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
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.
- Please note that there are no shopping facilities in Doubice directly, but A meal is available for favourable prices at nearby restaurants.
- Also there is 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.
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.
- The surrounding area is beautiful and invites for hiking, so do not forget proper shoes. We will also organize a hiking tour on one day with our own internal 'Wanderführer' and inform you of the meeting point on your arrival.
- In addition to dinner together, we have also planned an evening of traditional PowerPoint karaoke (short explanation: you get 10 random slides and have to give a spontaneous talk on them).
- NEW: A bioinformatics Escape Room. Since the Escape Room requires a bit of planning, it would be great if you let us know when you register if you want to try it out.
- 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.
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.
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:
- Introductory talk: 5 minutes
- Regular talk: 15 minutes
- Extended talk: 25 minutes
- Late night show: 45 minutes
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.
- ARRIVING BY CAR
Use the address Doubice 107, Doubice 40758, Czech Republic for your satnav. - ARRIVING BY TRAIN
- Please take the train to Krasna Lipa
- From Krasna Lipa you can either take
- the bus
- or a taxi. We recommend to book the taxi in advance.
Please be self-organized!
Registration will be open soon!
| # | Last name | First name | Affiliation | Talk title | Talk time | Payment status |
|---|---|---|---|---|---|---|
| 1 | Beier | Nora | Uni Leipzig Bioinformatik | RCLASS and how a database stands in your way to actually use their data (Graph reconstruction story) | 15 |  |
| 2 | Waldl | Maria | Uni Wien TBI | | ||
| 3 | Stadler | Peter F | Uni Leipzig Bioinformatik | Above, Below, or Equal? Identifying Horizontal Gene Transfer with Graph Theory | 45 | |
| 4 | Stadler | Baerbel | Companion | No talk | - | |
| 5 | Weinbauer | Klaus | Uni Leipzig Bioinformatik | No talk | - | |
| 6 | Salomon | Maximilian | Uni Leipzig Bioinformatik | Predicting intermediate GPCR conformations | 5 | |
| 7 | Kohlhaus | Victoria | Companion | No talk | - | |
| 8 | Valdivia | Dulce I. | Uni Leipzig Bioinformatik | Lost in tRNAslation: causes and consequences of tRNA abundance variation | 5 |  |
| 9 | Gärtner | Christiane | Uni Leipzig Bioinformatik | Sex-specific gene expression in Burkitt lymphoma | 15 | |
| 10 | Havgaard | Jakob Hull | RTH Copenhagen | No talk | - | |
| 11 | Laffitte | Marcos | Uni Leipzig Bioinformatik | Progressive Graph Alignment | 15 | |
| 12 | Anthon | Christian | RTH Copenhagen | Fair reporting of Deep Learning results in CRISPR | 15 | |
| 13 | Cassidy | Ella | Uni Leipzig Bioinformatik | Integrative analysis of Human Papillomavirus (HPV) detection, integration sites and transcriptome profiling using RNA-Seq. | 15 | |
| 14 | Klapproth | Christopher | Uni Leipzig Bioinformatik | A computational search for Telomere Template RNAs (TRs) in Nematodes | 15 | |
| 15 | Schmidt | Bruno Johann | MPI for Mathematics in the Sciences, Leipzig | Weighted Fitch Graph Optimization | 15 | |
| 16 | Domschke | Nico | Uni Leipzig Bioinformatik | Machine learning in chemistry and graph bipartitioning of molecules | 15 | |
| 17 | Gärtner | Fabian | Companion | No talk | - | |
| 18 | Gärtner | Janosch | Companion | No talk | - | |
| 19 | Gärtner | Mathilda | Companion | No talk | - | |
| 20 | Reinhardt | Franziska | Uni Leipzig Bioinformatik | Analysis of allosteric networks of receptor states | 15 | |
| 21 | Castro Guzman | Grover Enrique | University of Sao Paulo | Spectral density for graphs with short cycles | 15 | |
| 22 | Iha | Bruno | University of Sao Paulo | Dealing with uncertainties in bacterial metabolic simulations | 15 | |
| 23 | Onn | Amos | Uni Leipzig Bioinformatik | Single Cell Lineage Reconstruction using Short Tandem Repeats | 15 | |
| 24 | Balogh | Gabor | Uni Leipzig Bioinformatik | Automated analysis of epigenetic and transcriptomic biomarkers from public data to assist individualised treatment success predictions for patients with SCCs | 15 | |
| 25 | Ozerova | Julie | Uni Leipzig Bioinformatik | Weird mt-tRNAs and where to find them | 15 | |
| 26 | Slepchenkov | Aleksandr | Companion | No talk | - | |
| 27 | Nono Saha | Cyrille Merleau | MPI for Mathematics in the Sciences, Leipzig | No talk | - | |
| 28 | Vassena | Nicola | Uni Leipzig Bioinformatik | Instability is the new autocatalysis | 15 | |
| 29 | Vassena | Aglaia | Uni Leipzig Bioinformatik | No talk | - | |
| 30 | Eriksen | Casper Asbjørn | SDU | StructRecon: Reconciling Inconsistent Molecular Structures from Biochemical Databases | 15 | |
| 31 | Vladimirova | Daria | Free University Berlin | No talk | - | |
| 32 | Adrian | Geissler | RTH Copenhagen | Computational screen for conserved RNA structure motifs in cyanobacteria | 15 | |
| 33 | Sheng | Ziyi | RTH Copenhagen | Incorporating scaffold structure information for gRNA efficiency prediction by deep learning | 15 | |
| 34 | Sun | Ying | RTH Copenhagen | Enhanced CRISPR base editing design from data generation and deep learning | 15 | |
| 35 | Gao | Wenhao | RTH Copenhagen | A benchmark of CRISPRoff2 for assessing CRISPR off-target with mismatches and indels | 15 | |
| 36 | Gorodkin | Jan | RTH Copenhagen | No talk | - | |
| 37 | Vora | Dhvani | RTH Copenhagen | A binding energy model for CRISPR/Cas12a off-target analysis | 15 | |
| 38 | Lorenz | Ronny | Uni Wien TBI | No talk | - | |
| 39 | von Löhneysen | Sarah | Uni Leipzig Bioinformatik | Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction | 15 | |
| 40 | Bole | Martin | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | Loss of knowledge and what does metadata have to do with it | 15 | |
| 41 | Banke | Sissel | SDU | Detecting Hypercycles | 15 | |
| 42 | Bernhart | Stephan | Uni Leipzig Bioinformatik | No talk | - | |
| 43 | Golnik | Richard | Uni Leipzig Bioinformatik | Modelling isotope labeling in atom transition networks | 5 | |
| 44 | Hu | Die | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | Viral and prokaryotic genomes recovered from metagenomes as bioindicators of children with atopic eczema | 15 | |
| 45 | Wang | Gennuo | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | Influence of Bromoxynil on virus-prokaryote host interactions in grassland soil: insights from a genome-centric analysis of metagenomes in a microcosm succession study | 15 | |
| 46 | Liu | Zuopeng | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | | ||
| 47 | Mrsol | Manca | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | No talk | - | |
| 48 | Han | Xueer | RTH Copenhagen | The structural impact of SNPs on the secondary RNA structure of long non-coding RNAs | 15 | |
| 49 | Oni | Faith | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | Genome-centric analysis of an aromatics-degrading sulfate-reducing microbial community | 15 | |
| 50 | Korchmaros | Annachiara | Uni Leipzig Bioinformatik | Orthology pipeline: project and realization | 15 | |
| 51 | Kamath | Sanchita | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | Exploring the functional annotation of MAGs from terrestrial environment based on their Orthogroups. | 15 | |
| 52 | Muhammad | Kabiru Nata | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | Exploration of prokaryote carbon fixation in the marine environment | 15 | |
| 53 | Grissa | Dhouha | RTH Copenhagen | Probe design for pathogen detection by strand displacement | 15 | |
| 54 | Davoodi | Akbar | SDU | No talk | - | |
| 55 | Seemann | Carsten R. | Uni Leipzig Bioinformatik | Something about graphs ;) | 15 | |
| 56 | Varenyk | Yuliia | Uni Wien TBI | Modified nucleotides in tRNA structure | 15 | |
| 57 | Sami | Ioanna | Uni Leipzig Bioinformatik | No talk | - | |
| 58 | Scholz | Guillaume | Uni Leipzig Bioinformatik | Consensus Segmentation: Part 2. | 15 | |
| 59 | Yao | Hua-Ting | Uni Wien TBI | No talk | - | |
| 60 | Spicher | Thomas | Uni Wien TBI | Free energy calculation for modified nucleotides by molecular dynamics simulations | 15 | |
| 61 | Hofacker | Ivo | Uni Wien TBI | No talk | - | |
| 62 | Uhlir | Manuel | Uni Wien TBI | Predicting mass spectra using theoretically derived graph transformation rules | 5 | |
| 63 | Nunes da Rocha | Ulisses | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | Doctoral double degrees between Germany and the Global South | 15 | |
| 64 | Madruga de Brito | Mariana | UFZ - Helmholtz-Zentrum für Umweltforschung, Leipzig | No talk | - | |
| 65 | Ringbauer | Harald | Max Planck Institute for Evolutionary Anthropology Leipzig | Long shared haplotypes in ancient DNA - Inferring relatives and demography | 25 | |