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Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.
Nat Genet. 2023 Dec;55(12):2189-2199. doi: 10.1038/s41588-023-01551-3. Epub 2023 Nov 9.
Nat Genet. 2023.
PMID: 37945900
Free PMC article.
Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector.
Haas BJ, Dobin A, Ghandi M, Van Arsdale A, Tickle T, Robinson JT, Gillani R, Kasif S, Regev A.
Haas BJ, et al.
Cell Rep Methods. 2023 May 8;3(5):100467. doi: 10.1016/j.crmeth.2023.100467. eCollection 2023 May 22.
Cell Rep Methods. 2023.
PMID: 37323575
Free PMC article.
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Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response.
Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H.
Pagadala M, et al.
Nat Commun. 2023 May 12;14(1):2744. doi: 10.1038/s41467-023-38271-5.
Nat Commun. 2023.
PMID: 37173324
Free PMC article.
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3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.
Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L.
Okonechnikov K, et al.
Nat Commun. 2023 Apr 21;14(1):2300. doi: 10.1038/s41467-023-38044-0.
Nat Commun. 2023.
PMID: 37085539
Free PMC article.
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igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV).
Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP.
Robinson JT, et al.
Bioinformatics. 2023 Jan 1;39(1):btac830. doi: 10.1093/bioinformatics/btac830.
Bioinformatics. 2023.
PMID: 36562559
Free PMC article.
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