Abdallah E.

A bioinformatician with more than 7 years of experience in developing custom NGS pipelines for various “omics” experiments, and building solutions for maintaining and querying large genomics datasets. Competent in using Linux-based operating systems, with a deep knowledge of key programming languages and related resources such as Java, Python, R, Bioconductor, etc. Strong analytical and problem-solving skills. I have good expertise in the following: - Quality checks and detection of contamination in FASTQ files. - Whole-exome/genome sequencing: starting from raw FASTQ files to variant calling. Also, I do various analyses on the VCF files. - RNA-seq: starting from raw FASTQ files to FeatureCounts and Differential Expression analysis between two or more conditions, pathways analysis... - ChIP-seq and ATAC-seq: starting from FASTQ files to motif annotation and analysis. I can perform differential accessibility analysis. - Bisulfite sequencing: methylation analysis starting from FASTQ files. - Single-Cell RNA-seq: cells clustering analysis, differential expression analysis, pathways analysis... - Metagenomics analysis: identification of the content of the samples: Viruses, Bacterial... - Spatial transcriptomics. - Strong expertise in R, Docker. - Beginner in proteomics: I can work on output from MaxQuant, Differential Expression of proteins... - Good knowledge of Shiny R - Classical machine learning: supervised and unsupervised learning using Python