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Page 1
The variation and evolution of complete human centromeres.
Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Mao Y, Rautiainen M, Koren S, Nurk S, Porubsky D, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Alexandrov IA, Eichler EE. Logsdon GA, et al. Among authors: porubsky d. bioRxiv [Preprint]. 2023 May 30:2023.05.30.542849. doi: 10.1101/2023.05.30.542849. bioRxiv. 2023. Update in: Nature. 2024 May;629(8010):136-145. doi: 10.1038/s41586-024-07278-3 PMID: 37398417 Free PMC article. Updated. Preprint.
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Chaisson MJP, et al. Among authors: porubsky d. Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z. Nat Commun. 2019. PMID: 30992455 Free PMC article.
Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes.
Hsieh P, Vollger MR, Dang V, Porubsky D, Baker C, Cantsilieris S, Hoekzema K, Lewis AP, Munson KM, Sorensen M, Kronenberg ZN, Murali S, Nelson BJ, Chiatante G, Maggiolini FAM, Blanché H, Underwood JG, Antonacci F, Deleuze JF, Eichler EE. Hsieh P, et al. Among authors: porubsky d. Science. 2019 Oct 18;366(6463):eaax2083. doi: 10.1126/science.aax2083. Science. 2019. PMID: 31624180 Free PMC article.
Human-specific tandem repeat expansion and differential gene expression during primate evolution.
Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA; Human Genome Structural Variation Consortium; Warren WC, Pollen AA, Chaisson MJP, Eichler EE. Sulovari A, et al. Among authors: porubsky d. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23243-23253. doi: 10.1073/pnas.1912175116. Epub 2019 Oct 28. Proc Natl Acad Sci U S A. 2019. PMID: 31659027 Free PMC article.
Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads.
Vollger MR, Logsdon GA, Audano PA, Sulovari A, Porubsky D, Peluso P, Wenger AM, Concepcion GT, Kronenberg ZN, Munson KM, Baker C, Sanders AD, Spierings DCJ, Lansdorp PM, Surti U, Hunkapiller MW, Eichler EE. Vollger MR, et al. Among authors: porubsky d. Ann Hum Genet. 2020 Mar;84(2):125-140. doi: 10.1111/ahg.12364. Epub 2019 Nov 11. Ann Hum Genet. 2020. PMID: 31711268 Free PMC article.
Recurrent inversion toggling and great ape genome evolution.
Porubsky D, Sanders AD, Höps W, Hsieh P, Sulovari A, Li R, Mercuri L, Sorensen M, Murali SC, Gordon D, Cantsilieris S, Pollen AA, Ventura M, Antonacci F, Marschall T, Korbel JO, Eichler EE. Porubsky D, et al. Nat Genet. 2020 Aug;52(8):849-858. doi: 10.1038/s41588-020-0646-x. Epub 2020 Jun 15. Nat Genet. 2020. PMID: 32541924 Free PMC article.
Telomere-to-telomere assembly of a complete human X chromosome.
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM. Miga KH, et al. Among authors: porubsky d. Nature. 2020 Sep;585(7823):79-84. doi: 10.1038/s41586-020-2547-7. Epub 2020 Jul 14. Nature. 2020. PMID: 32663838 Free PMC article.
Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.
Maggiolini FAM, Sanders AD, Shew CJ, Sulovari A, Mao Y, Puig M, Catacchio CR, Dellino M, Palmisano D, Mercuri L, Bitonto M, Porubský D, Cáceres M, Eichler EE, Ventura M, Dennis MY, Korbel JO, Antonacci F. Maggiolini FAM, et al. Among authors: porubsky d. Genome Res. 2020 Nov;30(11):1680-1693. doi: 10.1101/gr.265322.120. Epub 2020 Oct 22. Genome Res. 2020. PMID: 33093070 Free PMC article.
68 results