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Education and qualifications (2)

Massachusetts Institute of Technology: Cambridge, MA, US

2019-08 to present | PhD Student (Electrical Engineering and Computer Science)
Education
Source: Self-asserted source
Samuel Sledzieski

University of Connecticut: Storrs, Connecticut, US

2015-08 to 2019-05 | Bachelor of Science (Computer Science and Engineering)
Education
Source: Self-asserted source
Samuel Sledzieski

Works (17)

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm

Nature Communications
2025-02-27 | Journal article
DOI: 10.1038/s41467-025-57148-3
Contributors: Meghana Kshirsagar; Artur Meller; Ian R. Humphreys; Samuel Sledzieski; Yixi Xu; Rahul Dodhia; Eric Horvitz; Bonnie Berger; Gregory R. Bowman; Juan Lavista Ferres et al.
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Crossref

Learning the language of antibody hypervariability

Proceedings of the National Academy of Sciences
2025-01-07 | Journal article
DOI: 10.1073/pnas.2418918121
Contributors: Rohit Singh; Chiho Im; Yu Qiu; Brian Mackness; Abhinav Gupta; Taylor Joren; Samuel Sledzieski; Lena Erlach; Maria Wendt; Yves Fomekong Nanfack et al.
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Crossref

Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC

2024-10-29 | Preprint
DOI: 10.1101/2024.10.25.620267
Contributors: Samuel Sledzieski; Charlotte Versavel; Rohit Singh; Faith Ocitti; Kapil Devkota; Lokender Kumar; Polina Shpilker; Liza Roger; Jinkyu Yang; Nastassja Lewinski et al.
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Crossref

Democratizing protein language models with parameter-efficient fine-tuning

Proceedings of the National Academy of Sciences
2024-06-25 | Journal article
DOI: 10.1073/pnas.2405840121
Contributors: Samuel Sledzieski; Meghana Kshirsagar; Minkyung Baek; Rahul Dodhia; Juan Lavista Ferres; Bonnie Berger
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Crossref

Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning

2023-11-10 | Preprint
DOI: 10.1101/2023.11.09.566187
Contributors: Samuel Sledzieski; Meghana Kshirsagar; Minkyung Baek; Bonnie Berger; Rahul Dodhia; Juan Lavista Ferres
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Crossref

TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions

Bioinformatics
2023-11-01 | Journal article
DOI: 10.1093/bioinformatics/btad663
Contributors: Samuel Sledzieski; Kapil Devkota; Rohit Singh; Lenore Cowen; Bonnie Berger; Arne Elofsson
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Crossref

Contrastive learning in protein language space predicts interactions between drugs and protein targets

Proceedings of the National Academy of Sciences
2023-06-13 | Journal article
DOI: 10.1073/pnas.2220778120
Contributors: Rohit Singh; Samuel Sledzieski; Bryan Bryson; Lenore Cowen; Bonnie Berger
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Crossref

Learning the Language of Antibody Hypervariability

2023-04-28 | Preprint
DOI: 10.1101/2023.04.26.538476
Contributors: Rohit Singh; Chiho Im; Yu Qiu; Brian Mackness; Abhinav Gupta; Taylor Sorenson; Samuel Sledzieski; Lena Erlach; Maria Wendt; Yves Fomekong Nanfack et al.
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Crossref

Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome

PLOS ONE
2023-02-03 | Journal article
DOI: 10.1371/journal.pone.0270965
Contributors: Lokender Kumar; Karl-Wilhelm Koch; Nathanael Brenner; Samuel Sledzieski; Monsurat Olaosebikan; Liza M. Roger; Matthew Lynn-Goin; Roshan Klein-Seetharaman; Bonnie Berger; Hollie Putnam et al.
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Crossref

Learning the Drug-Target Interaction Lexicon

2022-12-10 | Preprint
DOI: 10.1101/2022.12.06.519374
Contributors: Rohit Singh; Samuel Sledzieski; Lenore Cowen; Bonnie Berger
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Crossref

Adapting protein language models for rapid DTI prediction

2022-11-04 | Preprint
DOI: 10.1101/2022.11.03.515084
Contributors: Samuel Sledzieski; Rohit Singh; Lenore Cowen; Bonnie Berger
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Crossref

Contrasting drugs from decoys

2022-11-04 | Preprint
DOI: 10.1101/2022.11.03.515086
Contributors: Samuel Sledzieski; Rohit Singh; Lenore Cowen; Bonnie Berger
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Crossref

Topsy-Turvy: integrating a global view into sequence-based PPI prediction

Bioinformatics
2022-06-24 | Journal article
DOI: 10.1093/bioinformatics/btac258
Contributors: Rohit Singh; Kapil Devkota; Samuel Sledzieski; Bonnie Berger; Lenore Cowen
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Crossref

Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer’s Dementia

2022-04-22 | Preprint
DOI: 10.1101/2022.04.21.489103
Contributors: Maria Kousi; Carles Boix; Yongjin P. Park; Hansruedi Mathys; Samuel Sledzieski; Zhuyu Peng; David A. Bennett; Li-Huei Tsai; Manolis Kellis
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Crossref

Transfer of Knowledge from Model Organisms to Evolutionarily Distant Non-Model Organisms: The Coral Pocillopora damicornis Membrane Signaling Receptome

2021-10-18 | Other
DOI: 10.1101/2021.10.18.464760
Contributors: Lokender Kumar; Nathanael Brenner; Sam Sledzieski; Monsurat Olaosebikan; Matthew Lynn-Goin; Hollie Putnam; JK Yang; Nastassja Lewinski; Rohit Singh; Noah M. Daniels et al.
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Crossref

Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

2021-08-13 | Other
DOI: 10.1101/2021.08.12.456131
Contributors: Sumaira Zaman; Samuel Sledzieski; Bonnie Berger; Yi-Chieh Wu; Mukul S. Bansal
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Crossref

Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model

2021-01-25 | Preprint
DOI: 10.1101/2021.01.22.427866
Contributors: Samuel Sledzieski; Rohit Singh; Lenore Cowen; Bonnie Berger
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Crossref
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