Publications
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Filters: Author is Mahmoud, Medhat [Clear All Filters]
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 2021 ;10(9).
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Structural variant calling: the long and the short of it. Genome Biol. 2019 ;20(1):246.
. A strategy for building and using a human reference pangenome. F1000Res. 2019 ;8:1751.
. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021 ;31(4):635-644.
. Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data. bioRxiv. 2021 ;.
. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nat Commun. 2022 ;13(1):1321.
. Publisher Correction: Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol. 2024 ;.
. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 ;22(1):268.
. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol. 2021 ;39(9):1129-1140.
. Parliament2: Accurate structural variant calling at scale. Gigascience. 2020 ;9(12).
. Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism. Hum Mutat. 2022 ;43(12):2033-2053.
. Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration. Cancer Discov. 2023 ;13(4):910-927.
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Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biol. 2023 ;24(1):221.
. Genome-Wide Analysis of Structural Variants in Parkinson Disease. Ann Neurol. 2023 ;93(5):1012-1022.
. Fully resolved assembly of Cryptosporidium parvum. Gigascience. 2022 ;11.
. Fully resolved assembly of Cryptosporidium parvum. Gigascience. 2022 ;11.
. FixItFelix: improving genomic analysis by fixing reference errors. Genome Biol. 2023 ;24(1):31.
. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol. 2024 ;.
. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol. 2022 ;40(5):672-680.
. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience. 2022 ;11.
. Closing the gap: Solving complex medically relevant genes at scale. medRxiv. 2024 ;.
. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. 2021 ;39(3):309-312.
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