My Research

My research bridges the gap between computational modeling and experimental biology to decipher novel mechanisms. My research utilizes multi-omics, computational biology, and molecular and cellular biology approaches to elucidate biological functions and signalling pathways underlying diseases.

A. Motif-Functions-Pathway: I conceptualized and developed computational pipelines to analyze sequences and predict cellular pathways from small functional motifs. As a proof-of-concept, I analyzed viral proteomes (small datasets of <5,000 proteins per family) to identify their functions and pathways and to analyze host-specific differences. I found a MREL motif (conserved in the tubulin family) at the C-terminus of SARS-CoV-2 nsp1 protein (Sobhy 2021). Currently, 2 manuscripts are in preparation, refer to my GitHub. See the articles page for additional links, figures, and PDF files.

Publications:

Comparative and Functional Genomics, 2012; PMID: 23316117
COVID Journal 2021; doi: 10.3390/covid1010032
Proteomes 2018; PMID: 29786634
Proteomes 2016; PMID: 28248213
Virus Genes 2016; PMID: 28000080
Microbial Genomics 2015; PMID: 28348820

B. Gene expression: I studied gene regulation mechanisms and transcription regulators involved in development that contribute to multiple diseases, including CDK kinases and zinc finger (ZNF) and homeodomain (HD) proteins. Modeling 3D genome organization (Hi-C) data using a graph-based Markov model showed that highly connected regions are characterized by: (1) gene desert regions, (2) regulatory regions, (3) fragile regions (DNA damage), and (4) actively transcribed genes that contribute to cell adhesion and immune response pathways. ZNF can regulate RNA processing and splicing of genes related to cell integrity, cell proliferation, and cell adhesion in microglia (CNS immune cells). CDK and HD can regulate cell integrity in a multitude of cell types. The published results are listed below.