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Multiplexed 3D Analysis of Immune States and Niches in Human Tissue.
Yapp C, Nirmal AJ, Zhou F, Maliga Z, Tefft JB, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK; Human Tumour Atlas Network. Yapp C, et al. bioRxiv [Preprint]. 2024 Mar 28:2023.11.10.566670. doi: 10.1101/2023.11.10.566670. bioRxiv. 2024. PMID: 38014052 Free PMC article. Preprint.
Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment.
Hodis E, Torlai Triglia E, Kwon JYH, Biancalani T, Zakka LR, Parkar S, Hütter JC, Buffoni L, Delorey TM, Phillips D, Dionne D, Nguyen LT, Schapiro D, Maliga Z, Jacobson CA, Hendel A, Rozenblatt-Rosen O, Mihm MC Jr, Garraway LA, Regev A. Hodis E, et al. Science. 2022 Apr 29;376(6592):eabi8175. doi: 10.1126/science.abi8175. Epub 2022 Apr 29. Science. 2022. PMID: 35482859 Free PMC article.
Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer.
Launonen IM, Lyytikäinen N, Casado J, Anttila EA, Szabó A, Haltia UM, Jacobson CA, Lin JR, Maliga Z, Howitt BE, Strickland KC, Santagata S, Elias K, D'Andrea AD, Konstantinopoulos PA, Sorger PK, Färkkilä A. Launonen IM, et al. Nat Commun. 2022 Feb 11;13(1):835. doi: 10.1038/s41467-022-28389-3. Nat Commun. 2022. PMID: 35149709 Free PMC article.
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. Schapiro D, et al. Nat Methods. 2022 Mar;19(3):311-315. doi: 10.1038/s41592-021-01308-y. Epub 2021 Nov 25. Nat Methods. 2022. PMID: 34824477 Free PMC article.