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shari01/README.md

Hi 👋, I'm Sheryar Malik

Bioinformatics Engineer · AI Engineer · Data Scientist · Researcher

shari01

🧬 About Me

  • 🔭 Currently working as a Bioinformatics Engineer at Ayass Bioscience, Texas, USA
  • 🤖 Building disease-agnostic Agentic AI pipelines for drug discovery, biomarker identification, and pathway analysis — integrating LLM reasoning, PubMed mining, and multi-database validation (ChEMBL, DGIdb, OpenTargets)
  • 🎓 Pursuing MPhil in Bioinformatics at Hazara University, Mansehra
  • 🧠 Core expertise: Agentic AI · LLM Engineering · Computational Oncology · Multi-Omics · scRNA-seq · NGS
  • 👯 Open to collaborating on precision medicine, cancer genomics, LLM-driven bioinformatics, and drug repurposing projects
  • 📫 Reach me at sheryarmalik1403@gmail.com

"The convergence of agentic AI and multi-omics is unlocking disease mechanisms at a resolution that was unthinkable a decade ago."

🤝 Connect with Me

LinkedIn

🛠️ Languages & Tools

python R pandas scikit_learn pytorch tensorflow docker aws gcp bash linux java javascript opencv matlab anthropic claude huggingface chatgpt github copilot cursor

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  1. Oncocyrix_MultiCohort Oncocyrix_MultiCohort Public

    A comprehensive end-to-end single-cell RNA-seq analysis pipeline supporting multi cluster single and multi-sample 10x data analysis

    Python

  2. Fine-Tuning-DeepSeek-R1-on-Medical-Reasoning-Chain-of-Thought Fine-Tuning-DeepSeek-R1-on-Medical-Reasoning-Chain-of-Thought Public

    Fine-tuning DeepSeek-R1 for medical reasoning using Chain-of-Thought, LoRA, and clinical question datasets.

    Jupyter Notebook

  3. GenAI-Powered-Bioinformatics-Chatbot GenAI-Powered-Bioinformatics-Chatbot Public

    A full-stack LLM-powered chatbot designed for bioscience and clinical research queries — from pathway analysis to molecular Q&A.

    Python 3 1

  4. Oncocyrix Oncocyrix Public

    OncoCyrix: a modular Scanpy-based pipeline for single-sample 10x scRNA-seq cancer analysis

    Python 1 1

  5. Automated-Gene-Pathway-Enrichment-Analysis-with-STRING-API Automated-Gene-Pathway-Enrichment-Analysis-with-STRING-API Public

    This Python script automates the process of gene pathway enrichment analysis by integrating with the STRING Database API. It reads a list of genes from an input Excel file, queries the STRING datab…

    Python 1

  6. Immune-Deconvolution Immune-Deconvolution Public

    Python-based CIBERSORT runner for immune cell deconvolution using LM22, with automated QC, plotting, and seamless R integration.

    Python