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Page 1
ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.
Martín R, Gaitán N, Jarlier F, Feuerbach L, de Soyres H, Arbonés M, Gutman T, Puiggròs M, Ferriz A, Gonzalez A, Estelles L, Gut I, Capella-Gutierrez S, Stein LD, Brors B, Royo R, Hupé P, Torrents D. Martín R, et al. Among authors: stein ld. Cell Genom. 2024 Sep 11;4(9):100639. doi: 10.1016/j.xgen.2024.100639. Epub 2024 Aug 30. Cell Genom. 2024. PMID: 39216474 Free PMC article.
Early rhombic lip Protogenin+ve stem cells in a human-specific neurovascular niche initiate and maintain group 3 medulloblastoma.
Visvanathan A, Saulnier O, Chen C, Haldipur P, Orisme W, Delaidelli A, Shin S, Millman J, Bryant A, Abeysundara N, Wu X, Hendrikse LD, Patil V, Bashardanesh Z, Golser J, Livingston BG, Nakashima T, Funakoshi Y, Ong W, Rasnitsyn A, Aldinger KA, Richman CM, Van Ommeren R, Lee JJY, Ly M, Vladoiu MC, Kharas K, Balin P, Erickson AW, Fong V, Zhang J, Suárez RA, Wang H, Huang N, Pallota JG, Douglas T, Haapasalo J, Razavi F, Silvestri E, Sirbu O, Worme S, Kameda-Smith MM, Wu X, Daniels C, MichaelRaj AK, Bhaduri A, Schramek D, Suzuki H, Garzia L, Ahmed N, Kleinman CL, Stein LD, Dirks P, Dunham C, Jabado N, Rich JN, Li W, Sorensen PH, Wechsler-Reya RJ, Weiss WA, Millen KJ, Ellison DW, Dimitrov DS, Taylor MD. Visvanathan A, et al. Among authors: stein ld. Cell. 2024 Aug 22;187(17):4733-4750.e26. doi: 10.1016/j.cell.2024.06.011. Epub 2024 Jul 5. Cell. 2024. PMID: 38971152 Free article.
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.
Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M; PCAWG Evolution and Heterogeneity Working Group; SMC-Het Participants; Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Salcedo A, et al. Nat Biotechnol. 2024 Jun 11. doi: 10.1038/s41587-024-02250-y. Online ahead of print. Nat Biotechnol. 2024. PMID: 38862616
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G. Orlic-Milacic M, et al. Among authors: stein ld. Database (Oxford). 2024 May 7;2024:baae031. doi: 10.1093/database/baae031. Database (Oxford). 2024. PMID: 38713862 Free PMC article.
Oncogenic ETS fusions promote DNA damage and proinflammatory responses via pericentromeric RNAs in extracellular vesicles.
Ruzanov P, Evdokimova V, Pachva MC, Minkovich A, Zhang Z, Langman S, Gassmann H, Thiel U, Orlic-Milacic M, Zaidi SH, Peltekova V, Heisler LE, Sharma M, Cox ME, McKee TD, Zaidi M, Lapouble E, McPherson JD, Delattre O, Radvanyi L, Burdach SE, Stein LD, Sorensen PH. Ruzanov P, et al. Among authors: stein ld. J Clin Invest. 2024 Mar 26;134(9):e169470. doi: 10.1172/JCI169470. J Clin Invest. 2024. PMID: 38530366 Free PMC article.
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie M, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G. Orlic-Milacic M, et al. Among authors: stein ld. bioRxiv [Preprint]. 2023 Oct 21:2023.10.18.562964. doi: 10.1101/2023.10.18.562964. bioRxiv. 2023. Update in: Database (Oxford). 2024 May 7;2024:baae031. doi: 10.1093/database/baae031 PMID: 37904913 Free PMC article. Updated. Preprint.
JBrowse 2: a modular genome browser with views of synteny and structural variation.
Diesh C, Stevens GJ, Xie P, De Jesus Martinez T, Hershberg EA, Leung A, Guo E, Dider S, Zhang J, Bridge C, Hogue G, Duncan A, Morgan M, Flores T, Bimber BN, Haw R, Cain S, Buels RM, Stein LD, Holmes IH. Diesh C, et al. Among authors: stein ld. Genome Biol. 2023 Apr 17;24(1):74. doi: 10.1186/s13059-023-02914-z. Genome Biol. 2023. PMID: 37069644 Free PMC article.
240 results