Curriculum vitae
Download PDFEmployment
2024–
Postdoctoral Researcher, Department of Biochemistry and Molecular Medicine
Dennis Lab, Genome Center and MIND Institute, University of California, Davis
2020–2024
Graduate Student Researcher: scalable framework for massive-scale sequence QC
Titus Brown Lab, School of Veterinary Medicine, University of California, Davis
Education
2020–2024
PhD, Computer Science
University of California, Davis. Thesis: petabyte-scale sequence characterization
2017–2020
MSc, Communication and Information Technology
Nile University, Giza. Thesis: k-mer-based sequence partitioning
2011–2017
BSc, Electrical and Biomedical Engineering
Higher Technological Institute, Cairo. Thesis: ML-based taxonomic classification
Research funding
2022–2025
NIH R03 OD034502 ($312,000), project lead
Data-driven search of Common Fund datasets for better discoverability and novel meta-analysis
2022–2025
Morris Animal Foundation D22CLP-505 ($304,000), project lead
Maximizing the scientific utilization of the Golden Retriever Lifetime Study datasets
2023
Ferrini Research Award
Sequence-based quality control of canine SRA data, UC Davis School of Veterinary Medicine
Teaching
2023
Teaching Assistant, Gene Regulatory Networks workshop
Marine Biological Laboratory, Woods Hole
2023
Instructor, Data Analysis Collaboratory workshop
University of California, Davis
Selected talks and posters
2026
Invited talk
T2T face-to-face meeting, Santa Cruz
2026
Talk: "Chromosome-scale vole assemblies resolve a prairie vole-specific AVPR1A duplication"
Biology of Genomes, Cold Spring Harbor
2025
Poster: "CiFi: A Low-Input Long-Read Method to Unmask Hidden Chromatin"
Halloween Symposium, UC Davis Genome Center
2025
Talk: "Revolutionizing Canine SRA Dataset Analysis for Enhanced Comparative and Reusability Insights"
Plant and Animal Genome, San Diego
2025
Poster: "Structural Variant Discovery and Characterization from de novo Assembly of Khoe-Sān Genomes"
Biology of Genomes, Cold Spring Harbor
2022
Poster: "Fast Clustering of Hundreds of Microbiome Datasets"
Plant and Animal Genome, San Diego
Peer review
journal
Nature Biotechnology
1 manuscript
platform
Review Commons
1 manuscript
conference
RECOMB
1 paper
conference
NILES
2 papers
Skills
C++RustPythonprobabilistic data structuresgraph algorithmsde novo assemblystructural variantspopulation genomicsSnakemakeNextflowWDLHPCcontainersdata visualization
Links
orcid
0000-0002-3419-4785
github
github.com/mr-eyes