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Unbiased pangenome graphs.
Garrison E, Guarracino A. Garrison E, et al. Among authors: guarracino a. Bioinformatics. 2023 Jan 1;39(1):btac743. doi: 10.1093/bioinformatics/btac743. Bioinformatics. 2023. PMID: 36448683 Free PMC article.
Optimal gap-affine alignment in O(s) space.
Marco-Sola S, Eizenga JM, Guarracino A, Paten B, Garrison E, Moreto M. Marco-Sola S, et al. Among authors: guarracino a. Bioinformatics. 2023 Feb 3;39(2):btad074. doi: 10.1093/bioinformatics/btad074. Bioinformatics. 2023. PMID: 36749013 Free PMC article.
Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C; Human Pangenome Reference Consortium; Korbel JO, Paten B, Marschall T, Eichler EE. Porubsky D, et al. Genome Res. 2023 Apr;33(4):496-510. doi: 10.1101/gr.277334.122. Epub 2023 May 10. Genome Res. 2023. PMID: 37164484 Free PMC article.
Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y; Human Pangenome Reference Consortium; Marschall T, Li H, Paten B. Hickey G, et al. Nat Biotechnol. 2024 Apr;42(4):663-673. doi: 10.1038/s41587-023-01793-w. Epub 2023 May 10. Nat Biotechnol. 2024. PMID: 37165083 Free PMC article.
Increased mutation and gene conversion within human segmental duplications.
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M; Human Pangenome Reference Consortium; Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE. Vollger MR, et al. Nature. 2023 May;617(7960):325-334. doi: 10.1038/s41586-023-05895-y. Epub 2023 May 10. Nature. 2023. PMID: 37165237 Free PMC article.
Impact of radiotherapy dose, fractionation and immunotherapeutic partner in a mouse model of HR+ mammary carcinogenesis.
Buqué A, Bloy N, Petroni G, Jiménez-Cortegana C, Sato A, Iribarren C, Yamazaki T, Galassi C, Hensler M, Bhinder B, Guarracino A, Rippon B, Beltran-Visiedo M, Soler-Agesta R, Pannellini T, Fucikova J, Demaria S, Zhou XK, Elemento O, Formenti SC, Galluzzi L. Buqué A, et al. Among authors: guarracino a. J Natl Cancer Inst. 2024 Dec 11:djae329. doi: 10.1093/jnci/djae329. Online ahead of print. J Natl Cancer Inst. 2024. PMID: 39661487
Considerations in the search for epistasis.
Balvert M, Cooper-Knock J, Stamp J, Byrne RP, Mourragui S, van Gils J, Benonisdottir S, Schlüter J, Kenna K, Abeln S, Iacoangeli A, Daub JT, Browning BL, Taş G, Hu J, Wang Y, Alhathli E, Harvey C, Pianesi L, Schulte SC, González-Domínguez J, Garrisson E; Lorentz workshop on epistasis; Snyder MP, Schönhuth A, Sng LMF, Twine NA. Balvert M, et al. Genome Biol. 2024 Nov 19;25(1):296. doi: 10.1186/s13059-024-03427-z. Genome Biol. 2024. PMID: 39563431 Free PMC article. Review.
49 results