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Sunday, 12 Feb 2017 - Sunday, 19 Feb 2017


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

Registration Fee

270,- €

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 12 Feb 20176pmVilla Plemlj
RNA structures 13 Feb 20174pmHotel Astoria
Session Chair: Alexander Junge
Slides Speaker Talk Title
Ronny LorenzWelcome and opening of the TBI Winterseminar
Martin MannIntaRNA 2 - status and plans
Cedric SauleIncorporation of reactivity data in RNA secondary structure determination using Pareto optimization
Bioinformatics 13 Feb 20175pmHotel Astoria
Session Chair: Alexander Junge
Slides Speaker Talk Title
Ferhat AlkanPredicting off-targets in CRISPR technology
Nadezhda DonchevaPathway and network-based comparison of mammals
Computational Sciences 13 Feb 20178pmHotel Astoria
Session Chair: Martin Mann
Slides Speaker Talk Title
Wim HordijkAutocatalytic Sets and RNA Secondary Structure
Rojin KianianSomething on Computational Mass Spectrometry
Sarah BerkemerThe archaeal halting problem
Transcriptomics 14 Feb 20176pmHotel Astoria
Session Chair: Florian Eggenhofer
Slides Speaker Talk Title
Emanuel BarthA new statistical approach to identify differential expression in small RNA-Seq data
Anne HoffmannEvolution of Chemical Modifications
Alicja PacholewskaAnnotation of lncRNA in livestock
Lukas BartonekACROs and other RNAs interacting with RNA Pol-2
Mariam FarmanTranscriptomics of Bordetella and human phagocytes interplay
Franziska HufskyUpcoming events: a festival and a founding
RNA Structure 14 Feb 20178pmHotel Astoria
Session Chair: Sebastian Will
Slides Speaker Talk Title
Yann PontyThe BRaliBase dent-a tale of benchmark design and interpretation
Wei Wangk best suboptimal sequence structure alignment
Gregor EntzianSampling strategies to approximate RNA folding kinetics
Juraj MichalikNon-redundant sampling for RNA kinetics landscape reconstruction
Maria WaldlConservation in kinetic folding paths
Genomics 15 Feb 20178pmHotel Astoria
Session Chair: Jörg Fallmann
Slides Speaker Talk Title
Jan ZrimecStructural representation of DNA enables characterization of regulatory regions and properties involved in antimicrobial resistance transfer
Henrike IndrischekG protein evolution
Martin HölzerPoSeiDon: a web server for the detection of evolutionary recombination events and positive selection
Fabian ExternbrinkFrom Genomes to Supergenomes - How to deal with betweenness
Viruses 16 Feb 20174pmHotel Astoria
Session Chair: Markus Fricke
Slides Speaker Talk Title
Andrea TanzerStructured Regions in Flaviviridae
Michael WolfingerProbing assisted reconstruction of functional elements in Flaviviruses
Roman OchsenreiterStructuredness in viral genomes
Nelly F. Mostajo B.Ebola and ncRNAs (preliminary results)
Kevin LamkiewiczmiRNAs in RNA-Viruses
Graph Theory 16 Feb 20178pmHotel Astoria
Session Chair: Nicolas Wiesecke
Slides Speaker Talk Title
Tomaz PisanskiStable self-assembled polyhedra
Nino BasicA dynamic programming approach to generation of strong traces
Stefan MautnerGenerative adversarial training on structured domains
John AndersRepresenting horizontal gene transfer events in a tree structure
Paul KlemmGraph-based Adjustment of Orthology-Relations
Marc HellmuthFrom Gene Trees with HGT to Species Trees
Bioinformatics 17 Feb 20174pmHotel Astoria
Session Chair: Andrea Tanzer
Slides Speaker Talk Title
Veerendra GadekarPrediction and identification of functional cisNATs in plants
Dominik OttoA Factor Extraction in RNA-Seq Analysis
Anne WenzelThe RNA tools registry: A community effort to catalog RNA bioinformatics resources and their relationships
Halima SakerMultidimensional Segmentation
Carolin SchimmelpfennigDetection of Gene Fusions
Bioinformatics / RNA structure 17 Feb 20176pmHotel Astoria
Session Chair: Ronny Lorenz
Slides Speaker Talk Title
Peter KerpekievGenomic contact matrices: tiled, scaled and served for online consumption
Bernhard ThielCoarse grained RNA 3D structure prediction
Alexander JungeClustering conserved, structured RNAs
Milad MiladiA locality glitch in established RNA free-energy models
Ronny LorenzClosing remarks
Discussion Groups 18 Feb 20174pmVilla Plemlj
Discussion Groups 18 Feb 20178pmVilla Plemlj


Wim Hordijk captured a couple of very nice impressions here in Bled. You can find them at his blog. Take me there

Further Information

Find detailed information here.

Registered Participants

Name (headcount: 77) Email Affiliation
RonnyLorenzronny (at) Wien
AndreaTanzerat (at) Wien
YannPontyyann.ponty (at) lix.polytechnique.frCNRS Ecole Polytechnique
RojinKianianrojin (at) imada.sdu.dkBioinformatik Uni Leipzig
MichaelWolfingermichael.wolfinger (at) Wien
SebastianWillwill (at) Wien
DominikOttodominik.otto (at) izi.fraunhofer.deBioinformatik Uni Leipzig
FlorianEggenhoferegg (at) informatik.uni-freiburg.deUni Freiburg
JoergFallmannfall (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
WimHordijkwim (at) WorldWideWanderings.netKLI Klosterneuburg
ChristophFlammxtof (at) Wien
SarahBerkemerbsarah (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
NadezhdaDonchevadoncheva (at) rth.dkRTH Copenhagen
AlicjaPacholewskaalicja (at) rth.dkRTH Copenhagen
MariamFarmanfarman (at) Wien
MariaWaldlmaria (at) Wien
ChristinaWagnerchrisu (at) Wien
StefanMautnermautner (at) informatik.uni-freiburg.deUni Freiburg
FerhatAlkanferro (at) rth.dkRTH Copenhagen
Jakob HullHavgaardhull (at) rth.dkRTH Copenhagen
MartinMannmmann (at) informatik.uni-freiburg.deUni Freiburg
PeterStadlerstudla (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
JurajMichalikjuraj.michalik.2048 (at) gmail.comAMIB Palaiseau
Paul-RobertKästnerpaul-robert.kaestner (at) izi.fraunhofer.deFraunhofer IZI
ManuelaGeißmanuela.geiss (at) gmx.deBioinformatik Uni Leipzig
GregorEntzianentzian (at) Wien
HalimaSAKERhsaker (at) hotmail.comBioinformatik Uni Leipzig
MarkusFrickemarkus.fricke2 (at) uni-jena.deFSU Jena
MartinHölzermartin.hoelzer (at) uni-jena.deFSU Jena
MiladMiladimiladim (at) cs.uni-freiburg.deUni Freiburg
IvoHofackerivo (at) Wien
BernhardThielthiel (at) Wien
EmilyThielthiel (at) Wien
AlexanderJungeajunge (at) rth.dkRTH Copenhagen
FranziskaHufskyfranziska.hufsky (at) uni-jena.deFSU Jena
Nelly F.Mostajo B.nelly.mostajo (at) gmail.comFSU Jena
EmanuelBarthemanuel.barth (at) uni-jena.deFSU Jena
weiWANGWang.Wei (at) lri.frLaboratoire de recherche en informatique, Orsay
Jakob LykkeAndersenjlandersen (at) elsi.jpELSI Tokyo
KevinLamkiewiczkevin.lamkiewicz (at) gmail.comFSU Jena
RolfBackofenbackofen (at) informatik.uni-freiburg.deUni Freiburg
RomanOchsenreiterromanoch (at) Wien
FelixKuehnlfelix (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
SebastianKrautwurstraverjay (at) gmail.comFSU Jena
AnneWenzelwenzel (at) rth.dkRTH Copenhagen
NikolaiNøjgaardnnoej10 (at) student.sdu.dkSDU Odense
DanielMerkledaniel (at) imada.sdu.dkSDU Odense
StefanHammers.hammer (at) Wien
AnneHoffmannanneh (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
StephanBernhartberni (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
PaulKlemmpaulklemm (at) t-online.deEMAU Greifswald
CédricSaulesaule_cedric (at) yahoo.frInstitute for Integrative Biology of the Cell
CarolinSchimmelpfennigcaroschim (at) gmx.deBioinformatik Uni Leipzig
VeerendraGadekarveerendra (at) Wien
MarcHellmuthmhellmuth (at) mailbox.orgUniversity Greifswald
NicolasWiesekewieseke (at) informatik.uni-leipzig.dePaCoSy Leipzig
ZashaWeinbergzasha.weinberg (at) gmail.comBioinformatik Uni Leipzig
FabianExternbrinkfabianexe (at) gmail.comBioinformatik Uni Leipzig
RolfFagerbergrolf (at) imada.sdu.dkSDU Odense
HenrikeIndrischekhenrike (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
JohnAndersjohnanders (at) posteo.deBioinformatik Uni Leipzig
NinoBasicnino.basic (at) famnit.upr.siUniversity of Primorska, Koper
TomazPisanskiTomaz.Pisanski (at) upr.siUniversity of Primorska, Koper
MichaelUhluhlm (at) informatik.uni-freiburg.deUni Freiburg
NancyRetzlaffnancy (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
AminZarifsaffariamin (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
JosefLeydoldjosef.leydold (at) Wien
TeresaMüllermuellert (at) informatik.uni-freiburg.deUni Freiburg
MireilleRegniermireille.regnier (at) polytechnique.eduEcole polytechnique
SwetaSahayswetastar20 (at) gmail.comTBI Wien
RohitKolorarohit (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
JanGorodkingorodkin (at) rth.dkRTH Copenhagen
LukasBartoneklukas.bartonek (at) Wien
JensSteucksteuck (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
PeterKerpedjievpkerp (at) Medical
KristinReichekristin.reiche (at) izi.frauenhofer.deFraunhofer IZI
JanZrimecjanzrimec (at) gmail.comUniversity of Primorska, Koper