Omer S. Alkhnbashi

This paper identifies genomic loci and mutations associated with DDT metabolic resistance in Anopheles gambiae using bulk segregant analysis and confirms their selection in natural populations.

The paper identifies structural variants in MENA individuals using long-read sequencing, revealing previously unreported variants and population-specific disease-related variants.

The paper analyzes CRISPR array repeat mutations across prokaryotic genomes, revealing subtype-specific patterns and a link between repeat mutations and spacer dynamics.

CRISPR-evOr predicts CRISPR array orientation by analyzing evolutionary patterns, improving accuracy for arrays other tools cannot confidently resolve.

The paper introduces AVDB, a database of genetic variants from Arab populations, providing pathogenicity classifications and disease burden metrics to improve genomic screening and diagnostics.

PanScan is a tool for tertiary analysis of human pangenome graphs, enabling detection of duplicated genes, novel variants, and complex genomic regions.

The paper identifies a new subgroup of type V-K CAST systems in cyanobacteria through phylogenetic analysis and characterizes its unique features.

SpacerPlacer reconstructs ancestral CRISPR array evolution, revealing frequent spacer deletions and a decrease in deletion frequency towards both ends of arrays.

The paper benchmarks ORF prediction tools for bacterial Ribo-seq data, finding DeepRibo performs well but none detect all novel sORFs with high sensitivity.

CRISPRIdentify uses machine learning to detect CRISPR arrays with reduced false positives and provides certainty scores for identified regions.

The paper introduces a machine learning approach to identify and classify CRISPR-Cas systems by combining regression and classification models to improve protein cascade quality and subtype prediction.

The paper identifies 39 new Type III CRISPR-Cas associated gene families using comparative genomics and presents them in an online database.