Herbstseminar timeline: 17. | 16. | 15. | 14. | 13.

16. Herbstseminar der Bioinformatik

Oct 01, 2018 - Oct 06, 2018

Panorama Rosenberg

Welcome to the Herbstseminar website!

Please register for the conference via the small interface below.

Deadline for Registration is Sep 10, 2018.


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 01, 2018 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 01, 2018 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 slides can be found here.

Nanopore Workshop

This year's workshop will focus on Nanopore direct RNA sequencing.
We'll start on Monday with a live in-field sequencing demonstration of a "mystery sample", during which participants get some hands-on experience using the MinION sequencer.
Tuesday will provide the theoretical background on the previous day's experiment and introduce the Nanopore toolchain -- including preprocessing, mapping and assembly -- and focusing on typical strengths and weaknesses of the technology.
On Thursday we'll explore the data generated on day 1 using the skills obtained on day 2. Great fun is to be expected.

Traveling (map)

Panorama Rudolfstein


Registration will be open soon!

Registered participants

#Last nameFirst nameAffiliationTalk titleTalk timePayment status
1RetzlaffNancyUni Leipzig BioinformatikPhylogenetics beyond Biology15
2GärtnerFabianUni Leipzig BioinformatikSuperbubbles25
3StadlerPeterUni Leipzig BioinformatikNo talk-
4MockFlorianFSU Jenavirus host prediction through machine learning15
5HölzerMartinFSU JenaNo talk-
6FallmannJoergUni Leipzig BioinformatikNo talk-
7LeydoldJosefWU WienBlack box optimal important sampling?25
8LeydoldSandraCompanionNo talk-
9LeydoldSimonCompanionNo talk-
10LeydoldChristophCompanionNo talk-
11GeissManuelaUni Leipzig Bioinformatiksomething about graph-based orthology inference methods15
12EggenhoferFlorianALU FreiburgMe and uORFs15
13HammerStefanUni Leipzig BioinformatikNo talk-
14DesiroDanielFSU JenaInfluenza A Virus vRNP Networks15
15BernhartStephanUni Leipzig BioinformatikNo talk-
16EntzianGregorUni Wien TBIEfficient Sampling of the RNA Secondary Structure Space15
17LamkiewiczKevinFSU JenaFinding long-range RNA-RNA-Interaction with third generation sequencing techniques15
18KehrStephanieUni Leipzig BioinformatikNo talk-
19CollatzMaximilianFSU JenaEpitope prediction by protein structure analysis15
20ProhaskaSonjaUni Leipzig BioinformatikRunning Histone Code on a Chromatin Computer45
21WolfingerMichaelUni Wien TBINo talk-
22MeyerDariaFSU JenaSearching for EVEs - a Quest in Paradise5
23WiesekeNicolasUni Leipzig BioinformatikBeyond Fitch Orthology. Novel Relations for Homology Based Phylogeny Reconstruction25
24HellmuthMarcUni GreifswaldReconciling Event-Labeled Gene Trees with MUL-trees and Species Networks25
25BerkemerSarahUni Leipzig BioinformatikWho the COG is LUCA?15
26ReinhardtFranziskaUni Leipzig Bioinformatik Establishment of a method for the efficient determination of alternative poly-a sites and identification of Alzheimer's disease specific RNA isoforms5
27OchsenreiterRomanUni Wien TBINo talk-
28SeemannCarsten R. MPI for Mathematics in the Sciences, LeipzigGeneralized Fitch Relations25
29CorreaFelipeUFZTerrestrial "Microbial Big Data": what is out there?15
30Leonor Fernandes SaraivaJoao PedroUFZNo talk-
31ToscanRodolfoUFZHow does sample evenness influence recovery of metagenome assembled genomes from complex microbial communities?15
32RochaUlissesUFZUntangling microbial interactions from microbial Big Data25
33Gonzalez LaffitteMarcosNational Autonomous University of MexicoCommunity Detection in Biological Neural Networks15
34SteuckJensUni Leipzig BioinformatikNo talk-
35LataretuMarieFSU Jenato be announced5
36KrautwurstSebastianFSU JenaMultiplexed direct RNA nanopore sequencing with adapter barcoding15
37MadzgallaSaraFSU JenaNo talk-
38BeckmannIreneUni Wien TBIPrediction of RNA-RNA interaction in 3D with focus on kissing hairpins5
39Hoener zu SiederdissenChristianUni Leipzig BioinformatikNo talk-
40DrozdovaPolinaUni Leipzig BioinformatikAssembling large transcriptomes of Baikal endemic amphipods with limited computing power5
41Velandia HuertoCristian ArleyUni Leipzig BioinformatikAccessing to the miRNA complement in tunicate genomes, an in silico approach15
42HavgaardJakob HullRTH CopenhagenNo talk-
43BrandenburgVivianRuhr-Uni Bochumin vitro and in vivo RNA structurome of Y.pseudotuberculosis5
44Rodriguez FernandezAngel EduardoUni Leipzig BioinformatikAnalysis of some Fitness Landscapes 15
45EckertIrisUni Leipzig Bioinformatik
46BarfLisa-MarieFSU JenaWhole-genome comparison to elucidate bacterial host specificity and phylogeny5
47NunnAdamUni Leipzig Bioinformatikdeveloping a pipeline for bis-seq data from non-model plant species15
48ZhangPanpanThe French Research Institute for Development (IRD)From leaves to results: Arabidopsis and rice genomes composed of de novo use Nanopore MINION15
49WillSebastianUni Wien TBINo talk-
50WaldlMariaUni Wien TBI RNA-RNA Interaction Kinetics for Refining RNA Targeting Screens15
51KuehnlFelixUni Leipzig BioinformatikIn silico design of neomycine riboswitches 15
52YazbeckAliUni Leipzig BioinformatikThings about miRNA data and a pipeline25
53KirchnerFalcoUni Leipzig BioinformatikPartially Local Multi-Way Alignments15
54ScholzTomHochschule AnhaltNo talk-
55BonieckiMichalIIMCB (Warsaw/Poland)SimRNP: a new method for fully flexible modeling of protein-RNA complexes and for simulations of RNA-protein binding25
56HofackerIvoUni Wien TBINo talk-
57de CarvallhoAndreUniversity of Sao PauloAutoML in bioinformatics15