data
	Thomas Gatter	Comparison of Metabolic Networks
	Tieu Long Phan	SynCat: A light-weight model for reaction classification
	Nora Beier	Not Perfect, just Right - Suboptimal Solution as a Secret Igredient for Better Atom-toAtom Mappers
	Mikkel Posselt	Pushing Electrons from Positive to negative Partial Charge
	Aleksandra Olshanova	Graph Grammar Learning for Property-Driven Molecular Generation

Computational Biology 11 Feb 20253pmHotel Astoria

Session Chair: Ivo Hofacker
Slides	Speaker	Talk Title
	Tushar Patel	Gestational Age prediction using CpG clusters in regularized regression
	Elisa Israel	CUT&Tag in the Colorado Potato Beetle
	Mikkel Wolfhagen	Investigating off-targets for use in CRISPR-design
	Gül S. Demircan	Using Active Learning Techniques to Improve CRISPR/Cas9 Guide RNA Design
	Stefano Roncelli	Genetic Redundancy Prediction with Deep Learning
	Jose Antonio Ramirez Rafael	Reconstruction of evolutionary scenarios containing horizontal gene transfer

Graph Theory I 11 Feb 20255:25pmHotel Astoria

Session Chair: Sebastian Will
Slides	Speaker	Talk Title
	Richard Golnik	Modeling Isotope Labeling Experiments - Symmetries in Atom Transition Networks
	Marcos Emmanuel Gonzalez Laffitte	Partial Imaginary Transition State (ITS) Graphs - 2
	Bruno Johann Schmidt	Descendant Clusters
	Annachiara Korchmaros	Polynomial Solutions to hard Problems for undirected 2-Quasi Best Match Graphs
	Guillaume Scholz	Representing distance-hereditary graphs with trees

RNA 12 Feb 20253pmHotel Astoria

Session Chair: Michael T. Wolfinger
Slides	Speaker	Talk Title
	Leonhard Sidl	Designing artificial xrRNAs
	Denis Skibinski	RiboAI: Ribo-seq meets Machine Learning
	Patrick-Pascal Koller	Finding conserved disruptive base pairs in Multi-Sequence Alignments
	Stefan Badelt	Design of cotranscriptional folding paths
	Gupse Özcan	The Emerging Tumor Suppressor RFX7 is a Potential Regulator for Differentiation Therapy in Acute Myeloid Leukemia
	Xueer Han	Link cancer-related Single Nucleotide Polymorphisms in structured regions of Long Intergenic Non-Coding RNAs to function
	Gabriel Lencioni Lovate	Differential analzsis an de novo annotation of RNA-RNA interactions with RNAswarm
	Yitao Cai	Two tales of RNA folding
	Baerbel Stadler	A short history of the University of Vienna

Transcriptomics 12 Feb 20258pmHotel Astoria

Session Chair: Jan Gorodkin
Slides	Speaker	Talk Title
	Kanstantsin Siniuk	Convergent Promoters: Cooperation, Collision or Collision leading to Cooperation?
	Omid Omrani	Regeneration of aged intestinal epithelium: extrinsic and instrinsic players
	Anela Tosevska	Summarizing gene enrichment with SummArIzeR
	Rafael Nascimento	In silico identification of peptides encoded by small ORFs contained in lncRNAs
	Buwen Liang	A Comprehensive Survey of Available Datasets for Host-Bacterial Transcriptome Interactions

Cheminformatics II 13 Feb 20252:30pmHotel Astoria

Session Chair: Hua-Ting Yao, Maria Waldl, Nino Lauber
Slides	Speaker	Talk Title
	Stefan Müller	Elementary vectors for microbial communities
	Rupert Tscheliessnig	Metabolic Community Models: Exploring Interactions and Elementary Modes in Multi-Species Systems
	Maximilian Faissner	Beyond Affinity: Predicting Enzyme Kinetics from Computational Models
	Casper Asbjørn Eriksen	Creating Atom-Level Chemical Reaction Networks from Biochemical Models
	Anne-Susann Abel	Carbon Fixation Pathway Design and the Mystery of Thermodynamics
	Deza Amistas	Complexity of a Reaction Network
	Akbar Davoodi	Edge-Wise Graph Alignment: Theory, CHallenges, and Implementation
	Manuel Uhlir
	Christiane Gärtner	Sex Differences in Biomarker Levels Following Acute Coronary Syndrome (ACS)
	Thomas Gatter	Relevant Cuts for Chemical Networks

Graph Theory II 13 Feb 20258pmHotel Astoria

Session Chair: Marc Hellmuth
Slides	Speaker	Talk Title
	Anna Lindeberg	LCA or no LCA: A short story about simplifying networks
	Ella Cassidy	Class 2 CCA-adding Enzymes in Archaeal Lineages

Bioinformatics II 14 Feb 202510amHotel Astoria

Session Chair: Jakob Hull Havgaard
Slides	Speaker	Talk Title
	Atakan Ayden	Unraveling Epigenetic and Transcriptomic Trajectories in Hematopoiesis during Aging
	Ying Sun	Assessing and predicting the heterogeneity of topologically associating domain boundaries
	Christian Anthon	Pipeline for scoring of DNA probes against RNA targets

Photos

Registered Participants