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Sunday, 11 Feb 2024 - Friday, 16 Feb 2024


"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



Villa Plemelj
Prešernova 39
4260 Bled, Slovenia
Phone: +386 4 5743 023
GPS Coordinates: 46.371121,14.108504
Hotel Astoria
Prešernova 44
4260 Bled, Slovenia
Phone: +386 4 579 44 00
Fax:     +386 4 579 44 01

View Larger Map

How to get there
From Ljubljana airport you have the following options to get to the Winterseminar:
  • take a regular taxi (approx. 50 €)
  • public bus transfer, first to Ljubljana city and from there to Bled
  • Airport Shuttle ZUP prevozi (recommended, special rates for groups)
If you arrive via train at Lesce-Bled, you can take a taxi or go by bus to the main bus station (search for connections from Lesce to Bled)


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 PatelRegulatory aging clock
Isabell KrausUsing single-cell sequencing to investigate the epigenetic role in early embryonic development
Pierre HardouinDesign and High-throughput Screening of artificial SAM-I Aptamer by using SHAPE chemical probing method
Jannes Uwe SpangenbergRNA modifications: traces in the ONT signal
Vincent MessowBayesian Inference of Chromosome Structures at Multiple Scales from Single-Cell Hi-C Data
Gabor BaloghAutomated analysis of epigenetic and transcriptomic biomarkers from public data to assist individualised treatment success prediction
Sarah KrautwurstMulti-genome mapping: Are short-read mapping tools influenced by the order of reference sequences?
Tycho KirchnerGlobal transcriptional shutdown in RNA-seq data
Alexander CherkasovAbout single cell multiome of LZTR-1 depleted mice
Alena van BömmelNonlinear DNA methylation trajectories in aging mice
Graph Theory / Networks 12 Feb 20248pmHotel Astoria
Session Chair: Josef Leydold
Slides Speaker Talk Title
Marc HellmuthClustering Systems of Phylogenetic Networks
Guillaume ScholzArboreal Networks: What and Why?
Juri KolčákParameterless Identification of Microbial Interactions
Nicola VassenaStoichiometric mechanisms for oscillations and multistability in reaction networks
Tomaž PisanskiPolycirculant unit-distance graphs
RNA structure 13 Feb 20243pmHotel Astoria
Session Chair: Sebastian Will
Slides Speaker Talk Title
Yann PontyAutomated design of dynamic programming schemes for RNA folding with pseudoknots
Hua-Ting YaoSomething about probing
Thomas SpicherFree energy calculation of modified nucleotides by molecular dynamics simulations
Yuliia VarenykThe effect of modified nucleotides on RNA structure
Nan PanStructure modelling of RNA virus genomes
Leonhard SidlDesigning RNase-resistant Riboswitches
Stefan BadeltThe commit & delay model for exact coarse grained dynamics of RNA folding
Théo BourySearching for exact solutions for the inverse folding problem using graphs and parameterization
Casper AsbjørnSampling RNA Secondary Structures with Pseudoknots using Analytic Combinatorics
Cheminformatics 13 Feb 20248pmHotel Astoria
Session Chair: Thomas Gatter
Slides Speaker Talk Title
Maria WaldlMatomics Intro
Rupert TscheliessnigUnlocking Network Scalability in Communities
Nora BeierConverting KEGG RCLASS data into DPO graph rewriting rules
Richard GolnikModelling isotope labeling in atom transition networks
Tieu Long Phan + Klaus WeinbauerSynthesis Rebalancing Framework
Mikkel PoseltQuantum Mechanics and Chemical Graph Transformation
Jonas StisenCategories for Chemically Inspired Graph Transformation
Cheminformatics / Graph Theory 14 Feb 20243pmHotel Astoria
Session Chair: Christoph Flamm
Slides Speaker Talk Title
Peter StadlerElectron Pushing Diagrams and Atom-Atom Maps
Anne-Susann AbelNatural carbon assimilation and synthetic pathways: Exploring the chemical space of carbon fixation
Manuel UhlirChallenges in Mass Spectral Prediction
Maximilian FaissnerEnzyme Promiscuous Activity: Substrate Prediction based on 3-Dimensional Structure
Sissel BankeRealisability of Chemical Pathways
Yitao CaiExploring Chemical Reaction Space with Intrinsically Motivated Agent
Yingjie PanStoichiometric Conversion of Cellulosic Biomass by in Vitro Synthetic Enzymatic Biosystems
Thomas GatterSimulating the Unknown
*Omics 14 Feb 20248pmHotel Astoria
Session Chair: Cristian A. Velandia
Slides Speaker Talk Title
Christopher KlapprothSynthetic structured RNAs - playing with Genetic algorithms
Alan AzedeDeciphering the RNA structurome in the pathogenic bacterium Staphylococcus aureus
Amos OnnSingle Cell Lineage Reconstruction using Short Tandem Repeats
Karl KaetherAnnotation-Free Synteny Computation
Muriel RitschEndogenous Viral Elements in the Shadows: Challenges in Data Availability and Accessibility
Daria MeyerIdentifying tumor biomarkers based on Nanopore sequencing DNA methylation data
Kanstantsin SiniukConvergent promoters: collision or cooperation?
Graph Theory 15 Feb 20243pmHotel Astoria
Session Chair: Marc Hellmuth
Slides Speaker Talk Title
Annachiara KorchmarosThe Xenology Graph Completion Problem
Bruno SchmidtSorting by TDRL and iTDRL
Kasper BeiderLearning Graph Canonicalisation and Rule Inference
Akbar Davoodi + Daniel MerkleMaximum Common Subgraph Finding and Dynamic Programming for Mechanistic Explanation in Mass Spectrometry
Erika Herrera MachadoA Sensitivity Analysis for Rule-based Systems Chemistry
Marcos LaffitteProgressive Graph Alignment: ambiguous edges, mutants and heuristics
Alexander BlokhuisSome structural aspects of CRNS in theory and experiment
Nino LauberExpansion and Exploration of Prebiotic Chemical Reaction Spaces through Rule Based Modeling
Nino BašićNut 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 AydenDifferential histone marks between Clca3a1 high and low stem cells
Ioanna SamiUnveilling sex-differences: Exploring Methylation and Gene Expression in Multiple Sclerosis
Mara SteigerLive brain tumor classification from sparse epigenomic data using Naïve Bayesian modeling
Maria SchreiberNot everything gets bad when we get old
Zhihan ZhuDifferentially methylated region identification for multi-groups
Pablo Andres Perez MesaEvolution of plant specialized metabolism in Solanaceae from a multi-omics perspective
16 Feb 202411amHotel Astoria
Slides Speaker Talk Title
Ronny LorenzClosing Remarks


Further Information

Find detailed information here.

Registered Participants

Name (headcount: 91) Email Affiliation
RonnyLorenzronny (at) Wien
PeterStadlerstudla (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
BaerbelStadlerbaer (at) bioinf.uni-leipzig.deMPI MIS Leipzig
MariaWaldlmaria (at) Uni Leipzig
MurielRitschanne.muriel.christin.ritsch (at) uni-jena.deFSU Jena
MariaSchreibermaria.schreiber (at) uni-jena.deFSU Jena
DariaMeyerdaria.meyer (at) uni-jena.deFSU Jena
KlausWeinbauerweinbauer.klaus (at) gmail.comBioinformatik Uni Leipzig
JuriKolčákkolcak (at) imada.sdu.dkSDU Odense
EmanuelBarthemanuel.barth (at) uni-jena.deFSU Jena
SigridSchwarthoffsigrid.schwarthoff (at) outlook.deFamily
ChristianeGärtnerchristiane (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
Tieu LongPhanlong.tieu_phan (at) uni-leipzig.deBioinformatik Uni Leipzig
SarahKrautwurstsarah.krautwurst (at) uni-jena.deFSU Jena
NoraBeiernora (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
Anne-SusannAbelanne-susann.abel (at) Wien
YingjiePanpyj0474 (at) gmail.comTBI Wien
ChristophFlammxtof (at) Wien
JannesSpangenbergjannes.spangenberg (at) uni-jena.deFSU Jena
NicolaVassenanicola.vassena (at) uni-leipzig.deIZBI/LIFE Leipzig
ThomasGattergatter_thomas (at) hotmail.comBioinformatik Uni Leipzig
RichardGolnikrichard (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
StephanBernhartberni (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
MaximilianFaissnermax.faissner (at) gmail.comTBI Wien
Hua-TingYaohtyao (at) Wien
LeonhardSidlleonhard.paul.sidl (at) Wien
ChristopherKlapprothchristopher.klapproth (at) protonmail.comBioinformatik Uni Leipzig
IvoHofackerivo (at) Wien
ManjaMarzmanja (at) uni-jena.deFSU Jena
YitaoCaiyitao.cai (at) Wien
BrunoSchmidtbruno (at) bioinf.uni-leipzig.deMPI MIS Leipzig
NinoLaubernino.lauber (at) Wien
ManuelUhlirmanuel.uhlir (at) Wien
Casper AsbjørnEriksencasbjorn (at) imada.sdu.dkSDU Odense
JonasStisenjosti (at) sdu.dkSDU Odense
VincentMessowvincent.messow (at) uni-jena.deUKJ/FSU Jena
SebastianWillsebastian.will (at) polytechnique.eduCNRS/Ecole Polytechnique
YannPontyyann.ponty (at) lix.polytechnique.frCNRS/Ecole Polytechnique
NanPANpan (at) lix.polytechnique.frCNRS/Ecole Polytechnique
AmosOnnamos.onn (at) ukr.deIZBI/LIFE Leipzig
MichaelWolfinger Michael.wolfinger (at) Freiburg
AnnachiaraKorchmarosannachiara.korchmaros (at) uni-leipzig.deBioinformatik Uni Leipzig
ThéoBourytheo.boury (at) lix.polytechnique.frCNRS/Ecole Polytechnique
ElhamGholamzadehel.gholamzade7000 (at) gmail.comMax Planck Cognitive Brain Sience Leipzig
KajalSinglasingla (at) cbs.mpg.deMPI CBS, Leipzig
GuillaumeScholzguillaume (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
KarlKaetherkarl (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
TomažPisanskiTomaz.Pisanski (at) upr.siUniversity of Primorska
JosefLeydoldjosef.leydold (at) Wien
HeleneKretzmerkretzmer (at) molgen.mpg.deMPI for Molecular Genetics
GaborBaloghgabor.balogh (at) gmx.deBioinformatik Uni Leipzig
SteveHoffmannsteve.hoffmann (at) leibniz-fli.deFLI on Aging
MaraSteigersteigerm (at) molgen.mpg.deMPI for Molecular Genetics
AkbarDavoodiakb (at) sdu.dkSDU Odense
TychoKirchnerTycho.Kirchner (at) leibniz-fli.deFLI Jena
RobertSchwarzRobert.Schwarz (at) leibniz-fli.dFLI Jena
KatjanaSchwabKatjana.Schwab (at) leibniz-fli.deFLI Jena
Setenay GupseÖzcanGupse.Oezcan (at) leibniz-fli.deFLI Jena
DanielMerkledaniel.merkle (at) uni-bielefeld.deSDU Odense
Alenavan BömmelAlena.Vanboemmel (at) leibniz-fli.deFLI Jena
KanstantsinSiniukKanstantsin.Siniuk (at) leibniz-fli.deFLI Jena
TusharPatelTushar.Patel (at) leibniz-fli.deFLI Jena
AtakanAydenAtakan.Ayden (at) leibniz-fli.deFLI Jena
AlexanderCherkasovAlexander.Cherkasov (at) leibniz-fli.deFLI Jena
KonstantinRiegeKonstantin.Riege (at) leibniz-fli.deFLI Jena
JanGorodkingorodkin (at) rth.dkRTH Copenhagen
NinoBašićnino.basic (at) famnit.upr.siUniversity of Primorska
EllaCassidyella (at) bioinf.uni-leipzig.deIZBI/LIFE Leipzig
Isabelle Krausisa1.kraus (at) gmail.comMPI for Molecular Genetics
ZhihanZhuzzhu (at) molgen.mpg.deMPI for Molecular Genetics
AlexanderBlokhuisalex_blokhuis (at) hotmail.comIMDEA Nanociencia
MikkelPosseltmikkel (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
KasperBeiderkbeid20 (at) student.sdu.dkSDU Odense
SisselBankebanke (at) imada.sdu.dkSDU Odense
YuliiaVarenykyvarenyk (at) Wien
PierreHARDOUINpierre.hardouin (at) u-paris.frFaculté de Pharmacie - CiTCoM UMR 8038
ThomasSpichertspicher (at) Wien
MarcosLaffittemarcoslaffitte (at) gmail.comBioinformatik Uni Leipzig
AlanAZEDEalan.azede (at) Polytechnique
CristianVelandiacavelandiah (at) Wien
StefanBadeltstefan.badelt (at) Wien
Anela Tosevskaanela.tosevska (at) University of Vienna
RupertTscheliessnigrupert.tscheliessnig (at) gmail.comTBI Wien
IoannaSamishami.joanna (at) gmail.comBioinformatik Uni Leipzig
MarcHellmuthmarc.hellmuth (at) University
ErikaHerrera Machadoerikaherreramachado (at) gmail.comSDU Odense
LenaGladbachlenagl (at) imada.sdu.dkSDU Odense
JoeSmithjantonysmith2 (at) gmail.comTBI Wien
PatrickJakobsencontact (at) zelaven.comTBI Wien
DulceValdiviadulce (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
Pablo AndresPerez Mesapperezme (at) University of Colombia Bogotá, Cundinamarca, Colombia