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Herbstseminar der Bioinformatik

Design by Bruno Schmidt

Herbstseminar timeline: 19. | 18. | 17. | 16. | 15. | 14. | 13.

Panorama Rosenberg

Once again this year, the Herbstseminar Meeting will take place and we look forward to seeing as many faces as possible. Registration will be open from 01.08.2023 until 01.09.2023 and as usual, you can expect a week full of exciting talks.
In addition, there will be a workshop again this year on the topic: Data Science and Visualization libraries in Python.
But social bonding should not come too short, so we also have a few old and new offers for the free time.

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, Leipzig University.

In case of questions, feel free to contact us via email: herbstseminar@bioinf.uni-leipzig.de


There are two options for accommodation: On the one hand, there is the low-cost Hotel Jef where the seminar will take place. There are 2-4 person rooms, which means you will have to share a room with others. However, you can indicate in the registration form with whom you would like to share a room and we will do our best to make everyone happy. Another advantage is that there is also a breakfast buffet. Additional information about the hotel can be found here.

Phone: +420 412 381 429
email: doubice@hotel-jef.cz

Hotel Jef

The other option is the more extensive Chalupy, which is especially for professors. The furnishings here are more modern and the hotel is divided into family apartments for 4 people. The bedrooms are each equipped for two people. The Chalupy is also 3 Minutes walk from the Hotel Jef.


You are getting detailed information about the conference on Oct 02, 2023 at the registration desk.

Important to know

By Czech law, we are required to check your valid passport/ID upon arrival.
A driver's license is not sufficient. Please make sure to have your documents at hand upon check-in.
Additionally, by German law, you need to carry your valid passport/ID with you while entering / leaving Germany.

Further Information

Registration & Fee
135 EuroRegular fee for all participants
215 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 until the end of the registration deadline (per e-mail). Otherwise you have to pay the full fee.

Important! Please note that we cannot easily refund fees already paid.

The registration / check-in will be in the dining room of Hotel Jef on Oct 02, 2023 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.

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 & HDMI 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.


Speaker:Nono Saha Cyrille Merleau (ScaDS)
Title: Introduction to Pandas and other tools for Data Analysis in Python.

This workshop introduces the structure of Python programs in general, concepts such as object-oriented programming in Python, and give an example of Data Analysis software using such concepts, focussing on the Pandas Python library. A few techniques for preprocessing data in Python using pandas, e.g., checking for missing data, handling categorical data, visualisation etc. will be introduced as example applications. We will also address Pandas' limitations and introduce tools like Apache arrows, that offer a more in-depth functions for advanced uses.

Travelling & Arrival
Panorama Rudolfstein

Registration will be open soon!

Registered participants
#Last nameFirst nameAffiliationTalk titleTalk timePayment status
1BeierNoraUni Leipzig BioinformatikRCLASS and how a database stands in your way to actually use their data (Graph reconstruction story)15
2WaldlMariaUni Wien TBI
3StadlerPeter FUni Leipzig BioinformatikAbove, Below, or Equal? Identifying Horizontal Gene Transfer with Graph Theory45
4StadlerBaerbelCompanionNo talk-
5WeinbauerKlausUni Leipzig BioinformatikNo talk-
6SalomonMaximilianUni Leipzig BioinformatikPredicting intermediate GPCR conformations5
7KohlhausVictoriaCompanionNo talk-
8ValdiviaDulce I.Uni Leipzig BioinformatikLost in tRNAslation: causes and consequences of tRNA abundance variation5
9GärtnerChristianeUni Leipzig BioinformatikSex-specific gene expression in Burkitt lymphoma15
10HavgaardJakob HullRTH CopenhagenNo talk-
11LaffitteMarcosUni Leipzig BioinformatikProgressive Graph Alignment15
12AnthonChristianRTH CopenhagenFair reporting of Deep Learning results in CRISPR15
13CassidyEllaUni Leipzig BioinformatikIntegrative analysis of Human Papillomavirus (HPV) detection, integration sites and transcriptome profiling using RNA-Seq.15
14KlapprothChristopherUni Leipzig BioinformatikA computational search for Telomere Template RNAs (TRs) in Nematodes15
15SchmidtBruno JohannMPI for Mathematics in the Sciences, LeipzigWeighted Fitch Graph Optimization15
16DomschkeNicoUni Leipzig BioinformatikMachine learning in chemistry and graph bipartitioning of molecules15
17GärtnerFabianCompanionNo talk-
18GärtnerJanoschCompanionNo talk-
19GärtnerMathildaCompanionNo talk-
20ReinhardtFranziskaUni Leipzig BioinformatikAnalysis of allosteric networks of receptor states15
21Castro GuzmanGrover EnriqueUniversity of Sao PauloSpectral density for graphs with short cycles15
22IhaBrunoUniversity of Sao PauloDealing with uncertainties in bacterial metabolic simulations15
23OnnAmosUni Leipzig BioinformatikSingle Cell Lineage Reconstruction using Short Tandem Repeats15
24BaloghGaborUni Leipzig BioinformatikAutomated analysis of epigenetic and transcriptomic biomarkers from public data to assist individualised treatment success predictions for patients with SCCs15
25OzerovaJulieUni Leipzig BioinformatikWeird mt-tRNAs and where to find them15
26SlepchenkovAleksandrCompanionNo talk-
27Nono Saha Cyrille MerleauMPI for Mathematics in the Sciences, LeipzigNo talk-
28VassenaNicolaUni Leipzig BioinformatikInstability is the new autocatalysis15
29VassenaAglaiaUni Leipzig BioinformatikNo talk-
30EriksenCasper AsbjørnSDUStructRecon: Reconciling Inconsistent Molecular Structures from Biochemical Databases15
31VladimirovaDariaFree University BerlinNo talk-
32AdrianGeisslerRTH CopenhagenComputational screen for conserved RNA structure motifs in cyanobacteria15
33ShengZiyiRTH CopenhagenIncorporating scaffold structure information for gRNA efficiency prediction by deep learning15
34SunYingRTH CopenhagenEnhanced CRISPR base editing design from data generation and deep learning15
35GaoWenhaoRTH CopenhagenA benchmark of CRISPRoff2 for assessing CRISPR off-target with mismatches and indels15
36GorodkinJanRTH CopenhagenNo talk-
37VoraDhvaniRTH CopenhagenA binding energy model for CRISPR/Cas12a off-target analysis15
38LorenzRonnyUni Wien TBINo talk-
39von LöhneysenSarahUni Leipzig BioinformatikPhylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction15
40BoleMartinUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigLoss of knowledge and what does metadata have to do with it15
41BankeSisselSDUDetecting Hypercycles15
42BernhartStephanUni Leipzig BioinformatikNo talk-
43GolnikRichardUni Leipzig BioinformatikModelling isotope labeling in atom transition networks5
44HuDieUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigViral and prokaryotic genomes recovered from metagenomes as bioindicators of children with atopic eczema15
45WangGennuoUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigInfluence of Bromoxynil on virus-prokaryote host interactions in grassland soil: insights from a genome-centric analysis of metagenomes in a microcosm succession study15
46LiuZuopengUFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig
47MrsolMancaUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigNo talk-
48HanXueerRTH CopenhagenThe structural impact of SNPs on the secondary RNA structure of long non-coding RNAs15
49OniFaithUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigGenome-centric analysis of an aromatics-degrading sulfate-reducing microbial community15
50KorchmarosAnnachiaraUni Leipzig BioinformatikOrthology pipeline: project and realization15
51KamathSanchitaUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigExploring the functional annotation of MAGs from terrestrial environment based on their Orthogroups.15
52MuhammadKabiru NataUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigExploration of prokaryote carbon fixation in the marine environment15
53GrissaDhouhaRTH CopenhagenProbe design for pathogen detection by strand displacement15
54DavoodiAkbarSDUNo talk-
55SeemannCarsten R.Uni Leipzig BioinformatikSomething about graphs ;)15
56VarenykYuliiaUni Wien TBIModified nucleotides in tRNA structure15
57Sami IoannaUni Leipzig BioinformatikNo talk-
58ScholzGuillaumeUni Leipzig BioinformatikConsensus Segmentation: Part 2.15
59YaoHua-TingUni Wien TBINo talk-
60SpicherThomasUni Wien TBIFree energy calculation for modified nucleotides by molecular dynamics simulations15
61HofackerIvoUni Wien TBINo talk-
62UhlirManuelUni Wien TBIPredicting mass spectra using theoretically derived graph transformation rules5
63Nunes da RochaUlissesUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigDoctoral double degrees between Germany and the Global South15
64Madruga de BritoMarianaUFZ - Helmholtz-Zentrum für Umweltforschung, LeipzigNo talk-
65RingbauerHaraldMax Planck Institute for Evolutionary Anthropology LeipzigLong shared haplotypes in ancient DNA - Inferring relatives and demography25