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Time

Sunday, 10 Feb 2019 - Sunday, 17 Feb 2019

Topics

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

Registration Fee

275,- € (double room) / 375,- € (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.

Arrival and Get Together at the Villa 10 Feb 20196pmVilla Plemlj
Opening Session 11 Feb 20184pmHotel Astoria
Session Chair: Ronny Lorenz
Slides Speaker Talk Title
Ronny LorenzWelcome and opening of the TBI Winterseminar
Joerg Fallmann + Stephan BernhartBierinformatics
Bernhard ThielPredicting a lncRNA 3D structure with the help of SAXS data
Daniel DesiroSilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs
Giulia CorsiOn-target prediction and assessment of CRISPR/Cas9 cleavage efficiency
Networks and Cheminformatics 11 Feb 20198pmHotel Astoria
Session Chair: Christoph Flamm
Slides Speaker Talk Title
Cesim ErtenEmploying PPI Networks in Cancer Gene/Module Identification
Mariam FarmannHuman & Bordetella pertussis co-expression networks
Jakob Lykke AndersenIntroduction to Graphtheory in Cheminformatics
Tobias MadsenDecomposition and Evaluation of Graph Transformation Rules
Emil Houtved AndersenReduction of Graph-Grammar Models by grouping of tautomers
Thomas HansenGraph Canonicalization and Algorithmic Engineering
Nikolai NoejgaardA Generic Group Contribution Method
RNA Design 12 Feb 20174pmHotel Astoria
Session Chair: Yann Ponty
Slides Speaker Talk Title
Mario MoerlRNaseP riboswitch design and testing
Stefan HammerDesign objective functions (neg. design) and ligand triggered RNA switch
Sven FindeisssRNA triggered translational OFF switch
Felix KuehnlNeomycin Rioboswitch design and testing
Sebastian WillInfrared and sequence sampling (positiv design)
Sarah BerkemerExploring Neutral Networks for RNA sequences
Graph Theory 12 Feb 20198pmHotel Astoria
Session Chair: Christian Hoener zu Siederdissen
Slides Speaker Talk Title
Christoph FlammBeyond Boltzmann: A brief Intro to Dissipative Systems by Example
Manuela GeissHow to find false positive orthologs?
Carmen Bruckmann(Orthology-)Relations on rooted Median Graphs
Carsten R. SeemannR-Metrices and Mixing Hybrids
Angel Rodriguez FernandezFitness Landscape of the 2-spin model
Drago BokalTechnological valley of death as an emergent evolutionary phenomenon
Discrete Biomathematics Afternoon at the Adriatic Coast 2019 13 Feb 20199:30amFAMNIT, University of Primorska, Koper, Slovenia
Group Photo 14 Feb 20193:30pmHotel Astoria (Entrance)
RNA I 14 Feb 20194pmHotel Astoria
Session Chair: Zasha Weinberg
Slides Speaker Talk Title
Yann PontyIntegrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles
Vladimir ReinharzSequence covariations between a disordered protein and a structured RNA
Maria WaldlStructural alignment of kinetic trajectories reveals conserved transient structures
Gregor EntzianApproximate RNA folding kinetics
Irene K. BeckmannTrajectories of CopA-CopT under the "CPU microscope"
Alexandre PaschoalFeature Selection of Long Non-Coding RNAs in Plants
Omics I 14 Feb 20178pmHotel Astoria
Session Chair: Stephan Bernhart
Slides Speaker Talk Title
Sebastian KrautwurstDistributed representations of protein domains and genomes and their compositionality
Douglas DominguesIntertwining of transposable elements and non coding RNAs in plant genomes
Lisa-Marie BarfWhole genome comparison among bacteria
Polina DrozdovaAccessing size and complexity of the Eulimnogammarus verrucosus genome
Marie LataretuAnnotation and differential expression analysis of non-coding RNAs in 16 freely accessible bat genomes
Maximilian CollatzPrediction of B-Cell Epitopes
Paul KlemmNeed for Speed: Proteinortho Nitro
Jeremias ScheberaSuper Genome Browser
RNA II 15 Feb 20194pmHotel Astoria
Session Chair: Vladimir Reinharz
Slides Speaker Talk Title
Milad MiladiRNA alignment and folding with Markov chains
Teresa MuellerStructure-based RNA alignment: the trouble with locality
Rick GelhausenConstraint maximal inter-molecular helix lengths within RNA-RNA interaction prediction improves sRNA target prediction
Ferhat AlkanHow to decipher the structural secrets of an RNA behind its translational efficiency?
Alexander MitrofanovIdentification of CRISPR arrays using machine learning approach
Iris EckertDiscovering Ribosomal Leaders in Bacteria and Archaea
Pablo Cataldo6S RNA in Lactic Acid Bacteria
Omics II 15 Feb 20198pmHotel Astoria
Session Chair: Florian Eggenhofer
Slides Speaker Talk Title
Florian HeylCLIP-Explorer: CLIP-Seq data analysis in Galaxy
Adrian GeisslerThe BSGatlas: A fine-grained atlas of the Bacillus subtillis genome
John AndersUsing mass spectrometry to discover new proteins
Nadezhda DonchevaModeling of human pathways in animal models: possibilities and limitations
Natasha Andressa Nogueira JorgeNon coding RNAs high throughput sequencing data to classify human blood cell types and lung tumor samples.
Cristian Arley Velandia HuertoHow to improve the detection of miRNA homologs? an outlook from tunicate genomes.
Lukas BartonekVOLPES - an interactive visualization tool for physicochemical sequence properties
Workshops 16 Feb 20192pmVilla Plemelj

Photos

Further Information

Find detailed information here.

Registered Participants

Number Name Affiliation Talk Title Payment Status
1RonnyLorenzTBI Wien
2PeterStadlerBioinformatik Uni Leipzig
3RolfBackofenUni Freiburg
4VladimirReinharzIBS Center for Soft and Living MatterSequence covariations between a disordered protein and a structured RNA
5CesimErtenAntalya Bilim UniversityEmploying PPI Networks in Cancer Gene/Module Identification
6IvoHofackerTBI Wien
7MichaelWolfingerTBI Wien
8JoergFallmannBioinformatik Uni LeipzigBierinformatics
9Carsten R.SeemannMPI MIS LeipzigR-Metrices and Mixing Hybrids
10CarmenBruckmannBioinformatik Uni LeipzigTBA (something with "Median Graphs")
11SebastianWillTBI WienInfrared and sequence sampling (positiv design)
12Adrian SvenGeisslerRTH CopenhagenThe BSGatlas: A fine-grained atlas of the Bacillus subtillis genome
13JanGorodkinRTH Copenhagen
14EnriqueGonzalez TortueroRTH Copenhagen
16PabloCataldoUni Marburg6S RNA in Lactic Acid Bacteria
17PaulKlemmUni MarburgNeed for Speed: Proteinortho Nitro
18Jakob HullHavgaardRTH Copenhagen
19giuliacorsiRTH CopenhagenOn-target prediction and assessment of CRISPR/Cas9 cleavage efficiency
20JeremiasScheberaBSV Universität LeipzigSuper Genome Browser
21Jakob LykkeAndersenSDU Odense
22ZashaWeinbergBioinformatik Uni Leipzig
23Nadezhda TDonchevaRTH CopenhagenModeling of human pathways in animal models: possibilities and limitations
24Emil HoutvedAndersenSDU OdenseReduction of Graph-Grammar Models by grouping of tautomers
25ChristophFlammTBI Wiensay "Abg lrg qrpvqrq".trans: "A..Za..z"=>"N..ZA..Mn..za..m"
26MiladMiladiUni FreiburgRNA alignment and folding with Markov chains
27TobiasMadsenSDU OdenseDecomposition and Evaluation of Graph Transformation Rules
28IrisEckertBioinformatik Uni LeipzigRibosomal Leader in Bacteria
29FranziskaReinhardtBioinformatik Uni Leipzig
30PolinaDrozdovaBioinformatik Uni LeipzigAccessing size and complexity of the Eulimnogammarus verrucosus genome
31EmanuelBarthFSU Jena
32FlorianEggenhoferUni Freiburg
33AlexandrePaschoalUTFPRFeature Selection of Long Non-Coding RNAs in Plants
34SebastianKrautwurstFSU JenaDistributed representations of protein domains and genomes and their compositionality
35MaximilianCollatzFSU JenaPrediction of B-Cell Epitopes
36FlorianHeylUni FreiburgCLIP-Explorer: CLIP-Seq data analysis in Galaxy
37ThomasHansenSDU OdenseGraph Canonicalization and Algorithmic Engineering
38TharcisioAmorimUTFPR
39MartinHölzerFSU Jena
40StephanieKehrBioinformatik Uni Leipzig
41MarioMörlUni Leipzig BiochemieRNaseP riboswitch design and testing
42FerhatAlkanNetherlands Cancer InstituteHow to decipher the structural secrets of an RNA behind its translational efficiency?
43LukasBartonekMFPL WienVOLPES - an interactive visualization tool for physicochemical sequence properties
45ManuelaGeißBioinformatik Uni LeipzigHow to find false positive orthologs?
46StefanHammerIZBI/LIFE LeipzigDesign objective functions (neg. design) and ligand triggered RNA switch
47RomanOchsenreiterTBI WienStructural UTR evolution of NKV-FVs
48GregorEntzianTBI WienApproximate RNA folding kinetics
49SarahBerkemerBioinformatik Uni LeipzigExploring Neutral Networks for RNA sequences
50VictorPadilhaUni Freiburg
51AlexanderMitrofanovUni FreiburgIdentification of CRISPR arrays using machine learning approach
52RickGelhausenUni FreiburgConstraint maximal inter-molecular helix lengths within RNA-RNA interaction prediction improves sRNA target prediction
53YannPontyCNRS/Ecole PolytechniqueIntegrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles
54AngelRodriguez FernandezBioinformatik Uni LeipzigFitness Landscape of the 2-spin model
55AndreFujitaUniversity of São PauloStatistics on biological networks
57Cristian ArleyVelandia HuertoBioinformatik Uni LeipzigHow to improve the detection of miRNA homologs? an outlook from tunicate genomes.
59DragoBokalUM MariborTechnological valley of death as an emergent evolutionary phenomenon
60StephanBernhartBioinformatik Uni Leipzig
61MariaWaldlTBI WienStructural alignment of kinetic trajectories reveals conserved transient structures
64KevinLamkiewiczFSU Jenat.b.a (viral alignments... maybe)
66Teresa MüllerUni FreiburgStructure-based RNA alignment: the trouble with locality
67MarieLataretuFSU Jenatba
68FelixKuehnlTBI WienNeomycin Rioboswitch design and testing
69Irene K.BeckmannTBI WienTrajectories of CopA-CopT under the "CPU microscope"
70Natasha AndressaNogueira JorgeBioinformatik Uni LeipzigNon coding RNAs high throughput sequencing data to classify human blood cell types and lung tumor samples
71Lisa-MarieBarfFSU JenaWhole genome comoparison among bacteria
72DanielDesiròFSU JenaSilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs
73DouglasDominguesSão Paulo State University and UTFPRintertwining of transposable elements and non coding RNAs in plant genomes
74AnneWenzelBRIC, UCPHTBD
75ChristianHöner zu SiederdissenBioinformatik Uni Leipzig
76JosefLeydoldWU Wien
77JohnAndersBioinformatik Uni LeipzigUsing mass spectrometry to discover new proteins
78NikolaiNøjgaardSDU OdenseA Generic Group Contribution Method
79SvenFindeissBioinformatik Uni LeipzigsRNA triggered translational OFF switch
80MariamFarmanTBI WienHuman & Bordetella pertussis co-expression networks
81BernhardThielTBI WienPredicting a lncRNA 3D structure with the help of SAXS data