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Sunday, 14 Feb 2016 - Sunday, 21 Feb 2016


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

Registration Fee

270,- € (double room) / 370,- € (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 14 Feb 20166pmVilla Plemlj
RNA Structure 15 Feb 20174pmHotel Astoria
Session Chair: Stephan Bernhart
Slides Speaker Talk Title
Stefan HammerFlexible and universal multiple target sequence design
Roman OchsenreiterReliable Prediction of Viral RNA Structures
Dominik SteiningerRNA-RNA long range interactions in human introns
Markus FrickeRNA structure analysis and conserved long-range RNA-RNA interaction prediction of full viral RNA genomes
Anne WenzelRIsearch2, a method for large-scale RNA-RNA interaction prediction using suffix arrays
Cheminformatics 16 Feb 20178:30pmHotel Astoria
Session Chair: Christoph Flamm
Slides Speaker Talk Title
Jakob Lykke AndersenThermodynamic Feasibility of Pathways
Nikolai NøjgaardA Generic Group Contribution Method
Daniel MerkleAn Introduction to Counting
RNA Folding Kinetics 16 Feb 20174pmHotel Astoria
Session Chair: Ronny Lorenz
Slides Speaker Talk Title
Gregor EntzianApproximate RNA kinetics
Mario KoestlKinwalker parameter space analysis
Maria WaldlCompiling Data Sets from RNA Kinetic Simulations
Felix KuehnlThe Folding Kinetics of Riboswitches
Daniel OserKinfold 2.0 - Efficient Computation of RNA Folding Kinetics
Graph Theory 16 Feb 20178pmHotel Astoria
Session Chair: Nicolas Wiesecke
Slides Speaker Talk Title
Marc HellmuthTree-Representations of Binary Relations
Wilfried ImrichProducts of edge-transitive graphs
Transcriptomics 16 Feb 20179pmHotel Astoria
Slides Speaker Talk Title
Emanuel Barthnot known yet
Martin HölzerEvolutionary analyses of positively selected sites in the interferon-induced innate immunity factor Mx1 of bats
Fabrizio CostaAnalytical Systems for Life Sciences at the time of Big Data
Bioinformatics afternoon in Ljubljana 17 Feb 20173pm
Slides Speaker Talk Title
Michael Wolfinger + Andrea TanzerRewriting the history of Zika sfRNA evolution
Ronny LorenzConstraints in RNA Secondary structure prediction
Bernhard ThielIntegrating Cryo-EM with Coarse Grained RNA 3D Structure Prediction in ERNWIN
RNA secondary structure prediction 18 Feb 20174pmHotel Astoria
Session Chair: Sebastian Will
Slides Speaker Talk Title
Jérôme WaldispühlExploring RNA mutation landscapes
Teresa MüllerImproving the local alignment of LocARNA through automated parameter optimization
Alexander JungeRNAscClust - clustering RNAs using structure conservation and graph-based motifs
Mariam AlshaikhA graph kernel approach to the identification and characterisation of structured non-coding RNAs using multiple sequence alignment information
Bernhard ThielA genome wide RNAz screen for structured RNA elements in mouse
Peter KerpedjievJust what the doctors ordered: online cotranscriptional folding using Dr. Transformer and Dr. Forna
Daniel GerighausenRNApuzzler II
Genomics 18 Feb 20178pmHotel Astoria
Session Chair: Andrea Tanzer
Slides Speaker Talk Title
Fabian ExternbrinkGolden Genome
Helene KretzmerDNA Methylation in Splicing Regulation
Rohit KoloraHybrid assembly of non-model lizards
Philipp PetersAssembly of heterozygous Fodder beet
ncRNAs expression 19 Feb 20174pmHotel Astoria
Slides Speaker Talk Title
Alexandre PaschoalExploring the knowledge of the Non-coding RNA Databases
Ferhat AlkanIntegrated miRNA and mRNA Expression Profiling for Ulcerative Colitis
Clemens Thölken6S RNA: interaction & differential expression analysis
Gero DooseDifferential Alternative Splicing - an in silico detection approach
Anne HoffmannOrthologs, turn-over, and remolding of tRNAs in primates
Proteins 19 Feb 20178pmHotel Astoria
Session Chair: Ivo Grosse
Slides Speaker Talk Title
Mark DoerrHow machines learn protein engineering
Markus LechnerAssessing the functional significance of sequence change using molecular dynamics
Transcriptomics 20 Feb 20174pmHotel Astoria
Session Chair: Irma Lozada Chavez
Slides Speaker Talk Title
Ivo GrosseEmbryonic and post-embryonic hourglass patterns of plant development
Oana PalascaIntegration of tissue expression datasets in mammalian model organisms
Rebecca KirschTowards a Comprehensive Annotation of Structured RNAs in Drosophila
Xiaoyong PanInferring disease-associated lncRNAs using expression data and disease-associated protein coding genes
Grammars and Linguistics 20 Feb 20176pmHotel Astoria
Session Chair: Christian Hoener zu Siederdissen
Slides Speaker Talk Title
Sarah BerkemerThe Christmas Tree Dilemma
Trudie StraussStatistical Classification of Languages
Nancy RetzlaffStudying Paralogs in Linguistics


Further Information

Find detailed information here.

Registered Participants

Name (headcount: 81) Email Affiliation
AndreaTanzerat (at) Wien
PeterStadlerstudla (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
GeroDoosegero (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
NancyRetzlaffnancy (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
AlexandrePaschoalpaschoal (at)
DanielGerighausendaniel (at) bioinf.uni-leipzig.deBSV Uni Leipzig
SebastianWillwill (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
ChristianAnthonanthon (at) rth.dkRTH Copenhagen
AlexanderJungeajunge (at) rth.dkRTH Copenhagen
MichaelWolfingermichael.wolfinger (at) Wien
ChristophFlammxtof (at) Wien
AnneHoffmannanneh (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
UffeThorsenuthorsen (at) imada.sdu.dkSDU Odense
JanGorodkingorodkin (at) rth.dkRTH Copenhagen
StefanSeemannseemann (at) rth.dkRTH Copenhagen
RebeccaKirschrebecca (at) rth.dkRTH Copenhagen
Jakob LykkeAndersenjlandersen (at) imada.sdu.dkELSI Tokyo / SDU Odense
StefanHammers.hammer (at) Wien
MariaWaldlmaria (at) Wien
DominikOttodominik.otto (at) izi.fraunhofer.deFraunhofer IZI
SarahBerkemerbsarah (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
IvoHofackerivo (at) Wien
MarioKoestlmario (at) Wien
afafSaaidiafaf.saaidi (at) polytechnique.eduAMIB, Inria France
HeleneKretzmerhelene (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
StephanBernhartberni (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
RituparnoSenrituparno (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
WilfriedImrichimrich (at) Leoben
FelixKuehnlfelix (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
FabianExternbrinkfabianexe (at) gmail.comBioinformatik Uni Leipzig
XiaoyongPanpanxy (at) rth.dkRTH Copenhagen
TrudieStraussstrauss.trudie (at) gmail.comBioinformatik Uni Leipzig
HermanStraussstrauss.trudie (at) gmail.comBioinformatik Uni Leipzig
Jakob HullHavgaardhull (at) rth.dkRTH Copenhagen
DanielMerkledaniel (at) imada.sdu.dkSDU Odense
MarkusFrickemarkus.fricke2 (at) uni-jena.deFSU Jena
MartinHölzermartin.hoelzer (at) uni-jena.deFSU Jena
KonstantinRiegekonstantin.riege (at) uni-jena.deFSU Jena
BirgitTschiatschekbirgit.tschiatschek (at) Wien
JérômeWaldispühljeromew (at) cs.mcgill.caMcGill University
LydiaMüllerlydia (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
AgneseBaldisserribaldisser (at) math.unifi.itDepartment of Mathematics and Computer Science, University of Florence, Italy
OanaPalascaoana.palasca (at) gmail.comRTH Copenhagen
MarcHellmuthmhellmuth (at) mailbox.orgUniversity Greifswald
RojinKianianrojin (at) imada.sdu.dkBioinformatik Uni Leipzig
AnneWenzelwenzel (at) rth.dkRTH Copenhagen
FranziskaHufskyfranziska.hufsky (at) uni-jena.deFSU Jena
Flavia Cristinade Paula Freitasflaviacpfreitas (at) gmail.comRTH Copenhagen
MarcusLechnerlechner (at) staff.uni-marburg.deUni Marburg
ClemensThölkenclemens.thoelken (at) pharmazie.uni-marburg.deUni Marburg
DominikSteiningermili (at) Wien
JoergFallmannfall (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
RomanOchsenreiterromanoch (at) Wien
JensSteucksteuck (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
ChristianHoener zu Siederdissenchoener (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
FabrizioCostacosta (at) informatik.uni-freiburg.deUni Freiburg
MiladMiladimiladim (at) informatik.uni-freiburg.deUni Freiburg
TeresaMuellermuellert (at) informatik.uni-freiburg.deUni Freiburg
MarkDoerrmark.doerr (at) uni-greifswald.deInst. f. Biochemistry, Uni Greifswald
TorstenHouwaarthouwaart (at) informatik.uni-freiburg.deUni Freiburg
DanielOserdaniel.oser (at) gmx.atTBI Wien
JosefLeydoldjosef.leydold (at) Wien
NicolasWiesekewieseke (at) informatik.uni-leipzig.dePaCoSy Leipzig
BertramVogelbertram.vogel (at) uni-jena.deFSU Jena
MariamAlshaikhalshaikm (at) informatik.uni-freiburg.deUni Freiburg
AliAltinascoordinator (at) rth.dkRTH Copenhagen
RonnyLorenzronny (at) Wien
GregorEntzianentzian (at) Wien
FerhatAlkanferro (at) rth.dkRTH Copenhagen
PeterKerpedjievpkerp (at) Wien
EmanuelBarthemanuel.barth (at) uni-jena.deFSU Jena
SvenFindeisssven (at) Wien
AileenKlopschsven (at) Wien
IvoGrossegrosse (at) informatik.uni-halle.deMLU Halle
RolfBackofenbackofen (at) informatik.uni-freiburg.deUni Freiburg
IrmaLozada Chavezilozada (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
RohitKolorarohit (at) bioinf.uni-leipzig.deBioinformatik Uni Leipzig
NikolaiNørgaardnnoej10 (at) student.sdu.dkSDU Odense
BernhardThielthiel (at) Wien
PhilippPetersphilipp.peters (at) of Natural Resources and Life Sciences (BOKU), Vienna
ManjushaChintalapatim_chintalapati (at) eva.mpg.deUniversity of Leipzig