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Page 1
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler E, Phillippy AM. Makova KD, et al. Among authors: lewis ap. bioRxiv [Preprint]. 2023 Dec 1:2023.11.30.569198. doi: 10.1101/2023.11.30.569198. bioRxiv. 2023. Update in: Nature. 2024 Jun;630(8016):401-411. doi: 10.1038/s41586-024-07473-2 PMID: 38077089 Free PMC article. Updated. Preprint.
Noninvasive whole-genome sequencing of a human fetus.
Kitzman JO, Snyder MW, Ventura M, Lewis AP, Qiu R, Simmons LE, Gammill HS, Rubens CE, Santillan DA, Murray JC, Tabor HK, Bamshad MJ, Eichler EE, Shendure J. Kitzman JO, et al. Among authors: lewis ap. Sci Transl Med. 2012 Jun 6;4(137):137ra76. doi: 10.1126/scitranslmed.3004323. Sci Transl Med. 2012. PMID: 22674554 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: lewis ap. Science. 2019 Oct 18;366(6463):eaax2083. doi: 10.1126/science.aax2083. Science. 2019. PMID: 31624180 Free PMC article.
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Warren WC, et al. Among authors: lewis ap. Science. 2020 Dec 18;370(6523):eabc6617. doi: 10.1126/science.abc6617. Science. 2020. PMID: 33335035 Free PMC article.
Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Ebert P, et al. Among authors: lewis ap. Science. 2021 Apr 2;372(6537):eabf7117. doi: 10.1126/science.abf7117. Epub 2021 Feb 25. Science. 2021. PMID: 33632895 Free PMC article.
A high-quality bonobo genome refines the analysis of hominid evolution.
Mao Y, Catacchio CR, Hillier LW, Porubsky D, Li R, Sulovari A, Fernandes JD, Montinaro F, Gordon DS, Storer JM, Haukness M, Fiddes IT, Murali SC, Dishuck PC, Hsieh P, Harvey WT, Audano PA, Mercuri L, Piccolo I, Antonacci F, Munson KM, Lewis AP, Baker C, Underwood JG, Hoekzema K, Huang TH, Sorensen M, Walker JA, Hoffman J, Thibaud-Nissen F, Salama SR, Pang AWC, Lee J, Hastie AR, Paten B, Batzer MA, Diekhans M, Ventura M, Eichler EE. Mao Y, et al. Among authors: lewis ap. Nature. 2021 Jun;594(7861):77-81. doi: 10.1038/s41586-021-03519-x. Epub 2021 May 5. Nature. 2021. PMID: 33953399 Free PMC article.
Familial long-read sequencing increases yield of de novo mutations.
Noyes MD, Harvey WT, Porubsky D, Sulovari A, Li R, Rose NR, Audano PA, Munson KM, Lewis AP, Hoekzema K, Mantere T, Graves-Lindsay TA, Sanders AD, Goodwin S, Kramer M, Mokrab Y, Zody MC, Hoischen A, Korbel JO, McCombie WR, Eichler EE. Noyes MD, et al. Among authors: lewis ap. Am J Hum Genet. 2022 Apr 7;109(4):631-646. doi: 10.1016/j.ajhg.2022.02.014. Epub 2022 Mar 14. Am J Hum Genet. 2022. PMID: 35290762 Free PMC article.
Segmental duplications and their variation in a complete human genome.
Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AP, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga KH, Phillippy AM, Timp W, Ventura M, Eichler EE. Vollger MR, et al. Among authors: lewis ap. Science. 2022 Apr;376(6588):eabj6965. doi: 10.1126/science.abj6965. Epub 2022 Apr 1. Science. 2022. PMID: 35357917 Free PMC article.
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