Kayode Raheem, MS

Bioinformatics · Computational Oncology

Hi, I'm Kayode Raheem.

I build AI-driven, reproducible pipelines that turn multi-omics and spatial data into translational insights for cancer research — with a focus on how the spatial organization of tumors drives treatment resistance.

I work across bioinformatics, AI/ML, and translational medicine, integrating genomics and spatial/single-cell omics with digital pathology and clinical informatics to model tumor evolution, forecast therapy response, and discover biomarkers. Methodologically, I build graph neural networks and transformer models with causal and temporal analytics, delivered as reproducible pipelines (Nextflow/nf-core, containers, HPC/cloud).

I am especially interested in how the spatial architecture of the tumor microenvironment — cellular neighborhoods, niches, and tissue context — shapes therapy resistance, and in computational method development for spatial omics (Visium, Xenium, MERFISH, CODEX), including graph- and transformer-based models for cell-type deconvolution, niche detection, and spatially aware survival modeling. I also collaborate on computational drug discovery and pursue health equity through generalizable, fair evaluation.

  • Computational Oncology
  • Spatial Omics & Methods
  • Tumor Microenvironment
  • Therapy Resistance
  • GNNs & Transformers
  • Drug Discovery
  • Clinical Informatics
  • Reproducible Workflows
  • Health Equity
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News

  1. Jun 2026

    Competitively selected for the MONET Workshop — the NIH-funded Multi-Omics Network Analysis Workshop at the University of Colorado Anschutz Medical Campus.

  2. Apr 2026

    New paper out in In Silico Pharmacology: Personalized mRNA vaccine for breast cancer: in silico neoantigen discovery and immunogenic validation in a Pakistani patient cohort.

  3. Aug 2025

    Our paper, Kaempferols from Echinacea purpurea Demonstrate Anti-Cancer Potential by Targeting Anexelekto in Breast Cancer Therapy Using a Chemoinformatics Approach, was accepted to Discover Oncology.

  4. Dec 2024

    Joined the University of Nebraska Medical Center as a PhD student in Bioinformatics and Systems Biology.

  5. Jul 2022

    Presented work on the therapeutic capability of medicinal-plant bioactive constituents against the mutant ovarian TP53 gene at the 30th Conference on Intelligent Systems for Molecular Biology (ISMB), ISCB.

Research Interests

Cancer Genomics

Using NGS data to characterize tumor genomic landscapes and surface novel biomarkers.

Computational Drug Discovery

Structural bioinformatics for protein–ligand interaction studies and therapeutic design.

AI / Machine Learning

Applying deep learning to complex biological data for robust, interpretable prediction.

Selected Publications

Personalized mRNA vaccine for breast cancer: in silico neoantigen discovery and immunogenic validation in a Pakistani patient cohort.

Raheem, K., et al. (2026). In Silico Pharmacology. doi:10.1007/s40203-026-00631-6

Paper Code

Design of personalized neoantigen mRNA vaccines against breast cancer patients in Pakistan based on next-generation sequencing data.

Raheem, K., et al. (2024). Cancer Epidemiology, Biomarkers & Prevention.

Paper Code

Enhancing transformer-based segmentation for breast cancer diagnosis using auto-augmentation and search optimisation techniques.

Raheem, K., et al. (2023). arXiv preprint.

Paper Code

Therapeutic capability of selected medicinal plants' bioactive constituents against the mutant ovarian TP53 gene: a computational approach.

Raheem, K., et al. (2023). Advances in Biomarker Sciences and Technology.

Paper

A complete list is available on Google Scholar.

Featured Projects

Personalized Neoantigen Vaccines

Designing mRNA vaccines from NGS data.

cGEDs R Shiny App

Interactive cancer drug-sensitivity analysis.

Multi-Omics & Structural Analysis

Identifying biomarkers and drug targets.

Education

  1. 2024 – Present

    Doctor of Philosophy, Bioinformatics and Systems Biology

    University of Nebraska Medical Center, Omaha, NE, United States

  2. 2022 – 2024

    Master of Science, Bioinformatics

    COMSATS University Islamabad, Pakistan

  3. 2012 – 2017

    Bachelor of Science, Biochemistry

    Adekunle Ajasin University, Akungba-Akoko, Nigeria

Leadership & Service

  1. 2026 – Present

    Academic and Career Development Chair

    African Student Association, University of Nebraska Medical Center, Omaha, NE

    Lead mentorship programming, professional-development initiatives, and career-advancement activities for graduate students.

  2. 2025 – Present

    Event Supervisor & Leadership Committee Member

    Nebraska Science Olympiad, Omaha, NE

    Collaborate with state directors, coaches, and fellow supervisors to organize and oversee STEM competitions for middle- and high-school students; contribute to planning, judging, and event coordination in support of inquiry-based science education.

  3. 2025 – Present

    Discovery and Research Co-Chair

    American Cancer Society on Campus, Omaha, NE

    Coordinate campus-based cancer-research awareness initiatives; organize educational seminars and fundraising events; promote scientific literacy and research engagement among undergraduates.

Get in Touch

Open to discussing research, collaborations, or new opportunities in computational oncology, multi-omics, and AI for biomedicine.

kayoderaheem.y@gmail.com