Publications
* Equal contribution
Journal
Rapid and accurate prediction of protein homo-oligomer symmetry
Kshirsagar, Meller, Humphreys, Sledzieski, Xu, Dodhia, Horvitz, Berger, Bowman, Lavista Ferres, Baker, Baek, Nature Communications, 16(2017), 2025.
Learning the Language of Antibody Hypervariability
Singh, Im, Qiu, Macnkess, Gupta, Sorenson, Sledzieski, Erlach, Wendt, Nanfack, Bryson, Berger, Proceedings of the National Academy of Sciences, 122(1):e2418918121, 2024.
Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning
Sledzieski, Kshirsagar, Baek, Berger, Dodhia, Lavista Ferres, Proceedings of the National Academy of Sciences, 121(26):e2405840121, 2024.
TT3D: Leveraging Pre-Computed Protein Sequence Models to Predict Protein-Protein Interactions
Sledzieski*, Devkota*, Singh, Cowen, Berger, Bioinformatics, 39(11):btad663, 2023.
Contrastive learning in protein language space predicts interactions between drugs and protein targets
Singh*, Sledzieski*, Bryson, Cowen, Berger, Proceedings of the National Academy of Sciences, 120(24):e2220778120, 2023.
Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome
Kumar, Brenner, Sledzieski, Olaosebikan, Lynn-Goin, Putnam, Yang, Lewinski, Singh, Daniels, Cowen, Klein-Seetharaman, Plos one, 18(2):e0270965, 2023.
virDTL: Viral recombination analysis through phylogenetic reconciliation and its application to sarbecoviruses and SARS-CoV-2
Zaman*, Sledzieski*, Wu, Bansal, J Comput Biol, 30(1):3--20, 2023.
Topsy-Turvy: integrating a global view into sequence-based PPI prediction
Singh*, Devkota*, Sledzieski, Berger, Cowen, Bioinformatics, 38(Supplement 1):i264-i272, 2022.
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions
Sledzieski*, Singh*, Cowen, Berger, Cell Systems, 12(10):969-982, 2021.
Conference
Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC
Sledzieski, Versavel, Singh, Ocitti, Devkota, Kumar, Shhpilker, Roger, Yang, Lewinski, Putnam, Berger, Klein-Seetharaman, Cowen, Conference on Research in Computational Molecular Biology (RECOMB), 2024.
Parameter-Efficient Fine-Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions
Sledzieski, Kshirsagar, Baek, Berger, Dodhia, Lavista Ferres, Machine Learning for Structural Biology Workshop at NeurIPS, 2023.
Contrasting drugs from decoys
Sledzieski*, Singh*, Cowen, Berger, Machine Learning for Structural Biology Workshop at NeurIPS, 2022.
Adapting Protein Language Models for Rapid Drug-Target Interaction Prediction
Sledzieski*, Singh*, Cowen, Berger, Machine Learning for Structural Biology Workshop at NeurIPS, 2021.
Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model
Sledzieski*, Singh*, Cowen, Berger, Conference on Research in Computational Molecular Biology (RECOMB), 2021.
TreeFix-TP: Phylogenetic Error Correction for Accurate Reconstruction of Viral Transmission Networks
Sledzieski*, Zhang, Mandoiu, Bansal, Pacific Symposium on Biocomputing (PSB), 2021.
Preprint
Learning the language of protein-protein interactions
Ullanat, Jing, Sledzieski, Berger, bioRxiv, 2025.
Insulin Signaling and Pharmacology in Corals
Vizgaudis, Kumar, Olaosebikan, Roger, Brenner, Sledzieski, Yang, Lewinski, Singh, Daniels, Cowen, Klein-Seetharaman, Authorea Preprints, 2024.
Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimers Dementia
Kousi, Boix, Park, Mathys, Sledzieski, Peng, Bennett, Tsai, Kellis, bioRxiv, 2022.