Office
Campus E2.1,
room 1.13
room 1.13
Mails
Johanna Schmitz
Algorithmische Bioinformatik
Zentrum für Bioinformatik, Campus E2.1
Universität des Saarlandes
66123 Saarbrücken, Germany
Algorithmische Bioinformatik
Zentrum für Bioinformatik, Campus E2.1
Universität des Saarlandes
66123 Saarbrücken, Germany
Phone
+49 (681) 302-70848
I am a bioinformatician with a strong background in computer science and a focus on statistical modeling and data analysis. I am working in the Algorithmic Bioinformatics group, led by Sven Rahmann at Saarland University. My current topics are:
- Alignment-free methods for DNA sequence analysis
- Development of an efficient and accurate chromatin segmentation method based on epigenetic marks
- Investigating the diversity or species richness of a large population
Talks
| 2026 | DivQuant: Estimation of Species Richness and Entropy from Small Samples | WABI | L’Aquila |
| 2026 | Error correction algorithms for efficient gene expression quantification in single cell transcriptomics | DSB | Venice |
| 2026 | Smaller and more flexible Cuckoo Filters | Alenex | Vancouver |
| 2025 | Better Cuckoo Filters | DSB | Pisa |
| 2024 | EpiSegMix: Discovering chromatin states using a flexible distribution hidden Markov model with duration modeling | DSB | Montpellier |
Posters
| 2025 | Fast and low-resource alignment-free methods for sequence analysis | GCB | Düsseldorf |
| 2024 | From the 1940s until today: An introduction to the unseen species problem | GCB | Bielefeld |
| 2024 | EpiSegMix: Discovering chromatin states using a flexible distribution hidden Markov model with duration modeling | ISMB | Montreal |
| 2024 | From the 1940s until today: An introduction to the unseen species problem | HIPS Symposium | Saarbrücken |
| 2024 | EpiSegMix: Discovering chromatin states using a flexible distribution hidden Markov model with duration modeling | Functional Epigenomics Conference | Saarbrücken |
| 2023 | Discovering chromatin states using a flexible distribution hidden Markov model with duration modeling | GCB | Hamburg |
Tutorials
| 2024 | Just-in-Time Compiled Python for Bioinformatics Research | GCB | Bielefeld |
| 2024 | Just-in-time compiled Python for bioinformatics research | ISMB | Montréal |
Summer Schools
| 2024 | Computational Spatial Transcriptomics and Cell-Cell Communication with application in Biology and Medicine | Lipari |
| 2023 | Computational Single-Cell Analysis with application in Biology and Medicine | Lipari |
Participations
| 2026 | Organization | GCB | Saarbrücken |
| 2025 | Blocked Bloom Filters with Choices | Symposium on Experimental Algorithms | Venice |
| 2025 | Snakemake Hackathon | Geneva |
Thesis Topics
| Feb. 2023 | Master Thesis | Multivariate Hidden Markov Models with Flexible Distributions for Chromatin–State Discovery |
| Feb. 2021 | Bachelor Thesis | Identification of Key Transcriptional Regulators Using Single Cell Data |
Teaching
Courses
| SS | 26 | Statistical data compression | Proseminar | Saarland University |
| WS | 25/26 | Bioinformatik 1 | Tutorials | Saarland University |
| SS | 25 | Reproducible methods in metagenomics | (Pro-)Seminar | Saarland University |
| SS | 25 | Algorithms for Sequence Analysis | Tutorials | Saarland University |
| WS | 24/25 | BioStatsLab | Tutorials | Saarland University |
| SS | 2024 | Programming Course: Python | Tutorials | Saarland University |
| WS | 23/24 | BioStatsLab | Tutorials | Saarland University |
| SS | 2023 | Elementare Effiziente Algorithmen für Stochastische Fragestellungen | Proseminar | Saarland University |
| WS | 22/23 | Programming with Python | Tutorial | Saarland University |
| SS | 21 | Bioinformatics 2 | Tutorial | Saarland University |
| WS | 20/21 | Bioinformatics 1 | Tutorial | Saarland University |
| SS | 20 | Concurrent Programming | Tutorial | Saarland University |
| WS | 19/20 | Programming 1 | Tutorial | Saarland University |
Publications
Please visit my Google Scholar page.
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