Publications
* Equal contribution
Journal
- Singh, Im, Qiu, Macnkess, Gupta, Sorenson, Sledzieski, Erlach, Wendt, Nanfack, Bryson, Berger, "Learning the Language of Antibody Hypervariability," Proceedings of the National Academy of Sciences, In Review.
- Sledzieski, Kshirsagar, Baek, Berger, Dodhia, Lavista Ferres, "Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning," Proceedings of the National Academy of Sciences, 121.26 (2024): e2405840121. [PDF] [Code]
- Sledzieski*, Devkota*, Singh, Cowen, Berger, "TT3D: Leveraging Pre-Computed Protein Sequence Models to Predict Protein-Protein Interactions," Bioinformatics, 2023: btad663. [PDF] [Code] [Talk]
- Sledzieski*, Singh*, Bryson, Cowen, Berger, "Contrastive learning in protein language space predicts interactions between drugs and protein targets," Proceedings of the National Academy of Sciences, 120.24 (2023): e2220778120. [PDF] [Code]
- Kumar, Brenner, Sledzieski, Olaosebikan, Lynn-Goin, Putnam, Yang, Lewinski, Singh, Daniels, Cowen, Klein-Seetharaman, "Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome," Plos one, 18.2 (2023). 10.1371/journal.pone.0270965. [PDF]
- Zaman*, Sledzieski*, Wu, Bansal, "virDTL: Viral recombination analysis through phylogenetic reconciliation and its application to sarbecoviruses and SARS-CoV-2," J Comput Biol, 2022 Sep 20. doi: 10.1089/cmb.2021.0507. Epub ahead of print. PMID: 36125448. [PDF] [Code]
- Singh*, Devkota*, Sledzieski, Berger, Cowen, "Topsy-Turvy: integrating a global view into sequence-based PPI prediction," Bioinformatics, 38.Supplement_1 (July 2022): i264–i272. [PDF] [Code] [Talk]
- Sledzieski*, Singh*, Cowen, Berger, "D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions," Cell Systems, 12.10 (2021): 969-982. [PDF] [Code]
Conference
- Sledzieski, Kshirsagar, Baek, Berger, Dodhia, Lavista Ferres, "Parameter-Efficient Fine-Tuning of Protein Language Models Improves Prediction of Protein-Protein Interactions," Machine Learning for Structural Biology Workshop at NeurIPS. [PDF]
- Sledzieski*, Singh*, Cowen, Berger, "Contrasting drugs from decoys," Machine Learning for Structural Biology Workshop at NeurIPS. [PDF]
- Sledzieski*, Singh*, Cowen, Berger, "Adapting Protein Language Models for Rapid Drug-Target Interaction Prediction," Machine Learning for Structural Biology Workshop at NeurIPS. [PDF]
- Sledzieski*, Singh*, Cowen, Berger, "Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model," Conference on Research in Computational Molecular Biology (RECOMB). [PDF]
- Sledzieski*, Zhang, Mandoiu, Bansal, "TreeFix-TP: Phylogenetic Error Correction for Accurate Reconstruction of Viral Transmission Networks," Pacific Symposium on Biocomputing (PSB). [PDF] [Code]
Preprint
- Kousi, Boix, Park, Mathys, Sledzieski, Peng, Bennett, Tsai, Kellis, "Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer’s Dementia," bioRxiv, posted 22 April 2022, 10.1101/2022.04.21.489103. [PDF]