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2006 2
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75 results

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Page 1
Building pangenome graphs.
Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Golicz AA, Nahnsen S, Yang Z, Mwaniki MN, Nobrega FL, Wu Y, Chen H, de Ligt J, Sudmant PH, Huang S, Weigel D, Soranzo N, Colonna V, Williams RW, Prins P. Garrison E, et al. Among authors: prins p. Nat Methods. 2024 Nov;21(11):2008-2012. doi: 10.1038/s41592-024-02430-3. Epub 2024 Oct 21. Nat Methods. 2024. PMID: 39433878
A draft human pangenome reference.
Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichl… See abstract for full author list ➔ Liao WW, et al. Among authors: prins p. Nature. 2023 May;617(7960):312-324. doi: 10.1038/s41586-023-05896-x. Epub 2023 May 10. Nature. 2023. PMID: 37165242 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.
Tissue-specific mutation accumulation in human adult stem cells during life.
Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EE, Verstegen MM, van der Laan LJ, de Jonge J, IJzermans JN, Vries RG, van de Wetering M, Stratton MR, Clevers H, Cuppen E, van Boxtel R. Blokzijl F, et al. Among authors: prins p. Nature. 2016 Oct 13;538(7624):260-264. doi: 10.1038/nature19768. Epub 2016 Oct 3. Nature. 2016. PMID: 27698416 Free PMC article.
Building pangenome graphs.
Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Nahnsen S, Yang Z, Mwaniki MN, Nobrega FL, Wu Y, Chen H, de Ligt J, Sudmant PH, Soranzo N, Colonna V, Williams RW, Prins P. Garrison E, et al. Among authors: prins p. bioRxiv [Preprint]. 2024 Oct 2:2023.04.05.535718. doi: 10.1101/2023.04.05.535718. bioRxiv. 2024. Update in: Nat Methods. 2024 Nov;21(11):2008-2012. doi: 10.1038/s41592-024-02430-3. PMID: 37066137 Free PMC article. Updated. Preprint.
Recombination between heterologous human acrocentric chromosomes.
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C; Human Pangenome Reference Consortium; Gerton JL, Phillippy AM, Colonna V, Garrison E. Guarracino A, et al. Nature. 2023 May;617(7960):335-343. doi: 10.1038/s41586-023-05976-y. Epub 2023 May 10. Nature. 2023. PMID: 37165241 Free PMC article.
ODGI: understanding pangenome graphs.
Guarracino A, Heumos S, Nahnsen S, Prins P, Garrison E. Guarracino A, et al. Among authors: prins p. Bioinformatics. 2022 Jun 27;38(13):3319-3326. doi: 10.1093/bioinformatics/btac308. Bioinformatics. 2022. PMID: 35552372 Free PMC article.
Ten simple rules to run a successful BioHackathon.
Garcia L, Antezana E, Garcia A, Bolton E, Jimenez R, Prins P, Banda JM, Katayama T. Garcia L, et al. Among authors: prins p. PLoS Comput Biol. 2020 May 7;16(5):e1007808. doi: 10.1371/journal.pcbi.1007808. eCollection 2020 May. PLoS Comput Biol. 2020. PMID: 32379758 Free PMC article. No abstract available.
Cluster-efficient pangenome graph construction with nf-core/pangenome.
Heumos S, Heuer ML, Hanssen F, Heumos L, Guarracino A, Heringer P, Ehmele P, Prins P, Garrison E, Nahnsen S. Heumos S, et al. Among authors: prins p. Bioinformatics. 2024 Nov 1;40(11):btae609. doi: 10.1093/bioinformatics/btae609. Bioinformatics. 2024. PMID: 39400346 Free PMC article.
Highlights from the Era of Open Source Web-Based Tools.
Anderson KR, Harris JA, Ng L, Prins P, Memar S, Ljungquist B, Fürth D, Williams RW, Ascoli GA, Dumitriu D. Anderson KR, et al. Among authors: prins p. J Neurosci. 2021 Feb 3;41(5):927-936. doi: 10.1523/JNEUROSCI.1657-20.2020. Epub 2021 Jan 20. J Neurosci. 2021. PMID: 33472826 Free PMC article. Review.
75 results