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Genome Research|April 14, 2025
A Hitchhiker's Guide to long-read genomic analysisMedhat Mahmoud, Daniel P Agustinho, Fritz J SedlazeckGenome Biology|September 15, 2021
PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylationMedhat Mahmoud, Harshavardhan Doddapaneni, Winston Timp, et al.Genome Biology|October 5, 2023
Genomic variant benchmark: if you cannot measure it, you cannot improve itSina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, et al.Gigascience|September 25, 2021
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignmentYilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, et al.Nature Communications|March 15, 2022
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing dataYunxi Liu, Joshua Kearney, Medhat Mahmoud, et al.Biorxiv : the Preprint Server for Biology|September 14, 2021
Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing dataYunxi Liu, Joshua Kearney, Medhat Mahmoud, et al.Nature Methods|April 30, 2024
Unveiling microbial diversity: harnessing long-read sequencing technologyDaniel P Agustinho, Yilei Fu, Vipin K Menon, et al.Genome Biology|November 22, 2019
Structural variant calling: the long and the short of itMedhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, et al.Current Protocols in Human Genetics|November 20, 2019
Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinIONRoxanne R Zascavage, Courtney L Hall, Kelcie Thorson, et al.Nature Communications|June 22, 2024
MethPhaser: methylation-based long-read haplotype phasing of human genomesYilei Fu, Sergey Aganezov, Medhat Mahmoud, et al.Pageof 20