Programme

Research

Four strands, one question running through them — how do you turn sequence data into a decision somebody can act on?

Cancer Genomics

Genomic and transcriptomic profiling of bladder cancer and urothelial cell carcinoma — molecular drivers, therapeutic resistance and protein–protein interaction networks in oncogenic pathways.

  • Hub-gene discovery from PPI networks of transcriptomic expression
  • Candidate biomarkers for bladder cancer (CERS2, EN2)
  • Systematic synthesis of GWAS and biomarker evidence in bladder cancer

Oncolytic Virotherapy

Mechanisms of Newcastle disease virus (NDV) persistence in cancer cells — how a persistently infecting virus rewires the host transcriptome, and what that means for the therapeutic window.

  • In vitro models of NDV persistence in bladder cancer cell lines
  • Functional transcriptome analysis of persistently infected cells
  • Genomic alterations in persistently infecting NDV

Genomic Surveillance & Public Health

Computational pipelines for pathogen detection and population genomics, and the systems work of embedding sequencing into national public health institutes and regional hubs across West Africa.

  • Support to national public health institutes and regional sequencing hubs
  • Diagnostic assay performance against circulating African genotypes
  • Evidence for policy on molecular diagnostics and sequencing

Training & Open Science

Building bioinformatics capacity where it is scarcest — curricula, carpentry workshops, and the community infrastructure that keeps research open, reproducible and locally owned.

  • Certified Carpentries instructor; workshop design and delivery
  • Undergraduate and postgraduate genomics curricula
  • Founder, Open Science Community Nigeria

Software and resources

OncoSeq

Softwarebabasaraki/OncoSeq

Interests

  • Genomics
  • Pathogen Genomics
  • Transcriptomics
  • Association Mapping (GWAS)
  • Disease Genomics
  • Genomic Epidemiology
  • Data Science
  • Open Science

Methods and tools

Sequencing & data

  • Illumina, Oxford Nanopore and PacBio data
  • Next-generation sequencing analysis
  • Bulk RNA-Seq, scRNA-Seq, WGS, WES
  • NCBI Nucleotide, Pathogen Detection, SRA, KEGG

Computing

  • R / Bioconductor, Python, Bash, Git, LaTeX
  • Pipeline development and workflow automation
  • HPC with SLURM; working familiarity with AWS
  • NumPy, SciPy, pandas, seaborn, Jupyter

Research & leadership

  • Leading independent research projects
  • Teaching, mentoring and curriculum design
  • Technical, report and scientific writing
  • Open science and open data advocacy
Students and collaborators. I supervise undergraduate and postgraduate projects in genomics and bioinformatics, and I am glad to hear from people who want to work on any of the strands above. Write to me.