Biography

Hey, I am Umar!

I am an accomplished computational genomicist and the Head of the Anatomy Department at Bauchi State University, Nigeria. With a distinguished career in genetics and a focus on the regulatory pathways driving tumour recurrence and progression, my pioneering work primarily revolves around bladder cancer transcriptomics (RNA-Seq, scRNA-Seq, Microarray) and genomics (WGS, WES). I boasts a profound skill set in managing large scale genomic data, developing R/Bioconductor packages and utilising high-throughput sequence data analysis tools. As a passionate Open Science advocate, I founded the Open Science Community Nigeria to promote transparency and collaboration in scientific research and I am actively involved with an international team of scholarly professionals at AfricArXiv - the pan-African Open Access portal that increased discoverability of African research output. My role involves facilitating manuscript submission moderation and quality assurance.

Additionally, I have been actively involved in providing technical support to the National Public Health Institutes (NPHIs) and Regional Sequencing Hubs within the West African Region at Africa CDC. Specifically, I have been collaborating with institutions such as IPD Senegal, Nigeria CDC, NMIMR Ghana, ACEGID Nigeria and all the NPHIs. My role is to offer guidance and expertise to ensure effective implementation of the pathogen genomics programme across these laboratories and institutes. As the STO for Pathogen Genomics, I work closely with the NPHIs and Regional Hubs to enhance their capabilities in responding to outbreaks and improving infectious disease surveillance. This involves providing technical assistance, sharing best practices, and supporting the development and implementation of robust sampling methods, sequencing protocols, and data analysis techniques. Furthermore, my responsibilities include facilitating the establishment and functioning of a laboratory network within the Western RCC. This entails coordinating referrals, implementing quality assurance systems, and ensuring compliance with minimum quality standards for genomics laboratories.

I am passionate about the opportunities to collaborate with biologists, scientists, pathologists, data scientists to develop effective strategies to better understand and treat cancers and infectious diseases (pathogens). I am occasionally found on Twitter @babasaraky, sharing science and most of the time on Github, organising codes and repositories.

Interests

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

Skills

  • Next-generation sequencing data analysis
  • Pipeline development
  • Extensive experience with RNA- Seq
  • Genomics analysis
  • Programming: R, Bash, Python, Git and LaTeX
  • Packages: SciPy, Pandas, Jupyter Tools, Seanborn
  • Effective communication skills
  • Open Science and Open Data