Medhat Mahmoud

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

MethPhaser: methylation-based haplotype phasing of human genomes

MethPhaser improves haplotype phasing by using methylation signals from Oxford Nanopore data, increasing phase length N50 by 3-fold with minimal error increase.

Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions

The paper investigates how different genome references affect inversion detection, showing that T2T-CHM13 and long-read sequencing improve resolution of challenging inversions.

Closing the gap: Solving complex medically relevant genes at scale

The paper introduces a targeted sequencing framework, TADGP, that accurately calls variants in complex medically relevant genes at lower cost than HiFi-WGS, enabling scalable analysis of dark genomic regions.

Utility of long-read sequencing for All of Us

The paper compares short-read and long-read sequencing in the All of Us initiative, finding HiFi reads provide the most accurate variant calling and presents a cloud-based pipeline for long-read analysis.

Comprehensive Structural Variant Detection: From Mosaic to Population-Level

Sniffles2 improves SV detection accuracy and speed, enabling mosaic and population-level SV calling with applications in neurological disorders.

Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

Genome-wide analysis of Structural Variants in Parkinson's Disease using Short-Read Sequencing data

This study identifies 3,154 high-confidence structural variants in Parkinson's disease using short-read sequencing and validates some with long-read data, highlighting limitations of short-read methods.

Fixing reference errors efficiently improves sequencing results

The paper introduces FixItFelix and a modified GRCh38 reference to improve variant calling and expression analysis in genes with reference errors, showing benefits across multiple sequencing types and populations.

Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data

Variabel identifies low frequency intra-host variants from Oxford Nanopore sequencing data, outperforming existing tools for this task.

Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus

The paper presents an improved chromosome-scale genome assembly for the Syrian hamster using long-read sequencing, resulting in higher continuity and gene annotation accuracy.

Fully resolved assembly of Cryptosporidium parvum

The paper presents a high-quality, complete reference genome for Cryptosporidium parvum using Oxford Nanopore and Illumina reads, enabling comprehensive genomic studies.

Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment

Vulcan improves long-read mapping and structural variant calling by using dual-mode alignment, enhancing accuracy for Oxford Nanopore Technology reads.

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

This study analyzes over 7,000 SARS-CoV-2 datasets to reveal genomic diversity, showing iSNVs and small indels drive variation, and highlights implications for qRT-PCR and transmission tracking.

Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

The paper assesses DNA sequencing performance across multiple platforms using human and bacterial reference genomes to evaluate quality and reproducibility.

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.