Johann Wenckstern

BC 248, EPFL Lausanne, Switzerland

Hello! I am a Computer Science PhD student in the AIMM Lab at EPFL supervised by Charlotte Bunne. Before joining EPFL, I completed my bachelor’s and master’s degrees in Mathematics at ETH Zurich, where I was awarded the Willi Studer Prize for my master’s degree and the ETH Medal for my master’s thesis. I was also a visiting researcher at the Broad Institute of MIT and Harvard, where I worked with Gad Getz and David Sontag.

My research focuses on methods for representation learning and generative modeling, and on their application to spatial omics data. At the moment, I am particularly interested in (i) methods that bridge heterogeneous assays, which typically occur in omics data, and (ii) the modeling of temporal dynamics.

Selected Publications

The Virtual Tissues foundation model resolves spatial proteomics across scales

Johann Wenckstern, Eeshaan Jain, Benedikt Querfurth, and 9 more authors

Nature, 2026

Best Paper Award Bib PDF Code

Best Paper Award at the ICLR 2025 Workshop on Machine Learning for Genomics Explorations (MLGenX).

@article{wenckstern2026virtual,
  title = {{The Virtual Tissues foundation model resolves spatial proteomics across scales}},
  author = {Wenckstern, Johann and Jain, Eeshaan and von Querfurth, Benedikt and Cheng, Yexiang and Vasilev, Kiril and Pariset, Matteo and Cheng, Phil F. and Liakopoulos, Petros and Michielin, Olivier and Wicki, Andreas and Gut, Gabriele and Bunne, Charlotte},
  journal = {Nature},
  volume = {657},
  number = {8132},
  pages = {744--754},
  year = {2026},
  url = {https://www.nature.com/articles/s41586-026-10884-y},
}

spora: A Unified Multimodal Dataset and Platform for Spatial Proteomics

Benedikt Querfurth, Johann Wenckstern, Eeshaan Jain, and 9 more authors

In Advances in Neural Information Processing Systems (NeurIPS) Evaluations & Datasets (E&D) Track, 2026

Bib Code Website

@inproceedings{querfurth2026spora,
  title = {{spora: A Unified Multimodal Dataset and Platform for Spatial Proteomics}},
  author = {von Querfurth, Benedikt and Wenckstern, Johann and Jain, Eeshaan and Klein, Lukas and Cheng, Phil F. and Cheng, Yexiang and Vincent-Cuaz, Cédric and Frossard, Pascal and Haberecker, Martina and Wicki, Andreas and Michielin, Olivier and Bunne, Charlotte},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS) Evaluations & Datasets (E&D) Track},
  year = {2026},
  url = {https://spora.epfl.ch/},
}