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Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes.
Zaitsev A, Chelushkin M, Dyikanov D, Cheremushkin I, Shpak B, Nomie K, Zyrin V, Nuzhdina E, Lozinsky Y, Zotova A, Degryse S, Kotlov N, Baisangurov A, Shatsky V, Afenteva D, Kuznetsov A, Paul SR, Davies DL, Reeves PM, Lanuti M, Goldberg MF, Tazearslan C, Chasse M, Wang I, Abdou M, Aslanian SM, Andrewes S, Hsieh JJ, Ramachandran A, Lyu Y, Galkin I, Svekolkin V, Cerchietti L, Poznansky MC, Ataullakhanov R, Fowler N, Bagaev A. Zaitsev A, et al. Among authors: hsieh jj. Cancer Cell. 2022 Aug 8;40(8):879-894.e16. doi: 10.1016/j.ccell.2022.07.006. Cancer Cell. 2022. PMID: 35944503 Free article.
Single-cell Spatial Proteomic Revelations on the Multiparametric MRI Heterogeneity of Clinically Significant Prostate Cancer.
Pachynski RK, Kim EH, Miheecheva N, Kotlov N, Ramachandran A, Postovalova E, Galkin I, Svekolkin V, Lyu Y, Zou Q, Cao D, Gaut J, Ippolito JE, Bagaev A, Bruttan M, Gancharova O, Nomie K, Tsiper M, Andriole GL, Ataullakhanov R, Hsieh JJ. Pachynski RK, et al. Among authors: hsieh jj. Clin Cancer Res. 2021 Jun 15;27(12):3478-3490. doi: 10.1158/1078-0432.CCR-20-4217. Epub 2021 Mar 26. Clin Cancer Res. 2021. PMID: 33771855
Multiregional single-cell proteogenomic analysis of ccRCC reveals cytokine drivers of intratumor spatial heterogeneity.
Miheecheva N, Postovalova E, Lyu Y, Ramachandran A, Bagaev A, Svekolkin V, Galkin I, Zyrin V, Maximov V, Lozinsky Y, Isaev S, Ovcharov P, Shamsutdinova D, Cheng EH, Nomie K, Brown JH, Tsiper M, Ataullakhanov R, Fowler N, Hsieh JJ. Miheecheva N, et al. Among authors: hsieh jj. Cell Rep. 2022 Aug 16;40(7):111180. doi: 10.1016/j.celrep.2022.111180. Cell Rep. 2022. PMID: 35977503 Free article.
The somatic genomic landscape of chromophobe renal cell carcinoma.
Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network; Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. Davis CF, et al. Among authors: hsieh jj. Cancer Cell. 2014 Sep 8;26(3):319-330. doi: 10.1016/j.ccr.2014.07.014. Epub 2014 Aug 21. Cancer Cell. 2014. PMID: 25155756 Free PMC article.
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.
Şenbabaoğlu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA. Şenbabaoğlu Y, et al. Among authors: hsieh jj. Genome Biol. 2016 Nov 17;17(1):231. doi: 10.1186/s13059-016-1092-z. Genome Biol. 2016. PMID: 27855702 Free PMC article.
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH; Human Tumor Atlas Network. Rozenblatt-Rosen O, et al. Cell. 2020 Apr 16;181(2):236-249. doi: 10.1016/j.cell.2020.03.053. Cell. 2020. PMID: 32302568 Free PMC article. Review.
Targeting Aurora B kinase prevents and overcomes resistance to EGFR inhibitors in lung cancer by enhancing BIM- and PUMA-mediated apoptosis.
Tanaka K, Yu HA, Yang S, Han S, Selcuklu SD, Kim K, Ramani S, Ganesan YT, Moyer A, Sinha S, Xie Y, Ishizawa K, Osmanbeyoglu HU, Lyu Y, Roper N, Guha U, Rudin CM, Kris MG, Hsieh JJ, Cheng EH. Tanaka K, et al. Among authors: hsieh jj. Cancer Cell. 2021 Sep 13;39(9):1245-1261.e6. doi: 10.1016/j.ccell.2021.07.006. Epub 2021 Aug 12. Cancer Cell. 2021. PMID: 34388376 Free PMC article.
230 results