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ahmedhesham47/README.md

Hi there! πŸ‘‹ I'm Ahmed Saadawy

Typing SVG


🧬 About Me

  • πŸŽ“ PhD Student in Molecular & Cellular Biosciences @ University of Southern California
  • πŸ”¬ Graduate Research Assistant at CSI-Cancer β€” bridging liquid biopsy with computational biology
  • πŸŽ“ BSc in Computational Biology & Genomics (Minor: Information Engineering) from Zewail City for Science and Technology
  • πŸš€ Current research: Identifying rare cell populations in multiple myeloma using the HDSCA platform & developing multi-modal predictive models for clinical outcomes

πŸ” Research Interests

  • 🧬 Liquid Biopsy β€” cfDNA, ctDNA, fragmentomics, circulating tumor cells
  • 🧠 AI for Biology β€” interpretable ML/DL methods for biological data
  • πŸ§ͺ Systems Biology β€” network biology, cellular self-organization, virtual cell modeling
  • 🩺 Cancer Biology & Immunology β€” multiple myeloma heterogeneity, immunotherapy, tumor immune microenvironments

πŸ“š Publications & Projects

πŸ“– Publication πŸ“– Journal πŸ§ͺ Repository
AI in Healthcare: Using Bayesian Networks to Predict Response to Immune Checkpoint Blockades IEEE Xplore Bayesian Networks for ICB
The landscape of cyclin-dependent kinase 4/6 inhibitors in solid malignancies: Emphasis on immunotherapy combinatorial strategies Springer Nature, Medical Oncology CDK4_6-Inhibitors-In-silico-Analysis
Integrative multi-omics pipeline for analysis of checkpoint blockade therapy Springer Nature, Network Modeling Analysis in Health Informatics and Bioinformatics Integrative Multi-omics Pipeline for Analysis of Checkpoint Blockade Therapy
OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry Springer Nature, BMC Bioinformatics OpenIMC
Voltage‐dependent anion channels: key players in viral infection Wiley, Reviews in Medical Virology N/A
Trimetazidine mitigates methotrexate‐induced liver damage: Insights From biochemical, histological, and in silico analyses Wiley, Archiv der Pharmazie N/A

πŸ’» Languages

Python R C++ SQL MATLAB Bash


πŸ› οΈ Tech Tools

GitHub Jupyter VS Code SciPy Tmux SLURM HPC scikit-learn PyTorch


πŸ—„οΈ Bioinformatics Databases

NCBI GEO KEGG 1000 Genomes ClinVar Protein Data Bank UniProt PubChem Human Protein Atlas GTEx The Cancer Genome Atlas


πŸ”¬ Bioinformatics Tools

PyMol Cytoscape STRING CIBERSORTx xCell BLAST COBRApy treeWAS maftools UCSC Genome Browser DESeq2 limma Bioconductor g:Profiler AlphaFold Waltz IUPred2A Escher AMDock Reactome


πŸ“ˆ Profile Visitors

Visitor Count


πŸ“Š GitHub Achievements

GitHub Achievements


🌍 Outside of Work

  • β™ŸοΈ Chess enthusiast β€” Lichess: FuzzyBuzz
  • 🎡 Music fan β€” curated Spotify playlist
  • πŸŽ₯ Documentaries, science videos, and entertainment on YouTube

πŸ“« Reach Me

LinkedIn Email Google Scholar


πŸ’‘ β€œThe best way to predict the future is to create it.”

Pinned Loading

  1. Bayesian-Networks-for-Predicting-ICB-Response Bayesian-Networks-for-Predicting-ICB-Response Public

    Employing Bayesian Networks to quantify the probability of ICB response based on transcriptomic profiles

    Jupyter Notebook 2

  2. Genetic-Algorithms-for-Feature-Selection Genetic-Algorithms-for-Feature-Selection Public

    This project aims to utilize genetic algorithms for selecting a subset of features that maximize the classification accuracy for supervised machine learning tasks.

    Jupyter Notebook 1

  3. BreakHis-DL-Image-Classification BreakHis-DL-Image-Classification Public

    This project aims to classify breast cancer into one of eight subtypes based on the BreakHist dataset that contains around 8000 images using transfer learning techniques, Squeeze-and-Excite attenti…

    Jupyter Notebook 1

  4. PyAA PyAA Public

    A package that analyzes protein sequences, predicts secondary structure based on dihedral angles/Ramachandran plots and Chou and Fasman's statistical propensity method, among other cool things!

    Python 1

  5. PPIer PPIer Public

    Protein-Protein Interactions Network

    C++ 1

  6. Systems-Biology-Tutorials Systems-Biology-Tutorials Public

    A repo to store tutorials made for BMS 473 - Systems Biology in Fall 2024. The tutorials are using CobraPy on genome-scale metabolic models, mathematical modelling and numerical integration, and more.

    Jupyter Notebook 2