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A deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for accurate analysis of cell type ratios in complex tissue samples.
Guo S, Liu X, Cheng X, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Lee S, Sood AK, Kopetz S, Shen JP, Weinstein JN, DeAngelis MM, Chen R, Wang W. Guo S, et al. Among authors: shen jp. Genome Res. 2024 Nov 25:gr.278822.123. doi: 10.1101/gr.278822.123. Online ahead of print. Genome Res. 2024. PMID: 39586714
Molecular and Clinical Features of Pancreatic Acinar Cell Carcinoma: A Single-Institution Case Series.
Balachandran Pillai A, Yousef M, Yousef A, Alfaro-Munoz KD, Smaglo BG, Willis J, Wolff RA, Pant S, Hurd MW, Maitra A, Wang H, Katz MHG, Prakash LR, Tzeng CD, Snyder R, Castelnovo LF, Chen A, Kravets A, Kudriavtseva K, Tarasov A, Kryukov K, Ying H, Shen JP, Zhao D. Balachandran Pillai A, et al. Among authors: shen jp. Cancers (Basel). 2024 Oct 9;16(19):3421. doi: 10.3390/cancers16193421. Cancers (Basel). 2024. PMID: 39410042 Free PMC article.
Molecular, Socioeconomic, and Clinical Factors Affecting Racial and Ethnic Disparities in Colorectal Cancer Survival.
Yousef M, Yousef A, Chowdhury S, Fanaeian MM, Knafl M, Peterson J, Zeineddine M, Alfaro K, Zeineddine F, Goldstein D, Hornstein N, Dasari A, Huey R, Johnson B, Higbie V, Bent A, Kee B, Lee M, Morelli MP, Morris VK, Halperin D, Overman MJ, Parseghian C, Vilar E, Wolff R, Raghav KP, White MG, Uppal A, Sun R, Wang W, Kopetz S, Willis J, Shen JP. Yousef M, et al. Among authors: shen jp. JAMA Oncol. 2024 Nov 1;10(11):1519-1529. doi: 10.1001/jamaoncol.2024.3666. JAMA Oncol. 2024. PMID: 39264607
Consensus molecular subtyping of metastatic colorectal cancer expands biomarker-directed therapeutic benefit for patients with CMS1 and CMS2 tumors.
Chowdhury S, Xiu J, Ribeiro JR, Nicolaides T, Zhang J, Korn WM, Poorman KA, Lenz HJ, Marshall JL, Oberley MJ, Sledge GW Jr, Spetzler D, Kopetz S, Shen JP. Chowdhury S, et al. Among authors: shen jp. Br J Cancer. 2024 Nov;131(8):1328-1339. doi: 10.1038/s41416-024-02826-0. Epub 2024 Sep 4. Br J Cancer. 2024. PMID: 39227409
Clinical and molecular characteristics of patients with brain metastasis secondary to pancreatic ductal adenocarcinoma.
Yousef M, Hurd MW, Yousef A, Ludmir EB, Pillai AB, Peterson J, Koay EJ, Albarouki S, Tzeng CW, Snyder R, Katz MHG, Wang H, Overman MJ, Maitra A, Pant S, Smaglo BG, Wolff RA, Yao J, Shen JP, Zhao D. Yousef M, et al. Among authors: shen jp. Oncologist. 2024 Jul 16:oyae182. doi: 10.1093/oncolo/oyae182. Online ahead of print. Oncologist. 2024. PMID: 39014543 Free article.
Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome.
Jiang Y, Montierth MD, Yu K, Ji S, Guo S, Tran Q, Liu X, Shin SJ, Cao S, Li R, Tang Y, Lesluyes T, Kopetz S, Ajani J, Msaouel P, Subudhi SK, Aparicio A, Sharma P, Shen JP, Sood AK, Tarabichi M, Wang JR, Kimmel M, Loo PV, Zhu H, Wang W. Jiang Y, et al. Among authors: shen jp. bioRxiv [Preprint]. 2024 Jul 5:2024.07.03.601939. doi: 10.1101/2024.07.03.601939. bioRxiv. 2024. PMID: 39005348 Free PMC article. Preprint.
Defining the KRAS- and ERK-dependent transcriptome in KRAS-mutant cancers.
Klomp JA, Klomp JE, Stalnecker CA, Bryant KL, Edwards AC, Drizyte-Miller K, Hibshman PS, Diehl JN, Lee YS, Morales AJ, Taylor KE, Peng S, Tran NL, Herring LE, Prevatte AW, Barker NK, Hover LD, Hallin J, Sorokin A, Kanikarla PM, Chowdhury S, Coker O, Lee HM, Goodwin CM, Gautam P, Olson P, Christensen JG, Shen JP, Kopetz S, Graves LM, Lim KH, Wang-Gillam A, Wennerberg K, Cox AD, Der CJ. Klomp JA, et al. Among authors: shen jp. Science. 2024 Jun 7;384(6700):eadk0775. doi: 10.1126/science.adk0775. Epub 2024 Jun 7. Science. 2024. PMID: 38843331 Free PMC article.
186 results