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Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter.
Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Baker GJ, et al. Among authors: vallius t. bioRxiv [Preprint]. 2024 Mar 22:2023.11.01.565120. doi: 10.1101/2023.11.01.565120. bioRxiv. 2024. Update in: Nat Methods. 2024 Dec;21(12):2248-2259. doi: 10.1038/s41592-024-02328-0 PMID: 37961235 Free PMC article. Updated. Preprint.
Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer.
Launonen IM, Erkan EP, Niemiec I, Junquera A, Hincapié-Otero M, Afenteva D, Liang Z, Salko M, Szabo A, Perez-Villatoro F, Falco MM, Li Y, Micoli G, Nagaraj A, Haltia UM, Kahelin E, Oikkonen J, Hynninen J, Virtanen A, Nirmal AJ, Vallius T, Hautaniemi S, Sorger P, Vähärautio A, Färkkilä A. Launonen IM, et al. Among authors: vallius t. bioRxiv [Preprint]. 2024 Mar 20:2024.03.19.585657. doi: 10.1101/2024.03.19.585657. bioRxiv. 2024. Update in: Cancer Cell. 2024 Dec 9;42(12):2045-2063.e10. doi: 10.1016/j.ccell.2024.11.005 PMID: 38562799 Free PMC article. Updated. Preprint.
Quality control for single-cell analysis of high-plex tissue profiles using CyLinter.
Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Baker GJ, et al. Among authors: vallius t. Nat Methods. 2024 Dec;21(12):2248-2259. doi: 10.1038/s41592-024-02328-0. Epub 2024 Oct 30. Nat Methods. 2024. PMID: 39478175 Free PMC article.
Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer.
Launonen IM, Niemiec I, Hincapié-Otero M, Erkan EP, Junquera A, Afenteva D, Falco MM, Liang Z, Salko M, Chamchougia F, Szabo A, Perez-Villatoro F, Li Y, Micoli G, Nagaraj A, Haltia UM, Kahelin E, Oikkonen J, Hynninen J, Virtanen A, Nirmal AJ, Vallius T, Hautaniemi S, Sorger PK, Vähärautio A, Färkkilä A. Launonen IM, et al. Among authors: vallius t. Cancer Cell. 2024 Dec 9;42(12):2045-2063.e10. doi: 10.1016/j.ccell.2024.11.005. Cancer Cell. 2024. PMID: 39658541 Free article.
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. Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. Nat Methods. 2022. PMID: 35277708 Free PMC article.
Clinical Efficacy and Molecular Response Correlates of the WEE1 Inhibitor Adavosertib Combined with Cisplatin in Patients with Metastatic Triple-Negative Breast Cancer.
Keenan TE, Li T, Vallius T, Guerriero JL, Tayob N, Kochupurakkal B, Davis J, Pastorello R, Tahara RK, Anderson L, Conway J, He MX, Shannon E, Godin RE, Sorger PK, D'Andrea A, Overmoyer B, Winer EP, Mittendorf EA, Van Allen EM, Shapiro GI, Tolaney SM. Keenan TE, et al. Among authors: vallius t. Clin Cancer Res. 2021 Feb 15;27(4):983-991. doi: 10.1158/1078-0432.CCR-20-3089. Epub 2020 Nov 30. Clin Cancer Res. 2021. PMID: 33257427 Free PMC article. Clinical Trial.
SpatialCells: Automated Profiling of Tumor Microenvironments with Spatially Resolved Multiplexed Single-Cell Data.
Wan G, Maliga Z, Yan B, Vallius T, Shi Y, Khattab S, Chang C, Nirmal AJ, Yu KH, Liu D, Lian CG, DeSimone MS, Sorger PK, Semenov YR. Wan G, et al. Among authors: vallius t. bioRxiv [Preprint]. 2023 Nov 14:2023.11.10.566378. doi: 10.1101/2023.11.10.566378. bioRxiv. 2023. Update in: Brief Bioinform. 2024 Mar 27;25(3):bbae189. doi: 10.1093/bib/bbae189 PMID: 38014067 Free PMC article. Updated. Preprint.
35 results