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A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics.
Hoang DT, Dinstag G, Shulman ED, Hermida LC, Ben-Zvi DS, Elis E, Caley K, Sammut SJ, Sinha S, Sinha N, Dampier CH, Stossel C, Patil T, Rajan A, Lassoued W, Strauss J, Bailey S, Allen C, Redman J, Beker T, Jiang P, Golan T, Wilkinson S, Sowalsky AG, Pine SR, Caldas C, Gulley JL, Aldape K, Aharonov R, Stone EA, Ruppin E. Hoang DT, et al. Among authors: caldas c. Nat Cancer. 2024 Sep;5(9):1305-1317. doi: 10.1038/s43018-024-00793-2. Epub 2024 Jul 3. Nat Cancer. 2024. PMID: 38961276
Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups.
Rueda OM, Sammut SJ, Seoane JA, Chin SF, Caswell-Jin JL, Callari M, Batra R, Pereira B, Bruna A, Ali HR, Provenzano E, Liu B, Parisien M, Gillett C, McKinney S, Green AR, Murphy L, Purushotham A, Ellis IO, Pharoah PD, Rueda C, Aparicio S, Caldas C, Curtis C. Rueda OM, et al. Among authors: caldas c. Nature. 2019 Mar;567(7748):399-404. doi: 10.1038/s41586-019-1007-8. Epub 2019 Mar 13. Nature. 2019. PMID: 30867590 Free PMC article.
DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation.
Batra RN, Lifshitz A, Vidakovic AT, Chin SF, Sati-Batra A, Sammut SJ, Provenzano E, Ali HR, Dariush A, Bruna A, Murphy L, Purushotham A, Ellis I, Green A, Garrett-Bakelman FE, Mason C, Melnick A, Aparicio SAJR, Rueda OM, Tanay A, Caldas C. Batra RN, et al. Among authors: caldas c. Nat Commun. 2021 Sep 13;12(1):5406. doi: 10.1038/s41467-021-25661-w. Nat Commun. 2021. PMID: 34518533 Free PMC article.
Multi-omic machine learning predictor of breast cancer therapy response.
Sammut SJ, Crispin-Ortuzar M, Chin SF, Provenzano E, Bardwell HA, Ma W, Cope W, Dariush A, Dawson SJ, Abraham JE, Dunn J, Hiller L, Thomas J, Cameron DA, Bartlett JMS, Hayward L, Pharoah PD, Markowetz F, Rueda OM, Earl HM, Caldas C. Sammut SJ, et al. Among authors: caldas c. Nature. 2022 Jan;601(7894):623-629. doi: 10.1038/s41586-021-04278-5. Epub 2021 Dec 7. Nature. 2022. PMID: 34875674 Free PMC article.
Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4+ and PDPN+ CAFs to clinical outcome.
Friedman G, Levi-Galibov O, David E, Bornstein C, Giladi A, Dadiani M, Mayo A, Halperin C, Pevsner-Fischer M, Lavon H, Mayer S, Nevo R, Stein Y, Balint-Lahat N, Barshack I, Ali HR, Caldas C, Nili-Gal-Yam E, Alon U, Amit I, Scherz-Shouval R. Friedman G, et al. Among authors: caldas c. Nat Cancer. 2020 Jul;1(7):692-708. doi: 10.1038/s43018-020-0082-y. Epub 2020 Jun 29. Nat Cancer. 2020. PMID: 35122040 Free PMC article.
Prediction of cancer treatment response from histopathology images through imputed transcriptomics.
Hoang DT, Dinstag G, Hermida LC, Ben-Zvi DS, Elis E, Caley K, Sammut SJ, Sinha S, Sinha N, Dampier CH, Stossel C, Patil T, Rajan A, Lassoued W, Strauss J, Bailey S, Allen C, Redman J, Beker T, Jiang P, Golan T, Wilkinson S, Sowalsky AG, Pine SR, Caldas C, Gulley JL, Aldape K, Aharonov R, Stone EA, Ruppin E. Hoang DT, et al. Among authors: caldas c. Res Sq [Preprint]. 2023 Sep 15:rs.3.rs-3193270. doi: 10.21203/rs.3.rs-3193270/v1. Res Sq. 2023. Update in: Nat Cancer. 2024 Sep;5(9):1305-1317. doi: 10.1038/s43018-024-00793-2. PMID: 37790315 Free PMC article. Updated. Preprint.
Predictability of B cell clonal persistence and immunosurveillance in breast cancer.
Sammut SJ, Galson JD, Minter R, Sun B, Chin SF, De Mattos-Arruda L, Finch DK, Schätzle S, Dias J, Rueda OM, Seoane J, Osbourn J, Caldas C, Bashford-Rogers RJM. Sammut SJ, et al. Among authors: caldas c. Nat Immunol. 2024 May;25(5):916-924. doi: 10.1038/s41590-024-01821-0. Epub 2024 May 2. Nat Immunol. 2024. PMID: 38698238 Free PMC article.
A large-scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression-free survival.
Beddowes EJ, Ortega Duran M, Karapanagiotis S, Martin A, Gao M, Masina R, Woitek R, Tanner J, Tippin F, Kane J, Lay J, Brouwer A, Sammut SJ, Chin SF, Gale D, Tsui DWY, Dawson SJ, Rosenfeld N, Callari M, Rueda OM, Caldas C. Beddowes EJ, et al. Among authors: caldas c. Mol Oncol. 2025 Apr 15. doi: 10.1002/1878-0261.70015. Online ahead of print. Mol Oncol. 2025. PMID: 40231728 Free article.
718 results