The Sledzieski Lab at UC San Diego develops computational methods to better understand molecular structures and interactions, from modeling complex structural dynamics to building whole-organism interaction networks.

Our research Our team

Research

Learning the language of life

We train, investigate, and adapt large foundation models for biomolecular modeling.

Modeling dynamic allostery

We model the link between structural heterogeneity and molecular function through the lens of allostery.

Predicting molecular interactions

We build models for rapid and accurate prediction of protein-protein interaction networks.

Investigating function in diverse organisms

We develop high-throughput, robust, and generalizable models to study cellular systems across the tree of life.

Selected publications

Figure from PLANET-MD: Ultra-fast Proteome-scale Prediction of Allosteric Networks in Proteins

PLANET-MD: Ultra-fast Proteome-scale Prediction of Allosteric Networks in Proteinspreprint

Sledzieski, Hanson

bioRxiv, 2026

Paper Code

BibTeX

@article{sledzieski2026planetmd,
  title   = {PLANET-MD: Ultra-fast Proteome-scale Prediction of Allosteric Networks in Proteins},
  author  = {Sledzieski and Hanson},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.1101/2025.06.12.659353}
}

@article{sledzieski2026planetmd, title = {PLANET-MD: Ultra-fast Proteome-scale Prediction of Allosteric Networks in Proteins}, author = {Sledzieski and Hanson}, journal = {bioRxiv}, year = {2026}, doi = {10.1101/2025.06.12.659353} }

Figure from MIMIC: A Generative Multimodal Foundation Model for Biomolecules

MIMIC: A Generative Multimodal Foundation Model for Biomoleculespreprint

Golkar, Kovalic*, Espejo Morales*, Sledzieski*, Li*, Sokolova, Krawezik, Bietti, Skok Gibbs, Klypa, Xiong, Lanusse, Parker, Cho, Cranmer, Hehir, McCabe, Meyer, Morel, Mukhopadhyay, Pettee, Qu, Shen, Fouhey, Sotoudeh, Mulligan, Cossio, Hanson, Jones, Troyanskaya, Ho

arXiv, 2026

Project page Paper Code

BibTeX

@article{golkar2026mimic,
  title   = {MIMIC: A Generative Multimodal Foundation Model for Biomolecules},
  author  = {Golkar and Kovalic and {Espejo Morales} and Sledzieski and Li and Sokolova and Krawezik and Bietti and {Skok Gibbs} and Klypa and Xiong and Lanusse and Parker and Cho and Cranmer and Hehir and McCabe and Meyer and Morel and Mukhopadhyay and Pettee and Qu and Shen and Fouhey and Sotoudeh and Mulligan and Cossio and Hanson and Jones and Troyanskaya and Ho},
  journal = {arXiv},
  year    = {2026},
  doi     = {10.48550/arXiv.2604.24506}
}

@article{golkar2026mimic, title = {MIMIC: A Generative Multimodal Foundation Model for Biomolecules}, author = {Golkar and Kovalic and {Espejo Morales} and Sledzieski and Li and Sokolova and Krawezik and Bietti and {Skok Gibbs} and Klypa and Xiong and Lanusse and Parker and Cho and Cranmer and Hehir and McCabe and Meyer and Morel and Mukhopadhyay and Pettee and Qu and Shen and Fouhey and Sotoudeh and Mulligan and Cossio and Hanson and Jones and Troyanskaya and Ho}, journal = {arXiv}, year = {2026}, doi = {10.48550/arXiv.2604.24506} }

Decoding the functional interactome of non-model organisms with PHILHARMONIC

Sledzieski, Versavel, Singh, Ocitti, Devkota, Kumar, Shpilker, Roger, Yang, Lewinski, Putnam, Klein-Seetharaman, Berger, Cowen

Conference on Research in Computational Molecular Biology (RECOMB), 2025

Paper Code

BibTeX

@inproceedings{sledzieski2025decoding,
  title     = {Decoding the functional interactome of non-model organisms with PHILHARMONIC},
  author    = {Sledzieski and Versavel and Singh and Ocitti and Devkota and Kumar and Shpilker and Roger and Yang and Lewinski and Putnam and Klein-Seetharaman and Berger and Cowen},
  booktitle = {Conference on Research in Computational Molecular Biology (RECOMB)},
  year      = {2025},
  doi       = {10.1101/2024.10.25.620267}
}

@inproceedings{sledzieski2025decoding, title = {Decoding the functional interactome of non-model organisms with PHILHARMONIC}, author = {Sledzieski and Versavel and Singh and Ocitti and Devkota and Kumar and Shpilker and Roger and Yang and Lewinski and Putnam and Klein-Seetharaman and Berger and Cowen}, booktitle = {Conference on Research in Computational Molecular Biology (RECOMB)}, year = {2025}, doi = {10.1101/2024.10.25.620267} }

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News

Oct 14, 2026

The lab website is live! Sam will join the Halıcıoğlu Data Science Institute at UC San Diego as an Assistant Professor in July 2027, and the lab is recruiting at all levels: see Join.

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