Philip G Bradley (P Bradley, Philip Bradley, Phil Bradley)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 28

Top Topics

Genome Wide Association

Acute Lymphoblastic Leukemia

Protein Protein

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

Nature biotechnology

Science (New York, N.Y.)

This page only lists publications with an associated author ORCID identifier.

Publications

Michael N Pun, Andrew Ivanov, Quinn Bellamy, Zachary Montague, Colin LaMont, Philip G Bradley, Jakub Otwinowski, Armita Nourmohammad
Learning the shape of protein microenvironments with a holographic convolutional neural network. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Michael N Pun, Andrew Ivanov, Quinn Bellamy, Zachary Montague, Colin LaMont, Philip G Bradley, Jakub Otwinowski, Armita Nourmohammad
Learning the shape of protein microenvironments with a holographic convolutional neural network. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Michael N Pun, Andrew Ivanov, Quinn Bellamy, Zachary Montague, Colin LaMont, Philip G Bradley, Jakub Otwinowski, Armita Nourmohammad
Learning the shape of protein microenvironments with a holographic convolutional neural network. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Michael N Pun, Andrew Ivanov, Quinn Bellamy, Zachary Montague, Colin LaMont, Philip G Bradley, Jakub Otwinowski, Armita Nourmohammad
Learning the shape of protein microenvironments with a holographic convolutional neural network. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Michael N Pun, Andrew Ivanov, Quinn Bellamy, Zachary Montague, Colin LaMont, Philip G Bradley, Jakub Otwinowski, Armita Nourmohammad
Learning the shape of protein microenvironments with a holographic convolutional neural network. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Philip G Bradley
Structure-based prediction of T cell receptor:peptide-MHC interactions. eLife 12 (2023)
Lindsey A Doyle, Brittany Takushi, Ryan D Kibler, Lukas F Milles, Carolina T Orozco, Jonathan D Jones, Sophie E Jackson, Barry L Stoddard, Philip G Bradley
De novo design of knotted tandem repeat proteins. Nature communications 14 (1) (2023)
Philip G Bradley
Structure-based prediction of T cell receptor:peptide-MHC interactions. eLife 12 (2023)
Si Liu, Philip G Bradley, Wei Sun
Neural Network Models for Sequence-Based TCR and HLA Association Prediction. bioRxiv : the preprint server for biology (2023)
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Philip G Bradley
Structure-based prediction of T cell receptor:peptide-MHC interactions. eLife 12 (2023)
Philip G Bradley
Structure-based prediction of T cell receptor:peptide-MHC interactions. eLife 12 (2023)
Philip G Bradley
Structure-based prediction of T cell receptor:peptide-MHC interactions. eLife 12 (2023)
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Amir Motmaen, Justas Dauparas, Minkyung Baek, Mohamad H Abedi, Julien S Baker, Philip G Bradley
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America 120 (9) (2023)
Magdalena L Russell, Noah Simon, Philip G Bradley, Frederick A Matsen
Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming. eLife 12 (2023)
Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen, Philip G Bradley
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities. eLife 11 (2022)
Alexis Courbet, Jesse M Hansen, Yang Hsia, Neville P Bethel, Young-Jun Park, Chunfu Xu, A Moyer, Scott E Boyken, George Ueda, Una Nattermann, Deepesh Nagarajan, Daniel Adriano Silva, William Sheffler, Joel Quispe, Ashley L Nord, Neil P King, Philip G Bradley, David J Veesler, Justin M Kollman, Julien S Baker
Computational design of mechanically coupled axle-rotor protein assemblies. Science (New York, N.Y.) 376 (6591) (2022)
Jami R Erickson, Terry Stevens-Ayers, Florian Mair, Bradley Edmison, Michael J Boeckh, Philip G Bradley, Martin Prlic
Convergent clonal selection of donor- and recipient-derived CMV-specific T cells in hematopoietic stem cell transplant patients. Proceedings of the National Academy of Sciences of the United States of America 119 (6) (2022)
Koshlan Mayer-Blackwell, Stefan Schattgen, Liel Cohen-Lavi, Jeremy C Crawford, Aisha Souquette, Jessica A Gaevert, Tomer Hertz, Paul G Thomas, Philip G Bradley, Andrew-Fiore Gartland
TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs. eLife 10 (2021)
Stefan A Schattgen, Kate Guion, Jeremy Chase Crawford, Aisha Souquette, Alvaro Martinez Barrio, Michael J T Stubbington, Paul Glyndwr Thomas, Philip G Bradley
Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA). Nature biotechnology (2021)
Julia Koehler Leman, Brian D Weitzner, Steven M Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca F Alford, Melanie Aprahamian, Julien S Baker, Kyle A Barlow, Patrick Barth, Benjamin Basanta, Brian J Bender, Kristin Blacklock, Jaume Bonet, Scott E Boyken, Philip G Bradley, Chris Bystroff, Patrick Conway, Seth Cooper, Bruno E Correia, Brian Coventry, Rachel J Hagey, René M De Jong, Frank DiMaio, Lorna Dsilva, Roland L Dunbrack, Alexander S Ford, Brandon Frenz, Darwin Y Fu, Caleb Geniesse, Lukasz Goldschmidt, Ragul Gowthaman, Jeffrey J Gray, Dominik Gront, Sharon Guffy, Scott Horowitz, Po-Ssu Huang, Thomas Huber, Tim M Jacobs, Jeliazko R Jeliazkov, David K Johnson, Kalli Kappel, John Karanicolas, Hamed Khakzad, Karen R Khar, Sagar D Khare, Firas Khatib, Alisa Khramushin, Indigo C King, Robert Kleffner, Brian Koepnick, Tanja Kortemme, Georg Kuenze, Brian Kuhlman, Daisuke Kuroda, Jason W Labonte, Jason K Lai, Gideon Lapidoth, Andrew Leaver-Fay, Steffen Lindert, Thomas Linsky, Nir London, Joseph H Lubin, Sergey Lyskov, Jack Maguire, Lars Malmström, Enrique Marcos, Orly Marcu, Nicholas A Marze, Jens Meiler, Rocco Moretti, Vikram Khipple Mulligan, Santrupti Nerli, Christoffer Norn, Shane Ó'Conchúir, Noah Ollikainen, Sergey Ovchinnikov, Michael S Pacella, Xingjie Pan, Hahnbeom Park, Ryan E Pavlovicz, Manasi Pethe, Brian G Pierce, Kala Bharath Pilla, Barak Raveh, P Douglas Renfrew, Shourya S Roy Burman, Aliza Rubenstein, Marion F Sauer, Andreas Scheck, William R Schief, Ora Schueler-Furman, Yuval Sedan, Alexander M Sevy, Nikolaos G Sgourakis, Lei Shi, Justin B Siegel, Daniel-Adriano Silva, Shannon Smith, Yifan Song, Amelie Stein, Maria Szegedy, Frank D Teets, Summer B Thyme, Ray Yu-Ruei Wang, Andrew Watkins, Lior Zimmerman, Richard A Bonneau
Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature methods 17 (7) (2020)
Colin E Correnti, Jazmine P Hallinan, Lindsey A Doyle, Raymond O Ruff, Carla A Jaeger-Ruckstuhl, Yuexin Xu, Betty W Shen, Amanda Qu, Caley Polkinghorn, Della J Friend, Ashok D Bandaranayake, Stanley R Riddell, Brett K Kaiser, Barry L Stoddard, Philip G Bradley
Engineering and functionalization of large circular tandem repeat protein nanoparticles. Nature structural & molecular biology 27 (4) (2020)
Kristian Davidsen, Branden J Olson, William S DeWitt, Jean Feng, Elias Harkins, Philip G Bradley, Frederick A Matsen
Deep generative models for T cell receptor protein sequences. eLife 8 (2019)
Brian Kuhlman, Philip G Bradley
Advances in protein structure prediction and design. Nature reviews. Molecular cell biology 20 (11) (2019)
William S DeWitt, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen, Philip G Bradley
Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity. eLife 7 (2018)
Connor O McCoy, Trevor Felix Bedford, Vladimir N Minin, Philip G Bradley, Harlan S Robins, Frederick A Matsen
Quantifying evolutionary constraints on B-cell affinity maturation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 370 (1676) (2016)