Herbstseminar timeline: 15. | 14. | 13.

15. Herbstseminar der Bioinformatik

Oct 02, 2017 - Oct 07, 2017

Panorama Rosenberg

Welcome to the Herbstseminar website!

Please register for the conference via the small interface below.

Deadline for Registration is Sep 01, 2017.


The Herbstseminar-Meeting is organized by people from the Bioinformatics Group and from the Computational EvoDevo Group, both located at the Department of Computer Science, University of Leipzig.

In case of questions, feel free to contact us via:


The meeting takes place at Hotel Jef (Doubice 107, Doubice 40758, Czech Republic).

Hotel Jef (map)
Additional information about the hotel can be found here.
Phone: +420 412 381 429
email: doubice@hotel-jef.cz

Conference place

The hotel has 31 rooms for approximately 65 people. Each room has a bedroom and its own bathroom including a shower. If you prefer not to stay in Hotel Jef, we have the possibility to get rooms in another hotel - with student unfriendly prices - in the neighborhood. If this is the case, please make a note in the comment section.

You are getting detailed information about the conference on Oct 02, 2017 at the registration desk.

room example

Further information


Your family is welcome to join us in Doubice! Depending on the number of children and the size of the families, we will try to accommodate families separately from the party people and the lecture hall in a different accommodation. We will contact you after the registration to let you know the final prices for the kids and the details of your accommodation.

Registration and Fee

115 EuroRegular fee for all participants
175 EuroProfessor fee with option of upgraded accomodation
reducedIntended for the scientific offspring

The conference fee includes accommodation at Hotel Jef.

Please transfer the registration fee to the conference bank account in advance!
You will receive an email with all the details after successful registration, including payment information.
The conference fee can only be refunded if the registration is canceled at least eight days in advance. Otherwise you have to pay the full fee.

The registration / check-in will be in the dining room of Hotel Jef on Oct 02, 2017 from 2pm to 6pm. If you are arriving prior to registration, please do not check in with the hotel, but wait for the organizing team. We will hand you over the key and registration information. Please note that late-night registration will not be supported after 10 pm even for those running late.


No ATM available!
Payment with any cards will not be possible! You can pay in Euro, however with a "bad" rate, or in Czech korunas. Please, ensure that you have enough money for additional meals, drinks, etc.


WIFI is available in Hotel Jef, but might not cover all rooms equally.

Scientific Program

It is possible for every participant to present his/her scientific work. All diploma, master and PhD students should give a talk. This is not only a burden but also a good chance to present your scientific results to Peter, Ivo, Rolf and all the others of the Bompfünewerer consortium at the same time. We will have four kinds of talks:

A guide which talk format is the right for you can be found here.

A meaningful (preliminary) title should be given in the registration process in order to schedule talk sessions.

As usual, we provide a video projector (with VGA port) and a laser pointer for the presentations. If you cannot provide your talk as a PDF on USB stick, please bring all necessary equipment with you.

Approximate time table can be found here.

A PDF version of the time table can be found here.


The Herbstseminar will host a hands-on workshop on Galaxy this year, which will consist of two sessions. The workshop is organized by Matthias Bernt and Jörg Fallmann . For further information, please contact .

Session 1: Galaxy 101

We will show how to: Furthermore we will show you how to obtain further information.

Session 2: How to integrate tool XYZ (e.g. your tool) into galaxy

We will show you how a command line tool can be integrated into Galaxy: Please bring your own Laptop to both sessions.

Traveling (map)

Panorama Rudolfstein


Registration closed!

Registered participants

#Last nameFirst nameAffiliationTalk titleTalk timePayment status
1HammerStefanUni Leipzig BioinformatikHow an universal RNA design pipeline looks like25
2HoffmannAnneUni Leipzig BioinformatikAccurate Mapping of tRNA Reads15
3RetzlaffNancyUni Leipzig BioinformatikNo talk-
4StadlerPeter F. Uni Leipzig BioinformatikNo talk-
5StadlerBaerbelUni Leipzig BioinformatikNo talk-
6StadlerEliasUni Leipzig BioinformatikNo talk-
7FallmannJoergUni Leipzig BioinformatikNo talk-
8EggenhoferFlorianALU FreiburgNo talk-
9SAKERHalimaUni Leipzig Bioinformatikmultidimensional segmentation 15
10KehrStephanieUni Leipzig BioinformatikNo talk-
11KirchnerFalcoUni Leipzig BioinformatikPartially Local Multi-Way Alignments5
12GrosseIvoMLU Halle-WittenbergPhylogenetic footprinting with intra-motif dependencies25
13BerntMatthiasUFZ LeipzigNo talk-
14HellmuthMarcUniversity GreifswaldThe Matroid Structure of Representative Triple Sets25
15LamkiewiczKevinFSU JenaA machine-learning approach to identify viral miRNAs15
16HölzerMartinFSU JenaThe Dark Art of Next-Generation Sequencing25
17DesiròDanielFSU JenaInfluenza A Packaging15
18BarthEmanuelFSU JenaSomething about Transcriptome Data Statistics15
19De Anda ValerieEcology Institute UNAM, CSIC Zaragoza SpainMEBS: A new software platform to evaluate and classify ‘omic’ samples according to their metabolic machinery: the case of study of the biogeochemical sulfur cycle. 25
20CollatzMaximilianFSU JenaIn Silico enrichment of immunodominant proteins15
21GeissManuelaUni Leipzig BioinformatikReconstructing Gene Trees From Fitch’s Xenology Relation15
22KuehnlFelixUni Leipzig BioinformatikThe design of transcriptional neomycin riboswitches15
23BernhartStephanALU FreiburgNo talk-
24VidemPavankumarALU FreiburgAn integrated framework for annotation and visualization of chimeric reads25
25ThielBernhardUni Wien TBIHow to properly sample 3-way junctions in coarse-grained RNA 3D structure prediction15
26EmilyBernhardFamilyNo talk-
27GeisslerAdrianRTH CopenhagenBioinformatics pipeline for analyzing ncRNA in transcriptomics data15
28ThielElisabethFamilyNo talk-
29EntzianGregorUni Wien TBIHigh precision RNA folding kinetics15
30DonchevaNadezhdaRTH CopenhagenTissue-specific, orthology-based pathway comparison between human and animal models15
31BeckmannIreneUni Wien TBIPredicting Pseudoknots in RNA 3D structures5
32OchsenreiterRomanUni Wien TBIIdentifying Homolog and Analog Viral ncRNas15
33WillSebastianUni Wien TBINo talk-
34gorodkinjanRTH CopenhagenNo talk-
35KrautwurstSebastianFSU JenaPrediction of age-related non-coding RNAs in human15
36MockFlorianFSU JenaVirus host prediction machine learning5
37LataretuMarieFSU JenaSomething about fungi and mitochondria5
38GatterThomasUni Leipzig BioinformatikNew Methods for Transcript Isoform Assembly15
39WiedemannKarolinFraunhofer IZI, LeizigNo talk-
40GerighausenDanielUni Leipzig BSVRNApuzzler IV15
41BerkemerSarahUni Leipzig BioinformatikSMORE - prep roast eat15
42FeldhahnLasseMLU Halle-WittenbergA novel approach of transcriptome de novo assembly15
43ZötzscheSiegfriedUni Leipzig BioinformatikTraining and evaluation of a support vector regression model for standardized RNA folding energies25
44RadeMichaelFraunhofer IZI, LeizigLong non-coding RNAs related to MAPK-inhibitor resistance in melanoma15
45WagnerChristinaUni Wien TBIModelling Transcription Elongation15
46LeydoldJosefWU WienNo talk-
47Velandia HuertoCristian A.Uni Leipzig BioinformatikStudy of the genomic organization of ancestral domains of the immune system of basal chordates15
48FarmanMariamUni Wien TBIModulated SubPath Finder 15
49WenzelAnneRTH Copenhagen"RNA tools registry and ontologies"15
50OttoDominikFraunhofer IZI, LeizigIndependent Component Analysis as Signal Deconvolution15
51LeberechtChristophHS MittweidaSiNGA: Harnessing three-dimensional molecular structure data using graphs25
52IndrischekHenrikeUni Leipzig BioinformatikNo talk-
53HartmannTomPacosyNo talk-
54WaldlMariaUni Wien TBIsomething on RNA Interactions (seed kinetics or 3D structures)5
55Lozada-ChávezIrmaUni Leipzig BioinformatikNo talk-
56SenRituparnoUni Leipzig Bioinformatiksplice variants and classification of lncRNAs15
57LealWilmerUni Leipzig BioinformatikNo talk-
58LorenzRonnyUni Wien TBINo talk-
59RasmussenSimonRTH CopenhagenQuerying many RNA-seq data sets5
60Rodríguez F.Angel E.Uni Leipzig BioinformatikNeutrality and Ruggedness in Fitness Landscapes5
61KrautwurstSarahHS MittweidaTo be announced5
62ProhaskaSonjaUni Leipzig BioinformatikNo talk-
63EngelhardtJanUni Leipzig BioinformatikSomething about DNA methylation15
64AndersJohnUni Leipzig BioinformatikXenology relations in phyologenetic gene trees25
65BraunPatrickUni Wien TBIRandom-graph-models for chemical reaction-networks5
66HerbigNicoUni Leipzig BioinformatikFun and Trouble with Histone Modifications15
67WiesekeNicolasPacosyNo talk-
68GadekarVeerendraUni Wien TBINo talk-
69SahaySwetaUni Wien TBINo talk-
70HofackerIvoUni Wien TBINo talk-
71Corona-GomezJose AntonioCinvestavNo talk-