Publications

Filters: Author is Mahmoud, Medhat  [Clear All Filters]
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Mahmoud M, Doddapaneni H, Timp W, Sedlazeck FJ. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 ;22(1):268.
Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Publisher Correction: Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol. 2024 ;.
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Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data. bioRxiv. 2021 ;.
Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nat Commun. 2022 ;13(1):1321.
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Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RALeo, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Berry IMaljkovic, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021 ;31(4):635-644.
Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin C-S, 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. A strategy for building and using a human reference pangenome. F1000Res. 2019 ;8:1751.
Mahmoud M, Gobet N, Cruz-Dávalos DIvette, Mounier N, Dessimoz C, Sedlazeck FJ. Structural variant calling: the long and the short of it. Genome Biol. 2019 ;20(1):246.
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Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AAl, Mahmoud M, Paulin LF, Raza MSohail, Pfeifer SP, Agustinho DPaiva, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LChuin, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DMorgan, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRohit Raj, Kubica J, Lakra P, Lattimer D, Liew C-S, Lo B-W, Lo C, Lötter A, Majidian S, Mendem SKumar, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon C-L, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res. 2022 ;11:530.
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Fu Y, Mahmoud M, Muraliraman VVaibhav, Sedlazeck FJ, Treangen TJ. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 2021 ;10(9).