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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.
Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Foox J, et al. Among authors: mahmoud m. Nat Biotechnol. 2021 Sep;39(9):1129-1140. doi: 10.1038/s41587-021-01049-5. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504351 Free PMC article.
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: mahmoud m. 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.
Structural variant calling: the long and the short of it.
Mahmoud M, Gobet N, Cruz-Dávalos DI, Mounier N, Dessimoz C, Sedlazeck FJ. Mahmoud M, et al. Genome Biol. 2019 Nov 20;20(1):246. doi: 10.1186/s13059-019-1828-7. Genome Biol. 2019. PMID: 31747936 Free PMC article. Review.
Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.
Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IM, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck F, Treangen TJ. Sapoval N, et al. Among authors: mahmoud m. bioRxiv [Preprint]. 2020 Jul 2:2020.07.02.184481. doi: 10.1101/2020.07.02.184481. bioRxiv. 2020. Update in: Genome Res. 2021 Apr;31(4):635-644. doi: 10.1101/gr.268961.120 PMID: 32637955 Free PMC article. Updated. Preprint.
Chromosome-scale, haplotype-resolved assembly of human genomes.
Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H. Garg S, et al. Among authors: mahmoud m. Nat Biotechnol. 2021 Mar;39(3):309-312. doi: 10.1038/s41587-020-0711-0. Epub 2020 Dec 7. Nat Biotechnol. 2021. PMID: 33288905 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: mahmoud m. Gigascience. 2020 Dec 21;9(12):giaa145. doi: 10.1093/gigascience/giaa145. Gigascience. 2020. PMID: 33347570 Free PMC article.
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.
Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. Sapoval N, et al. Among authors: mahmoud m. Genome Res. 2021 Apr;31(4):635-644. doi: 10.1101/gr.268961.120. Epub 2021 Feb 18. Genome Res. 2021. PMID: 33602693 Free PMC article.
A strategy for building and using a human reference pangenome.
Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B. Llamas B, et al. Among authors: mahmoud m. F1000Res. 2019 Oct 14;8:1751. doi: 10.12688/f1000research.19630.2. eCollection 2019. F1000Res. 2019. PMID: 34386196 Free PMC article.
2,145 results