Author

Lucas Stalder

ETH Zurich

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 3 Bioinformatics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Approach:deep learning· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:proteomics· 2 Assay:scRNA-seq· 2

Frequent Co-Authors

Sai T. ReddyiD· 4 shared Alexander YermanosiD· 3 shared Daphne van GinnekeniD· 2 shared Kai‐Lin HongiD· 2 shared Alberto ValdeolivasiD· 1 shared Alessandro Genovese· 1 shared Ali NowrouziiD· 1 shared Anamay Samant· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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4 shared papersImmunology

Sai T. ReddyORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Spatial Transcriptomics and Single-Nucleus RNA Sequencing Reveal rAAV2- and rAAV9-Specific Transduction Signatures in the Mouse Liver

Bettina Amberg, Fabian Köchl, Nadine Kumpesa, Megana K. Prasad, Filip Bochner, Mar Hernandez-Obiols, Michael B. Otteneder, Lucas Stalder, Frances C. Shaffo, Ali Nowrouzi, David M. Markusic, Hélène Haegel, Rebecca Xicluna, Marc Sultan, Björn Jacobsen, , Kerstin Hahn

This study uses spatial transcriptomics and single-nucleus RNA sequencing to analyze rAAV2 and rAAV9 vector effects in mouse livers, revealing sex-specific transcriptomic changes and novel transgene co-expression factors.

Gene Therapy · Mar 11, 2026Peer-reviewedMolecular Biology

Contrastive learning for antibody-antigen sequence-to-specificity prediction

Hyunho Lee, Karla M. Castro, Sean Renwick, Lucas Stalder, Wiona Sophie Glänzer, Rachita K. Kumar, NingNing Chen, Andreas Scheck, Alexander Yermanos, Derek M. Mason, Sai T. Reddy

This paper introduces CALM, a model that predicts antibody-antigen binding from sequences using contrastive learning, achieving 7% top-1 retrieval on a test set.

bioRxiv · Feb 26, 2026 · PreprintImmunology

Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor‐Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T. Reddy, Alexander Yermanos

AntibodyForests quantifies inter- and intra-antibody repertoire evolution using protein language models and structure analysis.

Bioinformatics · Oct 1, 2025Peer-reviewedBioinformatics

Clonally expanded IgG antibody-secreting cells preferentially target influenza nucleoprotein following homologous and heterologous infections

Andreas Agrafiotis, Raphael Kuhn, Camilla Panetti, Marco Venerito, Hathaichanok Phandee, Lucas Stalder, Danielle Shlesinger, Vittoria Martinolli D’Arcy, Kai‐Lin Hong, Daphne van Ginneken, Alessandro Genovese, Nicole Joller, Annette Oxenius, Sai T. Reddy, Alexander Yermanos

The paper characterizes clonal dynamics of antibody-secreting cells in bone marrow following influenza infection, finding that IgG ASCs preferentially target nucleoprotein regardless of infection type.

The Journal of Immunology · Jul 26, 2025Peer-reviewedImmunology

Predicting TCR antigen specificity at proteome-scale with synthetic immune cells and machine learning

Kai‐Lin Hong, Beichen Gao, Lucas Stalder, Roy A. Ehling, Marton Horvath, Sarah Wehrle, Juliette L. Forster, Valentin Junet, Jakub Kucharczyk, Sébastien Lalevée, Marie‐Charlotte Diringer, Qinmei Yang, Rodrigo Vazquez-Lombardi, Sai T. Reddy

The paper presents a synthetic immune cell platform integrated with machine learning to predict TCR specificity to peptide-HLA antigens across the human proteome.

bioRxiv · Jul 23, 2025 · PreprintImmunology