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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: carroll a. 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.
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. Wenger AM, et al. Among authors: carroll a. Nat Biotechnol. 2019 Oct;37(10):1155-1162. doi: 10.1038/s41587-019-0217-9. Epub 2019 Aug 12. Nat Biotechnol. 2019. PMID: 31406327 Free PMC article.
A robust benchmark for detection of germline large deletions and insertions.
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. Zook JM, et al. Among authors: carroll a. Nat Biotechnol. 2020 Nov;38(11):1347-1355. doi: 10.1038/s41587-020-0538-8. Epub 2020 Jun 15. Nat Biotechnol. 2020. PMID: 32541955 Free PMC article.
A diploid assembly-based benchmark for variants in the major histocompatibility complex.
Chin CS, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazeck FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AM, Salit M, Marschall T, Dilthey AT, Zook JM. Chin CS, et al. Among authors: carroll a. Nat Commun. 2020 Sep 22;11(1):4794. doi: 10.1038/s41467-020-18564-9. Nat Commun. 2020. PMID: 32963235 Free PMC article.
Parliament2: Accurate structural variant calling at scale.
Zarate S, Carroll A, Mahmoud M, Krasheninina O, Jun G, Salerno WJ, Schatz MC, Boerwinkle E, Gibbs RA, Sedlazeck FJ. Zarate S, et al. Among authors: carroll a. Gigascience. 2020 Dec 21;9(12):giaa145. doi: 10.1093/gigascience/giaa145. Gigascience. 2020. PMID: 33347570 Free PMC article.
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, Rich SS, Rotter JI, Haussler D, Garrison E, Paten B. Sirén J, et al. Among authors: carroll a. Science. 2021 Dec 17;374(6574):abg8871. doi: 10.1126/science.abg8871. Epub 2021 Dec 17. Science. 2021. PMID: 34914532 Free PMC article.
A complete pedigree-based graph workflow for rare candidate variant analysis.
Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B. Markello C, et al. Among authors: carroll a. Genome Res. 2022 May;32(5):893-903. doi: 10.1101/gr.276387.121. Epub 2022 Apr 28. Genome Res. 2022. PMID: 35483961 Free PMC article.
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.
Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, McLean CY, Nattestad M, Chang PC, Carroll A. Baid G, et al. Among authors: carroll a. Nat Biotechnol. 2023 Feb;41(2):232-238. doi: 10.1038/s41587-022-01435-7. Epub 2022 Sep 1. Nat Biotechnol. 2023. PMID: 36050551
1,715 results