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Page 1
AIntibody: an experimentally validated in silico antibody discovery design challenge.
Erasmus MF, Spector L, Ferrara F, DiNiro R, Pohl TJ, Perea-Schmittle K, Wang W, Tessier PM, Richardson C, Turner L, Kumar S, Bedinger D, Sormanni P, Fernández-Quintero ML, Ward AB, Loeffler JR, Swanson OM, Deane CM, Raybould MIJ, Evers A, Sellmann C, Bachas S, Ruffolo J, Nastri HG, Ramesh K, Sørensen J, Croasdale-Wood R, Hijano O, Leal-Lopes C, Shahsavarian M, Qiu Y, Marcatili P, Vernet E, Akbar R, Friedensohn S, Wagner R, Kurella VB, Malhotra S, Kumar S, Kidger P, Almagro JC, Furfine E, Stanton M, Graff CP, Villalba SD, Tomszak F, Teixeira AAR, Hopkins E, Dovner M, D'Angelo S, Bradbury ARM. Erasmus MF, et al. Among authors: ruffolo j. Nat Biotechnol. 2024 Nov;42(11):1637-1642. doi: 10.1038/s41587-024-02469-9. Nat Biotechnol. 2024. PMID: 39496931 No abstract available.
Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.
Hutchinson M, Ruffolo JA, Haskins N, Iannotti M, Vozza G, Pham T, Mehzabeen N, Shandilya H, Rickert K, Croasdale-Wood R, Damschroder M, Fu Y, Dippel A, Gray JJ, Kaplan G. Hutchinson M, et al. Among authors: ruffolo ja. MAbs. 2024 Jan-Dec;16(1):2362775. doi: 10.1080/19420862.2024.2362775. Epub 2024 Jun 20. MAbs. 2024. PMID: 38899735 Free PMC article.
Designing proteins with language models.
Ruffolo JA, Madani A. Ruffolo JA, et al. Nat Biotechnol. 2024 Feb;42(2):200-202. doi: 10.1038/s41587-024-02123-4. Nat Biotechnol. 2024. PMID: 38361067 Review. No abstract available.
ProGen2: Exploring the boundaries of protein language models.
Nijkamp E, Ruffolo JA, Weinstein EN, Naik N, Madani A. Nijkamp E, et al. Among authors: ruffolo ja. Cell Syst. 2023 Nov 15;14(11):968-978.e3. doi: 10.1016/j.cels.2023.10.002. Epub 2023 Oct 30. Cell Syst. 2023. PMID: 37909046 Free article.
IgLM: Infilling language modeling for antibody sequence design.
Shuai RW, Ruffolo JA, Gray JJ. Shuai RW, et al. Among authors: ruffolo ja. Cell Syst. 2023 Nov 15;14(11):979-989.e4. doi: 10.1016/j.cels.2023.10.001. Epub 2023 Oct 30. Cell Syst. 2023. PMID: 37909045 Free PMC article.
SARS-CoV-2 infection establishes a stable and age-independent CD8+ T cell response against a dominant nucleocapsid epitope using restricted T cell receptors.
Choy C, Chen J, Li J, Gallagher DT, Lu J, Wu D, Zou A, Hemani H, Baptiste BA, Wichmann E, Yang Q, Ciffelo J, Yin R, McKelvy J, Melvin D, Wallace T, Dunn C, Nguyen C, Chia CW, Fan J, Ruffolo J, Zukley L, Shi G, Amano T, An Y, Meirelles O, Wu WW, Chou CK, Shen RF, Willis RA, Ko MSH, Liu YT, De S, Pierce BG, Ferrucci L, Egan J, Mariuzza R, Weng NP. Choy C, et al. Among authors: ruffolo j. Nat Commun. 2023 Oct 23;14(1):6725. doi: 10.1038/s41467-023-42430-z. Nat Commun. 2023. PMID: 37872153 Free PMC article.
44 results