Islam Salah, BSc,MSc
Area of Focus
- Genomics
- Biomarker
- Biostatistics
- Communications
- Whole genome sequencing
- Workflow Description Language (WDL)
- scRNA-seq
- RNAseq
- Education
- Project management
Biography
Islam Salah is a distinguished expert in the field of genomics data analysis with a robust foundation in utilizing R/Bioconductor tools such as DESeq2, EdgeR, and DEXSeq for RNA-Seq, microarrays, NGS, and sequence analysis. His work extends to in-depth DNA methylation analysis through both microarrays and NGS, employing tools like minfi, limma, bumphunter, and bsseq from the Bioconductor project.
Islam has proficiently analyzed data from cutting-edge technologies provided by Oxford Nanopore Technologies, including software such as Guppy and Minimap2, and tools like ONT Fast5 API, Porechop, Nanopolish, Medaka, and Flye. His expertise in SNPs and GWAS is well-established, utilizing SAMTOOLS, Vcftools, and bedtools. He is adept at Gene Set Enrichment Analysis (GSEA) and pathway analysis, notably with KEGG, enhancing his research into genomic function and expression.
With a strong proficiency in CHIP-Seq data analysis, Islam expertly examines transcriptional factors experiments data. His skills are complemented by his familiarity with a suite of computational tools essential for reproducible data analysis including Git/GitHub, RStudio, Spyder, and dynamic report generation using Rmarkdown, R Notebook, Jupyter, and Pandoc. His technical expertise also spans Bash, Linux, Docker, and cloud computing platforms like AWS SageMaker and Google Cloud, as well as HPC environments.
Islam is conversant with workflow languages and platforms like Nextflow, Cromwell, and CWL. His programming proficiency is evidenced by his strong Python skills, where he integrates packages such as Biopython, Pysam, NumPy, sci-kit-learn, Pandas, Altair, Matplotlib, and Colab into his work.
His capabilities extend to single-cell gene expression analysis using R and advanced machine learning techniques. Additionally, Islam is skilled in the use of MATLAB for biological data analysis and has familiarity with examining protein structures using PyMOL.
Islam’s experience includes designing and executing genetic experiments using simulation tools, reflecting his innovative approach to genetics research. He adheres to a lean and agile methodology, ensuring both high quality and efficiency in project delivery. As a PMP certified professional, Islam consistently delivers projects that meet rigorous standards on time and with exemplary quality.