| D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions S Sledzieski, R Singh, L Cowen, B Berger Cell Systems 12 (10), 969-982. e6, 2021 | 146* | 2021 |
| Contrastive learning in protein language space predicts interactions between drugs and protein targets R Singh, S Sledzieski, B Bryson, L Cowen, B Berger Proceedings of the National Academy of Sciences 120 (24), e2220778120, 2023 | 102* | 2023 |
| Topsy-Turvy: integrating a global view into sequence-based PPI prediction R Singh, K Devkota, S Sledzieski, B Berger, L Cowen Bioinformatics 38 (Supplement_1), i264-i272, 2022 | 56 | 2022 |
| Democratizing protein language models with parameter-efficient fine-tuning S Sledzieski, M Kshirsagar, M Baek, R Dodhia, J Lavista Ferres, B Berger Proceedings of the National Academy of Sciences 121 (26), e2405840121, 2024 | 28 | 2024 |
| TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions S Sledzieski, K Devkota, R Singh, L Cowen, B Berger Bioinformatics 39 (11), btad663, 2023 | 13 | 2023 |
| Learning the language of antibody hypervariability R Singh, C Im, Y Qiu, B Mackness, A Gupta, T Joren, S Sledzieski, ... Proceedings of the National Academy of Sciences 122 (1), e2418918121, 2025 | 12 | 2025 |
| Transfer of Knowledge from Model Organisms to Evolutionarily Distant Non-Model Organisms: The Coral Pocillopora damicornis Membrane Signaling Receptome L Kumar, N Brenner, S Sledzieski, M Olaosebikan, M Lynn-Goin, ... bioRxiv, 2021 | 11 | 2021 |
| TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference S Sledzieski, C Zhang, I Mandoiu, MS Bansal Pacific Symposium on Biocomputing 2021, 119-130, 2021 | 10 | 2021 |
| virDTL: Viral recombination analysis through phylogenetic reconciliation and its application to sarbecoviruses and SARS-CoV-2 S Zaman, S Sledzieski, B Berger, YC Wu, MS Bansal Journal of Computational Biology 30 (1), 3-20, 2023 | 6* | 2023 |
| Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer’s Dementia M Kousi, C Boix, YP Park, H Mathys, S Sledzieski, Z Peng, DA Bennett, ... bioRxiv, 2022.04. 21.489103, 2022 | 4 | 2022 |
| Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm M Kshirsagar, A Meller, I Humphreys, S Sledzieski, Y Xu, R Dodhia, ... Research Square, 2024 | 2 | 2024 |
| Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC S Sledzieski, C Versavel, R Singh, F Ocitti, K Devkota, L Kumar, ... bioRxiv, 2024.10. 25.620267, 2024 | | 2024 |
| Insulin Signaling and Pharmacology in Corals W Vizgaudis, L Kumar, M Olaosebikan, L Roger, N Brenner, S Sledzieski, ... | | 2024 |
| Learning the language of biomolecular interactions S Sledzieski Massachusetts Institute of Technology, 2024 | | 2024 |
| Structurally Motivated Deep Learning for Genome Scale Protein Interaction Prediction S Sledzieski Massachusetts Institute of Technology, 2021 | | 2021 |
Bonnie BergerMITVerified email at mit.edu