Hafiz M. Talha Malik

Senior Bioinformatician @23rd Pair

GB

NGS/WGS Analysis: Designed and maintained robust workflows for end-to-end NGS/WGS data analysis, including quality control, adapter trimming, alignment (BWA, STAR), de novo and reference-based genome assembly, variant calling (GATK, FreeBayes), and consensus sequence generation.RNA-seq & Transcriptomics: Led large-scale analysis of RNA-seq and single-cell RNA-seq (scRNA-seq) datasets using tools like STAR, HISAT2, Salmon, Kallisto, Seurat, DESeq2, and Scanpy to extract transcriptomic insights and identify differential expression across conditions.Single-Cell Omics: Implemented scalable pipelines for 10x Genomics data (e.g, Cell Ranger, Seurat) to explore cellular heterogeneity and gene expression patterns in high-resolution.Metagenomics & Pathogen Discovery: Deployed pathogen detection workflows using GUI (Geneious Prime, Galaxy) and CLI-based (Kraken2, MetaPhlAn, HUMAnN) tools on clinical metagenomics data for microbiome and pathogen profiling.Phylogenomics & Epidemiology: Performed evolutionary and transmission analysis of viruses (e.g, HIV, SARS-CoV-2) using Nextstrain, IQ-TREE2, MEGA, and MAFFT, enabling real-time phylogenetic tracking of outbreak strains.Pipeline Automation: Reproducible workflows using Nextflow, Snakemake, Bash, and Python, containerized with Docker, and managed environments with Conda for consistent deployments across cloud and HPC systems.Data Visualization & Reporting: Created high-quality, interactive visualizations and dashboards using R (ggplot2, Shiny) and Python (Plotly, seaborn, Matplotlib) to support data-driven decisions.Key Tools & Technologies:Workflow Management: Nextflow, Snakemake, Conda, Docker, Bash, PythonPlatforms: Illumina (NovaSeq, MiSeq, MiniSeq, iSeq), Oxford Nanopore (MinION), Ion TorrentCloud & DevOps: AWS, Azure, Git, GitHub Actions, HPC environmentsVisualization: R (ggplot2, Shiny), Python (seaborn, Plotly, matplotlib)

COMSATS Institute of Information and Technology

BS, BioInformatics

COMSATS Institute of Information and Technology

Master's degree, Bioinformatics