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Fragmentomic analysis of circulating tumor DNA-targeted cancer panels.
Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM, Bassetti M, Blitzer G, Floberg J, Sjöström M, Quigley DA, Dehm SM, Armstrong AJ, Beltran H, McKay RR, Feng FY, O'Regan R, Wisinski KB, Emamekhoo H, Wyatt AW, Lang JM, Zhao SG. Helzer KT, et al. Ann Oncol. 2023 Sep;34(9):813-825. doi: 10.1016/j.annonc.2023.06.001. Epub 2023 Jun 16. Ann Oncol. 2023. PMID: 37330052 Free PMC article.
The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. Sjöström M, et al. Cancer Res. 2022 Nov 2;82(21):3888-3902. doi: 10.1158/0008-5472.CAN-22-1123. Cancer Res. 2022. PMID: 36251389 Free PMC article.
Machine Learning & Molecular Radiation Tumor Biomarkers.
Rydzewski NR, Helzer KT, Bootsma M, Shi Y, Bakhtiar H, Sjöström M, Zhao SG. Rydzewski NR, et al. Semin Radiat Oncol. 2023 Jul;33(3):243-251. doi: 10.1016/j.semradonc.2023.03.002. Semin Radiat Oncol. 2023. PMID: 37331779 Free PMC article. Review.
Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer.
Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y; West Coast Dream Team Consortium; Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA, Lupien M, Feng FY. Zhao SG, et al. Nat Genet. 2024 Aug;56(8):1689-1700. doi: 10.1038/s41588-024-01826-3. Epub 2024 Jul 17. Nat Genet. 2024. PMID: 39020220 Free PMC article.
Clinical cell-surface targets in metastatic and primary solid cancers.
Sharifi MN, Shi Y, Chrostek MR, Callahan SC, Shang T, Berg TJ, Helzer KT, Bootsma ML, Sjöström M, Josefsson A, Feng FY, Huffman LB, Schulte C, Blitzer GC, Sodji QH, Morris ZS, Ma VT, Meimetis L, Kosoff D, Taylor AK, LeBeau AM, Lang JM, Zhao SG. Sharifi MN, et al. JCI Insight. 2024 Sep 24;9(18):e183674. doi: 10.1172/jci.insight.183674. JCI Insight. 2024. PMID: 39315546 Free PMC article.
Predicting dose response to prostate cancer radiotherapy: validation of a radiation signature in the randomized phase III NRG/RTOG 0126 and SAKK 09/10 trials.
Dal Pra A, Ghadjar P, Ryu HM, Proudfoot JA, Hayoz S, Michalski JM, Spratt DE, Liu Y, Schär C, Berlin AM, Zwahlen DR, Simko JP, Hölscher T, Efstathiou JA, Polat B, Sandler HM, Hildebrandt G, Parliament MB, Mueller AC, Dayes IS, Plasswilm L, Correa RJM, Robertson JM, Karrison TG, Davicioni E, Hall WA, Feng FY, Pollack A, Thalmann GN, Nguyen PL, Aebersold DM, Tran PT, Zhao SG. Dal Pra A, et al. Ann Oncol. 2025 May;36(5):572-582. doi: 10.1016/j.annonc.2025.01.017. Epub 2025 Feb 13. Ann Oncol. 2025. PMID: 39986927 Free article. Clinical Trial.
Longitudinal Molecular Profiling of Circulating Tumor Cells in Metastatic Renal Cell Carcinoma.
Bootsma M, McKay RR, Emamekhoo H, Bade RM, Schehr JL, Mannino MC, Singh A, Wolfe SK, Schultz ZD, Sperger J, Xie W, Signoretti S, Kyriakopoulos CE, Kosoff D, Abel EJ, Helzer KT, Rydzewski N, Bakhtiar H, Shi Y, Blitzer G, Bassetti M, Floberg J, Yu M, Sethakorn N, Sharifi M, Harari PM, Choueiri TK, Lang JM, Zhao SG. Bootsma M, et al. J Clin Oncol. 2022 Nov 1;40(31):3633-3641. doi: 10.1200/JCO.22.00219. Epub 2022 May 26. J Clin Oncol. 2022. PMID: 35617646 Free PMC article.