Moustafa Shokrof Ph.D. Email & Phone Number

New York, United States

Davis

The Great Genotyper:· Developed The Great Genotyper a population genotyper to study structural variants in 4K Whole genome sequencing datasets from diverse populations.· The Great Genotyper constructed colored counting debruijn graphs for 4.2K WGS, and it utilizes the graph to genotype variants in the population without needing the raw data.· Created an imputation panel for structural variants by utilizing the Human Pangenome and The Great Genotyper.· Constructed a list of structural variants demonstrating strong associations with SNPs identified in GWAS catalogs.Cattle Structural Variants Catalog:· Assembled a SV catalog for cattle breeds by calling SV from long-read samples, short-reads samples, and assemblies· Developed a machine learning-based method to integrate structural variant calls from various sources and filter out errors.· Calculated population allele frequency for the catalog by genotyping them in 1k short-read samples using The Great Genotyper.· Developed, Hosted, and Ran a successful workshop for 20 academics to use our SV calling/annotating snakemake workflow.MQF and kProcessor:· Implemented a compact hash table called MQF. It maps integer hashes to variable-length integer counter that can be scaled to Fast Flash Drives with acceptable performance.· Implemented kProcessor, a framework designed to facilitate the development of k-mer analysis software. It supports both procedural and functional programming paradigms and offers functionality through C++ and Python interfaces.

Menlo Park, California, United States

· Created a benchmarking workflow for whole genome sequencing (WGS) variant calling, focusing on both small and structural variants. · The workflow was constructed using the Workflow Description Language (WDL), with dependencies managed through Docker. For visualization, I utilized matplotlib, and the workflow's testing was conducted using pytest-workflow.

Riyadh, Saudi Arabia

· Developed solutions for challenges facing the operation team in the Saudi genome project.· Developed a novel compression algorithm(ioncram) for BAMs from ion torrent that achieves a 43% compression ratio by exploiting redundancy in the flow signal.· Developed a distributed version of the ion torrent variant calling workflow that take advantage of the HPC system.

Giza, Al Jizah, Egypt

· Developed a workflow to produce a high-quality draft for the Egyptian Buffalo Genome from hundreds of gigabytes of raw sequencing data.· Developed a streaming model in Tavaxy(workflow system) to enable jobs to in-memory communication.· Worked as a teaching assistant in a Machine learning course.· Redesign a c++ library for succinct data structures (SDSL).

Develop Information Extraction system from Biomedical papers using machine learning to recognize biological named entities like genes and data mining to find relations between those entities

Doctor Of Philosophy - Phd, Computer Science

Master'S Degree, Informatics,Bioinformatics

Bachelor'S Degree, Computer And Information Sciences, Bioinformatics

Bachelor Of Computer Science, Bioinformatics