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Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology.
Rosenthal J, Carelli R, Omar M, Brundage D, Halbert E, Nyman J, Hari SN, Van Allen EM, Marchionni L, Umeton R, Loda M. Rosenthal J, et al. Among authors: van allen em. Mol Cancer Res. 2022 Feb;20(2):202-206. doi: 10.1158/1541-7786.MCR-21-0665. Epub 2021 Dec 8. Mol Cancer Res. 2022. PMID: 34880124 Free PMC article.
Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib.
Wagle N, Grabiner BC, Van Allen EM, Hodis E, Jacobus S, Supko JG, Stewart M, Choueiri TK, Gandhi L, Cleary JM, Elfiky AA, Taplin ME, Stack EC, Signoretti S, Loda M, Shapiro GI, Sabatini DM, Lander ES, Gabriel SB, Kantoff PW, Garraway LA, Rosenberg JE. Wagle N, et al. Among authors: van allen em. Cancer Discov. 2014 May;4(5):546-53. doi: 10.1158/2159-8290.CD-13-0353. Epub 2014 Mar 13. Cancer Discov. 2014. PMID: 24625776 Free PMC article. Clinical Trial.
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.
Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Lohr JG, et al. Among authors: van allen em. Nat Biotechnol. 2014 May;32(5):479-84. doi: 10.1038/nbt.2892. Epub 2014 Apr 20. Nat Biotechnol. 2014. PMID: 24752078 Free PMC article.
Neoadjuvant-Intensive Androgen Deprivation Therapy Selects for Prostate Tumor Foci with Diverse Subclonal Oncogenic Alterations.
Sowalsky AG, Ye H, Bhasin M, Van Allen EM, Loda M, Lis RT, Montaser-Kouhsari L, Calagua C, Ma F, Russo JW, Schaefer RJ, Voznesensky OS, Zhang Z, Bubley GJ, Montgomery B, Mostaghel EA, Nelson PS, Taplin ME, Balk SP. Sowalsky AG, et al. Among authors: van allen em. Cancer Res. 2018 Aug 15;78(16):4716-4730. doi: 10.1158/0008-5472.CAN-18-0610. Epub 2018 Jun 19. Cancer Res. 2018. PMID: 29921690 Free PMC article.
Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites.
Nassar AH, Umeton R, Kim J, Lundgren K, Harshman L, Van Allen EM, Preston M, Dong F, Bellmunt J, Mouw KW, Choueiri TK, Sonpavde G, Kwiatkowski DJ. Nassar AH, et al. Among authors: van allen em. Clin Cancer Res. 2019 Apr 15;25(8):2458-2470. doi: 10.1158/1078-0432.CCR-18-3147. Epub 2018 Dec 28. Clin Cancer Res. 2019. PMID: 30593515
Genomic correlates of clinical outcome in advanced prostate cancer.
Abida W, Cyrta J, Heller G, Prandi D, Armenia J, Coleman I, Cieslik M, Benelli M, Robinson D, Van Allen EM, Sboner A, Fedrizzi T, Mosquera JM, Robinson BD, De Sarkar N, Kunju LP, Tomlins S, Wu YM, Nava Rodrigues D, Loda M, Gopalan A, Reuter VE, Pritchard CC, Mateo J, Bianchini D, Miranda S, Carreira S, Rescigno P, Filipenko J, Vinson J, Montgomery RB, Beltran H, Heath EI, Scher HI, Kantoff PW, Taplin ME, Schultz N, deBono JS, Demichelis F, Nelson PS, Rubin MA, Chinnaiyan AM, Sawyers CL. Abida W, et al. Among authors: van allen em. Proc Natl Acad Sci U S A. 2019 Jun 4;116(23):11428-11436. doi: 10.1073/pnas.1902651116. Epub 2019 May 6. Proc Natl Acad Sci U S A. 2019. PMID: 31061129 Free PMC article.
CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer.
Hwang JH, Seo JH, Beshiri ML, Wankowicz S, Liu D, Cheung A, Li J, Qiu X, Hong AL, Botta G, Golumb L, Richter C, So J, Sandoval GJ, Giacomelli AO, Ly SH, Han C, Dai C, Pakula H, Sheahan A, Piccioni F, Gjoerup O, Loda M, Sowalsky AG, Ellis L, Long H, Root DE, Kelly K, Van Allen EM, Freedman ML, Choudhury AD, Hahn WC. Hwang JH, et al. Among authors: van allen em. Cell Rep. 2019 Nov 19;29(8):2355-2370.e6. doi: 10.1016/j.celrep.2019.10.068. Cell Rep. 2019. PMID: 31747605 Free PMC article.
Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non-Small-Cell Lung Cancer.
Vokes NI, Liu D, Ricciuti B, Jimenez-Aguilar E, Rizvi H, Dietlein F, He MX, Margolis CA, Elmarakeby HA, Girshman J, Adeni A, Sanchez-Vega F, Schultz N, Dahlberg S, Zehir A, Jänne PA, Nishino M, Umeton R, Sholl LM, Van Allen EM, Hellmann MD, Awad MM. Vokes NI, et al. Among authors: van allen em. JCO Precis Oncol. 2019;3:PO.19.00171. doi: 10.1200/PO.19.00171. Epub 2019 Nov 12. JCO Precis Oncol. 2019. PMID: 31832578 Free PMC article.
Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer.
Barroso-Sousa R, Keenan TE, Pernas S, Exman P, Jain E, Garrido-Castro AC, Hughes M, Bychkovsky B, Umeton R, Files JL, Lindeman NI, MacConaill LE, Hodi FS, Krop IE, Dillon D, Winer EP, Wagle N, Lin NU, Mittendorf EA, Van Allen EM, Tolaney SM. Barroso-Sousa R, et al. Among authors: van allen em. Clin Cancer Res. 2020 Jun 1;26(11):2565-2572. doi: 10.1158/1078-0432.CCR-19-3507. Epub 2020 Feb 4. Clin Cancer Res. 2020. PMID: 32019858 Free PMC article.
286 results