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jonasscheid merged 2 commits into from
May 5, 2026
Merged

Add bioRxiv preprint citation #18

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544d050
Add bioRxiv preprint citation
jonasscheid May 5, 2026
56dc222
Link PR #18 in changelog entry
jonasscheid May 5, 2026
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,11 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]

### Changed
- Added bioRxiv preprint citation in README and Gradio app help tab ([doi:10.64898/2026.04.08.717021](https://doi.org/10.64898/2026.04.08.717021)) ([#18](https://github.com/AG-Walz/immunotype/pull/18))

## [1.0.3]

### Fixed
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18 changes: 13 additions & 5 deletions README.md
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Expand Up @@ -130,11 +130,19 @@ sample_0 A HLA-A*02:01 0.0000 0.1945 0.0584

## 📚 Citation

If you use immunotype in your research, please cite our preprint:

> Pilz M, Scheid J, Bauer A, Lemke S, Sachsenberg T, Bauer J, Nelde A, Stadelmaier J, Walter A, Rammensee H-G, Nahnsen S, Kohlbacher O, Walz JS.
> **Deep learning enables direct HLA typing from immunopeptidomics data.** *bioRxiv* (2026).
> [doi:10.64898/2026.04.08.717021](https://doi.org/10.64898/2026.04.08.717021)

```bibtex
@software{immunotype,
title={immunotype: Peptide-based HLA typing from immunopeptidomics data},
author={Pilz, Matteo and Scheid, Jonas},
url={https://github.com/AG-Walz/immunotype},
year={2026}
@article{immunotype,
title = {Deep learning enables direct HLA typing from immunopeptidomics data},
author = {Pilz, Matteo and Scheid, Jonas and Bauer, Alina and Lemke, Steffen and Sachsenberg, Timo and Bauer, Jens and Nelde, Annika and Stadelmaier, Josua and Walter, Axel and Rammensee, Hans-Georg and Nahnsen, Sven and Kohlbacher, Oliver and Walz, Juliane Sarah},
journal = {bioRxiv},
year = {2026},
doi = {10.64898/2026.04.08.717021},
url = {https://doi.org/10.64898/2026.04.08.717021}
}
```
6 changes: 5 additions & 1 deletion src/immunotype/constants.py
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Max peptides, batch size, and GPU settings do not affect lookup-only predictions.

### Citation
If you use immunotype in your research, please cite TODO.
If you use immunotype in your research, please cite our preprint:

> Pilz M, Scheid J, Bauer A, Lemke S, Sachsenberg T, Bauer J, Nelde A, Stadelmaier J, Walter A, Rammensee H-G, Nahnsen S, Kohlbacher O, Walz JS.
> **Deep learning enables direct HLA typing from immunopeptidomics data.** *bioRxiv* (2026).
> [doi:10.64898/2026.04.08.717021](https://doi.org/10.64898/2026.04.08.717021)
"""
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