American University in Cairo (AUC)
Bioinformatics Consultant, Egypt Center for Research and Regenerative Medicine (ECRRM), Ministry of Defense
Adjunct Scientist, J. Craig Venter Institute (JCVI)
Lead, Systems Genomics Lab
About
I am a Professor of Bioinformatics and Genomic Data Science at the American University in Cairo (AUC), where I lead the Systems Genomics Lab. My research connects population genomics, microbiome science, and machine learning to improve genomic interpretation for precision medicine, with a particular focus on populations underrepresented in global genomic research.
I also serve as a bioinformatics consultant at the Egypt Center for Research and Regenerative Medicine (ECRRM), Ministry of Defense, and as an adjunct scientist at the J. Craig Venter Institute (JCVI). Through the Egypt Genome Project, my work supports large-scale genomic analysis, studies of population diversity, and the bioinformatics infrastructure behind national genomics efforts.
Earlier in my career, I worked as a software engineer, and later contributed to the sequencing and analysis of human genomes at Human Longevity, Inc. (HLI). I earned my PhD in Computational Genetics from the University of Iowa and my BSc in Computer Science from Alexandria University.
Research Focus
My group develops computational approaches to study human and microbial diversity, with emphasis on populations, diseases, and environments that are underrepresented in global datasets. Our main areas are:
- Population genomics and precision medicine
- Microbiome, metagenomics, and viromes
- Machine learning for genomic data
- Bioinformatics infrastructure and tools
Featured Work
Egypt Genome Project (EGP1K). A national initiative that sequenced and characterized the genomes of 1,024 Egyptians to map population structure and genetic diversity. I contribute to its bioinformatics effort (preprint).
DeepTaxa. A hybrid CNN–BERT deep-learning framework for 16S rRNA taxonomic classification, developed to support microbiome analysis workflows. Open source and published in Bioinformatics Advances (paper).
Selected Publications
Population genomics and precision medicine
- EGP1K: Whole-Genome Sequencing of 1,024 Egyptians Characterizes Population Structure and Genetic Diversity. bioRxiv, 2026.
- The Egypt Genome Project. Nature Genetics, 2024.
Microbiome and virome
- The blood DNA virome in 8,000 humans. PLOS Pathogens, 2017.
- Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease. Clinical and Translational Gastroenterology, 2018.
Evolutionary genomics
- Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science, 2009.
- An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Science Advances, 2019.
For the complete list, see Publications or the curriculum vitae.