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 develops and applies computational methods for genomics, metagenomics, microbiome analysis, and precision medicine, with a particular interest in underrepresented populations.
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.
Current Focus
- Population genomics and the Egypt Genome Project
- Machine learning and deep learning for genomic and microbiome data
- Bioinformatics infrastructure supporting precision medicine research in Egypt and Africa
Featured Tool: DeepTaxa
DeepTaxa is a hybrid CNN–BERT deep-learning framework for 16S rRNA taxonomic classification, developed to support microbiome analysis workflows. It is open source and published in Bioinformatics Advances (paper).
Research Interests
Our research applies computational, statistical, and machine-learning methods to large-scale genomic, metagenomic, and transcriptomic data. We are broadly interested in precision and population genomics and in how microbial communities shape the health of their hosts and environments.
- Precision medicine and population genomics
- Machine learning and deep learning for genomics
- The human microbiome in health and disease
- Metagenomics, pathogen surveillance, and viromes
- Comparative and evolutionary genomics
- Bioinformatics pipelines, tools, and data science
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.
- Deep Sequencing of 10,000 Human Genomes. PNAS, 2016.
Microbiome and virome
- The blood DNA virome in 8,000 humans. PLOS Pathogens, 2017.
- Microbial metagenome of urinary tract infection. Scientific Reports, 2018.
- 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.