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mtariqi/README.md

AI-driven computational biology and precision medicine

🧬 AI-Driven Computational Biology for Precision Medicine

Bioinformatics Β· Cancer Genomics Β· Healthcare Data Engineering Β· Scientific Machine Learning

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About Me

I am a Research Scientist, Bioinformatician, and Data Scientist working at the intersection of computational biology, cancer genomics, artificial intelligence, biostatistics, and precision medicine.

My research combines genomics, transcriptomics, multi-omics integration, machine learning, and large language models to transform complex biological and health data into evidence for:

  • Biomarker discovery
  • Therapeutic-target prioritization
  • Precision oncology
  • AI-assisted drug discovery
  • Reproducible biomedical research

I currently contribute to cancer-genomics research as a Bioinformatician at the University of Arkansas for Medical Sciences (UAMS), developing scalable NGS workflows and analyzing TCGA and CPTAC datasets. I am also pursuing an MSc in Bioinformatics at Northeastern University, strengthening my expertise in translational bioinformatics, machine learning, and trustworthy biomedical AI.

Beyond biomedical research, I independently reproduced and extended machine-learning workflows for streamflow prediction and National Water Model bias correction. My HYDRO-FLOW-AI project builds on open workflows from the Alabama Water Institute’s NWM-ML project and research involving a University of West Florida researcher, while remaining an independent project with no claim of institutional affiliation.

My long-term goal is to build trustworthy computational systems that connect biological evidence, clinical data, and artificial intelligence to accelerate scientific discovery and improve patient outcomes.


Research Interests

  • 🧬 Computational biology and bioinformatics
  • πŸŽ—οΈ Cancer genomics and precision oncology
  • πŸ§ͺ NGS analysis and variant interpretation
  • πŸ”— Multi-omics integration
  • πŸ’Š Computational drug discovery
  • πŸ€– Artificial intelligence and deep learning
  • πŸ“š Biomedical large language models
  • ⚑ Agentic AI and retrieval-augmented generation
  • ☁️ Cloud-based scientific computing
  • πŸ₯ Healthcare data engineering
  • 🌊 Scientific machine learning for hydrology

Featured Research Projects

Project Research focus Repository
RTK/NRTK TNBC Patient-level kinase alterations and drug-target prioritization in triple-negative breast cancer View project
HYDRO-FLOW-AI Extreme-aware streamflow prediction and National Water Model bias correction View project
NIH Clinical Trials Lakehouse Reproducible healthcare data engineering for clinical-trial analytics View project
CDC Healthcare Streaming ETL Streaming ingestion, validation, transformation, and public-health analytics View project
TCGA–CPTAC Kafka Platform Event-driven processing of large-scale cancer multi-omics data View project
Synthetic Variant Calling Benchmark Reproducible benchmarking of NGS variant-calling workflows View project
Genomic Foundation Models Transformer-based representation learning for genomic sequences View project
USAG1 Validation Computational evidence synthesis and therapeutic-target validation View project

🌊 HYDRO-FLOW-AI

License: MIT Python 3.10+ Stage 1

HYDRO-FLOW-AI is an independent, extreme-aware machine-learning framework for streamflow prediction and site-specific National Water Model bias correction at USGS gauges.

Current capabilities

  • Leakage-safe temporal training, validation, and testing
  • Historical USGS streamflow and climate-data integration
  • Site-specific model-performance diagnostics
  • Evaluation using RMSE, MAE, bias, and NSE
  • Q95 and Q99 high-flow evaluation
  • Peak-magnitude error analysis
  • Extreme-event detection and threshold-based assessment

Planned extensions

  • XGBoost residual bias correction
  • Quantile-regression uncertainty intervals
  • LSTM and Transformer-based forecasting
  • River-network graph neural networks
  • Explainability and model-drift monitoring

πŸ§ͺ Selected Scientific Contributions

Hybrid-CORE

Computational framework for rational drug-combination prioritization using complementary biological and pharmacological evidence.

RTK/NRTK Network Analysis

Identification of compensatory kinase alteration patterns and potential drug-target combinations using TCGA cancer-genomics data.

Biomedical Agentic RAG

LLM-supported retrieval, evaluation, and synthesis of biomedical evidence for research decision support.

Genomic Foundation Models

Transformer-based representation-learning approaches for genomic sequences and downstream biological prediction.

Healthcare Data Engineering

Reproducible lakehouse and streaming architectures for clinical-trial, public-health, and biomedical data.


βš™οΈ Technology Stack

Programming and Analytics

Python R SQL Bash Git Linux

Artificial Intelligence

PyTorch TensorFlow scikit-learn Hugging Face LangChain Amazon Bedrock

Bioinformatics

GATK BWA DeepVariant Snakemake Nextflow

Cloud and Infrastructure

AWS Azure GCP Docker Terraform PostgreSQL


πŸ“ˆ Current Research Focus

  • AI for precision oncology
  • Computational drug discovery
  • Cancer multi-omics
  • Biomedical large language models
  • Genomic foundation models
  • Agentic AI for scientific discovery
  • Trustworthy and explainable AI
  • Scalable scientific computing
  • Extreme-aware streamflow forecasting

πŸŽ“ Education

  • MSc Bioinformatics β€” Northeastern University (in progress)
  • MSc Molecular Biology (Bioinformatics) β€” UmeΓ₯ University
  • BSc Biotechnology and Genetic Engineering β€” Khulna University
  • Advanced Diploma in Data Science and Data Engineering
  • Graduate Certificate in Project Management

πŸ“œ Professional Development

  • Health Informatics β€” Johns Hopkins University
  • Business Analytics and Data-Driven Decision-Making β€” University of Toronto
  • Project Management
  • Cloud Computing
  • Machine Learning and Data Science

🌱 Currently Learning

  • Trustworthy and causal AI
  • Agentic and multi-agent systems
  • Biomedical large language models
  • Genomic foundation models
  • Scalable multi-omics analytics

πŸ“Š GitHub Statistics

GitHub statistics

Most-used programming languages


🀝 Collaboration

I welcome research and open-source collaboration in:

  • Computational biology and bioinformatics
  • Cancer genomics and precision medicine
  • Biomedical artificial intelligence
  • Computational drug discovery
  • Healthcare data engineering
  • Scientific machine learning
  • Reproducible research software

Transforming biological and health data into evidence for intelligent therapeutic discovery

LinkedIn Β· ORCID Β· Portfolio Β· Email

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