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MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA; Human Tumor Atlas Network; Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. Schapiro D, et al. Among authors: xie y. Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. Nat Methods. 2022. PMID: 35277708 Free PMC article.
Regenerative lineages and immune-mediated pruning in lung cancer metastasis.
Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y, Masilionis I, Carr AJ, Kottapalli S, Allaj V, Mattar M, Rekhtman N, Xavier JB, Mazutis L, Poirier JT, Rudin CM, Pe'er D, Massagué J. Laughney AM, et al. Among authors: xie y. Nat Med. 2020 Feb;26(2):259-269. doi: 10.1038/s41591-019-0750-6. Epub 2020 Feb 10. Nat Med. 2020. PMID: 32042191 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.
Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer.
Chan JM, Quintanal-Villalonga Á, Gao VR, Xie Y, Allaj V, Chaudhary O, Masilionis I, Egger J, Chow A, Walle T, Mattar M, Yarlagadda DVK, Wang JL, Uddin F, Offin M, Ciampricotti M, Qeriqi B, Bahr A, de Stanchina E, Bhanot UK, Lai WV, Bott MJ, Jones DR, Ruiz A, Baine MK, Li Y, Rekhtman N, Poirier JT, Nawy T, Sen T, Mazutis L, Hollmann TJ, Pe'er D, Rudin CM. Chan JM, et al. Among authors: xie y. Cancer Cell. 2021 Nov 8;39(11):1479-1496.e18. doi: 10.1016/j.ccell.2021.09.008. Epub 2021 Oct 14. Cancer Cell. 2021. PMID: 34653364 Free PMC article.
Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis.
Burdziak C, Alonso-Curbelo D, Walle T, Reyes J, Barriga FM, Haviv D, Xie Y, Zhao Z, Zhao CJ, Chen HA, Chaudhary O, Masilionis I, Choo ZN, Gao V, Luan W, Wuest A, Ho YJ, Wei Y, Quail DF, Koche R, Mazutis L, Chaligné R, Nawy T, Lowe SW, Pe'er D. Burdziak C, et al. Among authors: xie y. Science. 2023 May 12;380(6645):eadd5327. doi: 10.1126/science.add5327. Epub 2023 May 12. Science. 2023. PMID: 37167403 Free PMC article.
The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1.
Romero R, Chu T, González-Robles TJ, Smith P, Xie Y, Kaur H, Yoder S, Zhao H, Mao C, Kang W, Pulina MV, Lawrence KE, Gopalan A, Zaidi S, Yoo K, Choi J, Fan N, Gerstner O, Karthaus WR, DeStanchina E, Ruggles KV, Westcott PMK, Chaligné R, Pe'er D, Sawyers CL. Romero R, et al. Among authors: xie y. bioRxiv [Preprint]. 2024 Apr 11:2024.04.09.588557. doi: 10.1101/2024.04.09.588557. bioRxiv. 2024. PMID: 38645223 Free PMC article. Preprint.
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