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Time

Sunday, 12 Feb 2023 - Friday, 17 Feb 2023

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

Location(s)

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)

Registration


In case you have further questions, please send an email to the organizers:
bled (at) viennarna (dot) at

Program

Find the Program calendar here.

Find the pdf version of the Program here.

Arrival and Get Together at the Villa 12 Feb 20235pmVilla Plemlj
Opening Session 13 Feb 202311amHotel Astoria
Session Chair: Ivo Hofacker
Slides Speaker Talk Title
Ivo HofackerWelcome notes and dinner planning
Computational Biology / RNA Structure 13 Feb 20203pmHotel Astoria
Session Chair: Stephan Bernhart
Slides Speaker Talk Title
Gabor BaloghPEVO basket trial, combining immunotherapy with an epidrug in squamous cell carcinomas
Maximilian FeussnerCRISPR-Cas and associated RNA secondary structures
Thomas SpicherComputatonal estmation of energy parameters
Yuliia VarenykThe effect of modified nucleotides on secondary structure prediction in tRNA
Maria WaldlRNA-RNA interaction dynamics
Hua-Ting YaoSalt concentration correction in ViennaRNA package
Graph Theory 13 Feb 20208pmHotel Astoria
Session Chair: Daniel Merkle
Slides Speaker Talk Title
Wilfried ImrichApproximate Graph Products
Nino BašićNut graphs are not edge transitive
Tomaž PisanskiOn vertex-transitive nut graphs that are notcirculant graphs
Sandhya Thekkumpadan Puthiyaveeduk-Median Graphs
Phylogeny / Transcriptomics 14 Feb 20233pmHotel Astoria
Session Chair: Jan Gorodkin
Slides Speaker Talk Title
Ben Luis HackA quartet-based approach to infer phylogenetically informative characters from phenotypic data
Vivian BrandenburgA quartet-based approach to inferphylogenetically informative characters from phenotypic data
Franziska ReinhardtEvolution of Neuropeptide Y/RFamide-likereceptors in Nematodes
Elisa IsraelEvolution of the CCA-adding Enzyme in early-branchingMetazoa
Jannes SpangenbergMagnipore: Differential single nucleotide changesof ONT signals
Daria MeyerDNA methylation analysis using Nanopore sequencing
Robert SchwarzLocus-specific expression analysis of TransposableElements
Christiane GärtnerThe impact of methylation patterns in lymphoma onallele-specific expression
Graph Theory / Cheminfo 14 Feb 20238pmHotel Astoria
Session Chair: Peter Stadler
Slides Speaker Talk Title
Daniel MerkleTACsy : Training Alliance for Comput-ational SystemsChemistry
Nora BeierAtom Transition Networks for Atom Tracing
Casper Asbjørn EriksenA Petri-Net Based Framework for Atom-Tracingin Chemical Networks
Nico DomschkeSynthesizability of molecules
Marcos LaffitteComparison of Atom Maps
Akbar DavoodiAn Application of Graph Products in Rule Inference
Genomics / Other 15 Feb 20238pmHotel Astoria
Session Chair: Sven Findeiß
Slides Speaker Talk Title
Muriel RitschNonretroviral RNA viruses integrated into the humangenome
Tycho KirchnerBashing irreproducibility with shournal
Axel MosigTheory is Dead! Long Live Theory!
Graph Theory 16 Feb 20233pmHotel Astoria
Session Chair: Josef Leydold
Slides Speaker Talk Title
Elina WiechensPromoters revisited
Lena GladbachBubble Structures in Digraphs
Annachiara KorchmarosQuasi Best Match Graphs
Bruno SchmidtDirected Permutation Graphs
Carsten R. SeemannNesting of Polygons
Mehmet Aziz YirikCORENET: Complex chemical reaction networks for breakthrough scalable reservoir computing
Christoph FlammRandomization of chemical reaction networks
Bioinformatics 16 Feb 20238pmHotel Astoria
Session Chair: Ivo Hofacker
Slides Speaker Talk Title
Konstantin RiegeBashbone: NGS Bash library
Shahram SaghaeiVirJenDB: the virus genome database based at FSUJena
Carmen BruckmannAutomated gating of flow cytometry data
Gabriel Lencioni LovateDifferential analysis of RNA cross-linkedHTS reads with RNAswarm
Sarah KrautwurstApproaching RNA-protein interaction predictionsfrom an evolutionary perspective using co-alignments
Ying SunPrediction of base editing outcomes by deep learning
Genomics 17 Feb 202310amHotel Astoria
Session Chair: Steve Hoffmann
Slides Speaker Talk Title
Adrian GeisslerScreen for conserved RNA structures in cyanobacteria
Cristian VelandiaDe-novo canonical microRNA annotation: Insightsusing iterative models
Martin FischerGenome regulation by tumor suppressors andoncoproteins
Arne SahmDeciphering the molecular causes of exceptional agingphenomens in the animal kingdom by applying multi-omics
Karl KaetherAnnotation-free Identification of Synteny Anchors
Thomas GatterGenomics on a Shoestring Budget

Further Information

Find detailed information here.

Registered Participants

Number Name Affiliation Talk Title Payment Status
1ChristianeGärtnerBioinformatik Uni LeipzigThe impact of methylation patterns in lymphoma on allele-specific expression
2ChristophFlammTBI WienRandomization of chemical reaction networks.
3MurielRitschFSU Jenatba
4DariaMeyerFSU Jenatba
5NicoDomschkeBioinformatik Uni LeipzigTBA
6NoraBeierBioinformatik Uni LeipzigAtom Transition Networks for Atom Tracing
7ChristopherKlapprothBioinformatik Uni LeipzigSvift & STRICT: Annotation of conserved non-coding RNAs (WiP)
8EmanuelBarthFSU Jena
9SigridSchwarthoffNot applicable
10PeterStadlerBioinformatik Uni Leipzig
11BärbelStadlerBioinformatik Uni Leipzig
13SarahKrautwurstFSU Jenatba
14KarlKaetherBioinformatik Uni Leipzigtba
15BrunoSchmidtMPI MIS Leipzigtba
16JannesSpangenbergFSU JenaMagnipore: Differential single nucleotide changes of ONT signals
17KevinLamkiewiczFSU Jena
18StephanBernhartBioinformatik Uni Leipzig
19MaximilianFeussnerBioinformatik Uni Leipzigtba
20SteveHoffmannFLI Jena
21TychoKirchnerFLI JenaBashing irreproducibility with shournal
22ArneSahmFLI JenaDeciphering the molecular causes of exceptional aging phenomens in the animal kingdom by applying multi-omics
23ElinaWiechensFLI JenaPromoters revisited
24RobertSchwarzFLI JenaLocus-specific expression analysis of Transposable Elements
25MartinFischerFLI JenaGenome regulation by tumor suppressors and oncoproteins
26KatjanaSchwabFLI Jena
27KonstantinRiegeFLI JenaBashbone: NGS Bash library
28EllaCassidyBioinformatik Uni Leipzig
29SvenFindeißBioinformatik Uni Leipzig
30CarmenBruckmannBioinformatik Uni LeipzigAutomated gating of flow cytometry data
31AxelMosigRuhr University BochumTheory is Dead! Long Live Theory!
34Ben LuisHackRuhr University BochumA quartet-based approach to infer phylogenetically informative characters from phenotypic data
35WilfriedImrichUni LeobenApproximate Graph Products
36LenaGladbachBioinformatik Uni Leipzigtba
37Hua-TingYaoTBI Wientba
39ThomasGatterBioinformatik Uni LeipzigTba
40AnnachiaraKorchmarosBioinformatik Uni LeipzigQuasi Best Match Graphs
41SarahBerkemerCNRS/Ecole Polytechnique
42MarcosLaffitteBioinformatik Uni Leipzigtba
43VivianBrandenburgRuhr University BochumA quartet-based approach to infer phylogenetically informative characters from genomic data
44YuliiaVarenykTBI WienThe effect of modified nucleotides on secondary structure prediction in tRNA
45ThomasSpicherTBI WienComputatonal estmation of energy parameters
46JosefLeydoldWU Wien
47NinoBašićUniversity of PrimorskaNut graphs are not edge transitive
48GaborBaloghBioinformatik Uni Leipzigtba
49IvoHofackerTBI Wien
50Mehmet AzizYirikSDU OdenseCORENET: Complex chemical reaction networks for breakthrough scalable reservoir computing
51Casper AsbjørnEriksenSDU OdenseTBA
52GabrielLencioni LovateFSU JenaDifferential analysis of RNA cross-linked HTS reads with RNAswarm
53JanGorodkinRTH Copenhagen
54Carsten R.SeemannMPI MIS LeipzigNesting of Polygons
55TomažPisanskiUniversity of PrimorskaOn vertex-transitive nut graphs that are not circulant graphs
56AdrianGeisslerRTH CopenhagenScreen for conserved RNA structures in cyanobacteria
57AkbarDavoodiSDU Odensetba
58DanielMerkleSDU OdenseTACsy : Training Alliance for Comput­ational Systems Chemistry
59FranziskaReinhardtBioinformatik Uni LeipzigEvolution of Neuropeptide Y/RFamide-like receptors in Nematodes
60MariaWaldlTBI Wiensomething on rna-rna interaction dynamics
61ElisaIsraelBioinformatik Uni Leipzigtba
63SandhyaThekkumpadan PuthiyaveeduStockholm Universityk-Median Graphs
64ShahramSaghaeiFSU JenaVirJenDB: the virus genome database based at FSU Jena
65YingSunRTH CopenhagenPrediction of base editing outcomes by deep learning
66CristianVelandiaTBI Wientba