Systems Genomics Lab
Computational research group at the American University in Cairo
The Systems Genomics Lab is a computational research group working in population genomics, microbiome science, machine learning, and bioinformatics tool development. Much of our work is collaborative, with projects connected to national genomics efforts, microbiome studies, and open-source software development. For research themes and representative publications, see the Research and Publications pages.
Alumni and Completed Theses
Selected graduate theses and dissertations I supervised or co-supervised, with emphasis on computational genomics, microbiome science, machine learning, and bioinformatics.
- Eman Adel — MSc, 2027
Sex stratification of gene expression changes in Parkinson’s disease - Aya Galal — PhD, 2026
Proteo-metabolomic integration identifies stage-specific candidate biomarkers for Parkinson’s disease - Sherine Saber — MSc, 2026
Cell-type-specific regulon activity alterations across Alzheimer’s disease, Parkinson’s disease, and frontotemporal dementia - Rana Salah — MSc, 2026
Characterization of the gut microbiome in Egyptian patients with schizophrenia and bipolar disorder - Marwa A. Zahra — PhD, 2026
Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients - Khlood AbdElaal — MSc, 2026
Characterization of the oral microbiome in Egyptian patients with schizophrenia and bipolar disorders - Maryam Ibrahim — MSc, 2026
Identifying neuronal connectivity in the rat lateral geniculate nucleus (LGN) from spike train data - Ahmed M. Kazlak — MSc, 2025
Multitasking deep learning framework for functional discovery of novel prokaryotic Argonaute proteins in metagenomes - Lobna Ghonaim — MSc, 2025
Identification of novel Argonaute proteins using a metagenomic mining approach - Rowan Abdelbary — PhD, 2025
The interplay between FOXO1 and non-coding RNAs in liver cancer - Tasnim Ghanim — MSc, 2024
Integrative genomic insights into coral resilience: adaptive and acclimatory responses to seasonal environmental shifts - Iman Sultan — MSc, 2024
Deciphering the microbial fingerprint of COVID-19: a multi-layered exploration of the oral and gut microbiome dysbiosis - Ahmed El Hosseiny — MSc, 2023
Computational identification of circulating microRNAs associated with the early stage of ovarian cancer - Ahmed Adel Aboushanab — MSc, 2022
A predictive model for geographical location using microbiome composition and COVID-19 based analysis - Sarah Halawa — PhD, 2020
Profiling genome-wide DNA methylation patterns in human aortic and mitral valves - Dina Abou-Raiya — MSc, 2019
Modulation of stress response in rice via genome editing of splicing factors - Marwa Nassar — PhD, 2017
Characterization of aggresome formation in choroid plexus carcinoma - Diana Abou El Hassan — MSc, 2016
Transcriptomic profiling of the extremophile Eutrema salsugineum response to environmental stressors - Moustafa Abohawya — MSc, 2016
Genome-wide transcriptomic analysis of alternative splicing modulation in Arabidopsis thaliana - Yasmeen Howeedy — MSc, 2015
Transcription regulatory networks in medulloblastoma - Hazem Sharaf — MSc, 2014
Genome-wide reconstruction of the metabolic network of Phaeodactylum tricornutum - Hadeel El Bardisy — MSc, 2014
Polyketide synthase III isolated from uncultured deep-sea Proteobacterium from the Red Sea: functional and evolutionary characterization - Mariam R. Rizkallah — MSc, 2014
Transcriptomics of iron limitation in Phaeocystis antarctica
Joining and Collaboration
Prospective students and collaborators are welcome to get in touch with a brief description of their background, research interests, and potential project ideas. Most projects are computational and may involve genomics, microbiome analysis, machine learning, or bioinformatics software development.