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Education, appointments, honors, funding, and service. The full publication list is on the publications page.

General Information

Full Name Nourhan E. H. Abdelfattah, Ph.D.
Position Instructor, Houston Methodist Academic Institute; Research Associate, Houston Methodist Research Institute
Location Houston, TX, USA
Email neabdelfattah@gmail.com
Links Google Scholar · ORCID · GitHub · NCBI Bibliography
Research areas Cancer immunology · tumor microenvironment · neuroimmunology · single-cell & spatial multi-omics · open-source scientific software

Research Focus

  • How biological sex shapes immune function, therapeutic response, and neuroimmune disease biology — at the intersection of cancer immunology, sex biology, and computational biology. My research adopts an integrated wet-lab and computational program combining mouse genetics, single-cell and spatial multi-omics, functional immunology, protein-interaction biology, and open-source software development.

Education

  • 2018
    Ph.D., Cancer Biology
    UT Health Science Center at San Antonio, San Antonio, TX
  • 2011
    Post-Baccalaureate, Chemistry
    Cairo University, Giza, Egypt
  • 2010
    B.Sc., Biotechnology
    Cairo University, Giza, Egypt — Excellent with Highest Honors, Top 1%

Postdoctoral Training

  • 2018–2023
    Postdoctoral Fellow — Brain Cancer, Tumor Immunology, Single-Cell Genomics
    Houston Methodist Research Institute, Houston, TX (Mentor: Kyuson Yun)
  • 2009–2013
    Research Internships
    University of Windsor (2013) · LMU Munich (2012) · AGERI, Giza (2011) · Medical Genetics Center, Cairo (2009)

Academic & Professional Appointments

  • 2024–Present
    Instructor
    Houston Methodist Academic Institute, Houston, TX
  • 2023–Present
    Research Associate
    Houston Methodist Research Institute, Houston, TX
  • 2024–Present
    Independent Bioinformatician
    Remote — single-cell, Visium/HD spatial, and bulk RNA-seq workflows
  • 2011–2013
    Demonstrator / Teaching Assistant
    Faculty of Science, Cairo University, Giza, Egypt

Software & Tools Built

  • 2025
    scSidekick
    Open-source R package for reproducible single-cell & spatial transcriptomics analysis — automated reporting, methods text, legends, PowerPoint exports; CellChat, inferCNV, cNMF, pseudotime, pseudobulk, ssGSEA, survival correlation. Submitted to Bioinformatics.
  • 2024
    RNAseqWizard
    An interactive Shiny app for end-to-end bulk RNA-seq analysis. It takes raw count matrices and a sample metadata file and walks you through a complete pipeline: library-size QC, density-based filtering, and PCA for quality control; TMM normalization and edgeR GLM-based differential expression (two-group, all pairwise, or omnibus); volcano plots, MA plots, and expression heatmaps for visualization; CPM boxplots with pairwise statistics for genes of interest; and pathway analysis via GSEA (fgsea), GSVA, or over-representation analysis (ORA) against MSigDB collections or custom GMT files. Results can be exported as publication-ready PDFs and a compiled R Markdown report.
  • 2025
    ScrubPDF
    A browser-based, fully client-side PDF utility for reducing PDF file size without compromising quality. It preserves text and vector elements, removes unwanted “ghost” content from cropped areas, and includes a target-size option that rasterizes only problematic pages when needed.
  • 2026
    MatchLR
    R framework (in development) for orphan ligand–receptor prediction — interactome, scRNA-seq, and surfaceome evidence fused with an XGBoost binding-probability ensemble, Pfam domain compatibility, CellChat, and AlphaFold via reciprocal rank fusion.
  • 2026
    Lumos
    Cross-platform desktop app for interactive figure building for non-bioinformaticians (internal release).

Technical Skills

  • Omics & Analysis
    • sc/snRNA-seq · spatial transcriptomics · single-cell multiome · bulk RNA-seq · ChIP-seq · scATAC-seq
    • Proteomics integration · long-read (PacBio) · TCR/BCR-seq · pseudobulk · meta-analysis
  • Perturbation Biology
    • High-throughput functional screens · Cas9 KO · LNP-delivered CRISPR · CRISPR off-target analysis
    • miRNA perturbation · nanoparticle synthesis · intracranial injection
  • AI & Agentic Tools
    • Agentic workflow design · generative-AI prompt engineering · AI-augmented pipeline automation
    • LLM-assisted R/Python/Bash development · pipeline debugging · documentation generation · reproducible workflow automation
  • Programming
    • R (expert) · Python · JavaScript/HTML · Bash · shell scripting · HPC/SLURM
  • Experimental & In Vivo Biology
    • Intracranial surgery · flow cytometry · single-cell library prep · confocal microscopy · ELISA
    • Animal modeling · tissue processing · nanoparticle synthesis · LNP delivery
  • Communication
    • First-author publications in Cancer Cell & Nature Communications · international conference presenter
    • Clinical stakeholder communication · scientific visualization · workshop instructor

Honors, Fellowships & Competitive Awards

  • 2026
    • Presidential Award, Excellence in Peer-Reviewed Publication — Houston Methodist Academic Institute
  • 2025
    • Presidential Award, Excellence in Peer-Reviewed Publication — Houston Methodist Academic Institute
  • 2023
    • SITC Women in Cancer Immunotherapy Network Leadership Program
  • 2021
    • Outstanding Grant Recipient Award — Houston Methodist Office of Graduate Studies and Trainee Affairs
  • 2020–2023
    • Horizon Award (PI) — Department of Defense Peer Reviewed Cancer Research Program
  • 2019
    • Barbara H. Bowman Graduate Student of the Year Award
  • 2016–2018
    • Schlumberger Foundation Faculty for the Future Predoctoral Fellowship
  • 2014–2016
    • Greehey Graduate Fellowship in Children’s Health
  • 2012
    • Nano-systems Initiative Munich Student Research Award
    • Partnership and Ownership Initiative Scholarship, Egyptian Ministry of Higher Education

Research Support

  • 2026–2029
    NCI K22 (1K22CA307633-01A1) — PI (pending)
    Sex-specific differences in the Yap1–Cd276 axis in medulloblastoma immune suppression
  • 2020–2023
    DOD Horizon Award CA191052 — PI
    Yap1 function in sex-biased medulloblastoma tumorigenesis, progression, and protumor immunity
  • 2016–2018
    Schlumberger Foundation Faculty for the Future Fellowship — PI
    MicroRNAs as therapeutic adjuvants to treat pediatric medulloblastoma
  • 2014–2016
    Greehey Graduate Fellowship in Children’s Health — PI
    MicroRNAs as therapeutic adjuvants to treat pediatric medulloblastoma

Service to the Profession

  • Peer reviewer for Nature Communications, Cancer Research, Clinical Cancer Research, npj Precision Oncology, Molecular Cancer Research, Molecular Cancer Therapeutics, Cancer Research Communications, Neuro-Oncology Advances, and Scientific Reports (2021–present).

Teaching & Mentoring

  • 2020–2026
    Instructor & curriculum developer — faculty and trainee development workshops
    Houston Methodist Research Institute (e.g. Creating a Research Poster; Statistics for Biologists)
  • 2015–2018
    Teaching Assistant — graduate biomedical science courses
    UT Health San Antonio (Molecular Biology; Cancer Biology Core; Methods in Cell Biology)
  • 2011–2013
    Instructor — molecular biology & bioinformatics workshops
    LabLog Scientific Training & Development / Medical Genetics Center, Cairo University
  • 2018–Present
    Mentoring
    Mentored 15+ graduate students, postdoctoral fellows, and research staff in single-cell/spatial analysis, experimental design, scientific visualization, and reproducible computational workflows, with a teach-to-independence model.