Font size: Increase font size Decrease font size Switch style sheet from default to highcontrast and back


Sunday, 10 Feb 2019 - Sunday, 17 Feb 2019


"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



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 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


Further Information

Find detailed information here.

Registered Participants

Name (headcount: 74) Email Affiliation
RonnyLorenzronny (at) Wien
PeterStadlerstudla (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
RolfBackofenrbnet (at) informatik.uni-freiburg.deUni Freiburg
VladimirReinharzvreinharz (at) Center for Soft and Living Matter
CesimErtencesimerten (at) gmail.comAntalya Bilim University
IvoHofackerivo (at) Wien
MichaelWolfingerMichael.wolfinger (at) Wien
JoergFallmannfall (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
Carsten R.Seemanncarsten (at) bioinf.uni-leipzig.deMPI MIS Leipzig
CarmenBruckmanncarmen (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
SebastianWillwill (at) Wien
Adrian SvenGeissleradrian (at) rth.dkRTH Copenhagen
JanGorodkingorodkin (at) rth.dkRTH Copenhagen
EnriqueGonzalez Tortueroenriquegleztortuero (at) gmail.comRTH Copenhagen
PabloCataldopablocataldo93 (at) gmail.comUni Marburg
PaulKlemmklemmp (at) staff.uni-marburg.deUni Marburg
Jakob HullHavgaardhull (at) rth.dkRTH Copenhagen
giuliacorsigiulia (at) rth.dkRTH Copenhagen
JeremiasScheberaschebera (at) informatik.uni-leipzig.deBSV Universität Leipzig
Jakob LykkeAndersenjlandersen (at) imada.sdu.dkSDU Odense
ZashaWeinbergzasha.weinberg (at) gmail.comBioinformatik Uni Leipzig
Nadezhda TDonchevadoncheva (at) rth.dkRTH Copenhagen
Emil HoutvedAndersenemila14 (at) student.sdu.dkSDU Odense
ChristophFlammxtof (at) Wien
MiladMiladimiladim (at) cs.uni-freiburg.deUni Freiburg
TobiasMadsentobma14 (at) student.sdu.dkSDU Odense
IrisEckertiris (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
FranziskaReinhardtfranziska (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
PolinaDrozdovapolina (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
EmanuelBarthemanuel.barth (at) uni-jena.deFSU Jena
FlorianEggenhoferegg (at) informatik.uni-freiburg.deUni Freiburg
AlexandrePaschoalpaschoal (at)
SebastianKrautwurstsebastian.krautwurst (at) uni-jena.deFSU Jena
MaximilianCollatzmaximilian.collatz (at) uni-jena.deFSU Jena
FlorianHeylheylf (at) informatik.uni-freiburg.deUni Freiburg
ThomasHansenDryvnt (at) gmail.comSDU Odense
TharcisioAmorimamorim (at)
MartinHölzermartin.hoelzer (at) uni-jena.deFSU Jena
StephanieKehrsteffi (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
MarioMörlmoerl (at) uni-leipzig.deUni Leipzig Biochemie
FerhatAlkanf.alkan (at) nki.nlNetherlands Cancer Institute
LukasBartoneklukas.bartonek (at) Wien
ManuelaGeißmanuela (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
StefanHammerstefan.hammer (at) uni-leipzig.deIZBI/LIFE Leipzig
RomanOchsenreiterromanoch (at) Wien
GregorEntzianentzian (at) Wien
SarahBerkemerbsarah (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig (at) gmail.comUni Freiburg
AlexanderMitrofanovalexander.v.mitrofanov (at) gmail.comUni Freiburg
RickGelhausengelhausr (at) informatik.uni-freiburg.deUni Freiburg
YannPontyyann.ponty (at) lix.polytechnique.frCNRS/Ecole Polytechnique
AngelRodriguez Fernandezaerfangel (at) gmail.comBioinformatik Uni Leipzig
AndreFujitaandrefujita (at) usp.brUniversity of São Paulo
Cristian ArleyVelandia Huertocristian (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
DragoBokaldrago.bokal (at) um.siUM Maribor
StephanBernhartberni (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
MariaWaldlmaria (at) Wien
KevinLamkiewiczkevin.lamkiewicz (at) uni-jena.deFSU Jena
Teresa Müllermuellert (at) informatik.uni-freiburg.deUni Freiburg
MarieLataretumarie.lataretu (at) uni-jena.deFSU Jena
FelixKuehnlfelix (at) bioinf.uni-leipzig.deTBI Wien
Irene K.Beckmannirene (at) Wien
Natasha AndressaNogueira Jorgenitandressa (at) gmail.comBioinformatik Uni Leipzig
Lisa-MarieBarflisa-marie.barf (at) uni-jena.deFSU Jena
DanielDesiròdaniel.desiro (at) uni-jena.deFSU Jena
DouglasDominguesdouglas.domingues (at) unesp.brSão Paulo State University and UTFPR
AnneWenzelanne.wenzel (at) bric.ku.dkBRIC, UCPH
ChristianHöner zu Siederdissenchoener (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
JosefLeydoldjosef.leydold (at) Wien
JohnAndersjohnanders (at) posteo.deBioinformatik Uni Leipzig
NikolaiNøjgaardnnoej10 (at) gmail.comSDU Odense
SvenFindeisssven (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
MariamFarmanfarman (at) Wien
BernhardThielbernhardthiel (at) hotmail.comTBI Wien