Omar Y. Ahmed

This paper identifies challenges in GWAS integration and fine-mapping for variant interpretation and suggests a multi-modal approach for prioritizing causal variants.

The paper integrates multi-omic QTLs and predictive models to identify regulatory variants in CD4+ T cells and their role in immune-related GWAS loci.

This paper introduces a run-length compressed metagenomic read classification method that outperforms existing tools in accuracy and runtime while maintaining efficient memory usage.

This paper extends Chromap to provide peak-based quality control metrics for single-cell ATAC-seq without peak calling, improving downstream analysis by identifying low-quality cells missed by other methods.

The paper introduces a new open-source tool for efficient genomic sequence digestion using minimizers, modimizers, or syncmers.

Movi is a fast pangenome index that enables efficient querying of nanopore sequencing reads using move structures, achieving faster speeds than existing methods.

Sigmoni classifies nanopore signals using a compressed pangenome index, enabling efficient and accurate classification of reads against large references.

Cliffy improves 16S rRNA classification by reducing index size and increasing accuracy compared to Kraken2 and Bracken.

The paper introduces MEMO, a pangenome indexing method that efficiently handles k-mer queries and conservation analysis across pangenomes.

DandD measures sequence growth and similarity in genome assemblies using a new metric called delta, estimating how much new sequence is added and when discoveries will plateau.

SPUMONI enables fast and accurate targeted nanopore sequencing using efficient pangenome indexes, outperforming minimap2 in speed and memory usage.

Megadepth efficiently quantifies coverage in BigWig and BAM files, outperforming existing tools in speed and memory usage.