Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries

Konstantinos Antonopoulos; Olof Nordenstorm; Avlant Nilsson

doi:10.1371/journal.pcbi.1014100

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Open Access

Peer-reviewed

Research Article

Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries

Konstantinos Antonopoulos,

Roles Conceptualization, Formal analysis, Methodology, Visualization, Writing – original draft

Affiliations Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Cell and Molecular Biology, SciLifeLab, Karolinska Institutet, Stockholm, Sweden

https://orcid.org/0000-0003-2781-3872

⨯
Olof Nordenstorm,

Roles Methodology, Writing – review & editing

Affiliation Department of Cell and Molecular Biology, SciLifeLab, Karolinska Institutet, Stockholm, Sweden

https://orcid.org/0009-0003-5711-376X

⨯
Avlant Nilsson

Roles Conceptualization, Funding acquisition, Supervision, Writing – review & editing

* E-mail: avlant.nilsson@ki.se

Affiliation Department of Cell and Molecular Biology, SciLifeLab, Karolinska Institutet, Stockholm, Sweden

https://orcid.org/0000-0002-9476-4516

⨯

Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries

Konstantinos Antonopoulos,
Olof Nordenstorm,
Avlant Nilsson

Published: March 18, 2026
https://doi.org/10.1371/journal.pcbi.1014100

About the Authors

Konstantinos Antonopoulos

Roles Conceptualization, Formal analysis, Methodology, Visualization, Writing – original draft

Affiliations Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden, Department of Cell and Molecular Biology, SciLifeLab, Karolinska Institutet, Stockholm, Sweden

https://orcid.org/0000-0003-2781-3872

Olof Nordenstorm

Roles Methodology, Writing – review & editing

Affiliation Department of Cell and Molecular Biology, SciLifeLab, Karolinska Institutet, Stockholm, Sweden

https://orcid.org/0009-0003-5711-376X

Avlant Nilsson

Roles Conceptualization, Funding acquisition, Supervision, Writing – review & editing

* E-mail: avlant.nilsson@ki.se

Affiliation Department of Cell and Molecular Biology, SciLifeLab, Karolinska Institutet, Stockholm, Sweden

https://orcid.org/0000-0002-9476-4516

Competing Interests

The authors have declared that no competing interests exist.

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Signaling networks
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Phosphorylation
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Interpolation
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Signal inhibition
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Drug interactions
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MAPK signaling cascades
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Protein interaction networks
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Recurrent neural networks
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