Science at Home: A Summer of Bioinformatics in Ghana

Natalie's summer research collaboration in Ghana through the Expanding Horizon's Fellowship.

Introduction

Hi, my name is Natalie Kokroko, a 2nd-year PhD student in the Computer Science Department at Rice University. My research focuses on developing and applying computational tools for microbiome and metagenomic sequencing data analysis. As someone who grew up in Ghana and now conducts advanced research in the U.S., returning home not just for vacation but to foster scientific collaboration was a fulfilling experience. It felt like weaving together two worlds I love, home and science.

I was excited for the opportunity to contribute to the growing bioinformatics scene in Ghana by spending part of my summer at the West African Centre for Cell Biology of Infectious Pathogens WACCBIP where I once was an intern in the Genomics and Bioinformatics unit.

Acknowledgement

Before I take you through my experience, I would like to acknowledge the Expanding Horizons Fellowship sponsor, Dr. Walter Loewenstern for making this dream a reality. I would also like to thank my PhD advisor, Dr. Todd Treangen for supporting my interest in building research connections back home, and to Prof.Samuel Duodu at the University of Ghana for welcoming me into his research group and exploring opportunities for collaboration.

From Houston to Accra

From Houston to Accra, the journey was long but deeply fulfilling. It began with a 3.5-hour flight to Washington, D.C., followed by an 11-hour overnight flight across the Atlantic to Accra, Ghana. After months of planning and anticipation, I was finally home. Waiting for me at the airport were two familiar faces, my sister and our dog, Sibeau, ready with warm hugs and wagging tails.

About WACCBIP

The West African Centre for Cell Biology of Infectious Pathogens is a world-class biomedical research institute based at the University of Ghana, my Alma Mater. WACCBIP’s research focuses on genomic and molecular biology which involves generating lots of sequencing data: from human samples, pathogens or microbiomes. With this knowledge, I sought to apply the bioinformatics skills I have been equipped with over the course of my PhD to some data in Ghana.

One of the first people I connected with was Prof. Samuel Duodu from the Department of Biochemistry at the University of Ghana. Prof. Duodu expressed a strong interest in establishing a collaboration, and we arranged meetings to discuss ongoing projects, data needs, and potential joint research directions. I also had the chance to work closely with one of his research assistants, whose focus is on building bioinformatics pipelines. Together, we compared workflows, exchanged ideas, and discussed how different computational approaches could improve analysis outcomes.

During my first week, I had the opportunity to meet a number of the new interns from my alma mater which is University of Ghana where the research centre(WACCBIP) is located. It was a pleasure telling them about my graduate school experience and the kind of research in Bioinformatics I am currently doing. I was thrilled to see my undergraduate research advisor, Prof. Samuel Kwofie, the Head of the Biomedical Engineering Department. These conversations were a key part of my visit’s capacity-building mission: inspiring early-career scientists and strengthening Ghana’s next generation of bioinformatics researchers.

The Scientific Focus

During my stay,Prof. Duodu took me through some of the projects his research group is working on and the need for bioinformatics pipelines that would be able to make the projects go a long way. I was introduced to an exciting ongoing research project focused on non-malarial febrile illnesses. Cases where patients present with fever symptoms, but test negative for Plasmodium, the parasite responsible for malaria. These illnesses are often caused by a wide range of bacterial and viral pathogens, and identifying their exact etiology is crucial for effective diagnosis and treatment. The team’s approach is not just to detect pathogens, but also to understand the host’s immune response to these infections.

They are currently working with a large collection of biological samples gathered from patients in the field. These samples, collected from individuals experiencing febrile illness but without malaria, offer a valuable resource for both host transcriptomic analysis and pathogen detection. On the pathogen side, they plan to use metagenomic sequencing to comprehensively identify the bacteria, viruses, fungi, or parasites present in the samples.

The next step in this project involves using metagenomic sequencing to detect and identify the pathogens present in these samples. Once the sequencing is completed, the data will require a full bioinformatics pipeline; from raw read processing to taxonomic classification and downstream analysis. This is where my expertise from the Treangen Lab comes in.

I introduced several tools and resources developed in the Treangen Lab, including our GitHub repositories and relevant documentation. These tools, designed for metagenomic data analysis, could be adapted to help process the sequencing data once available. I also had productive discussions with the research team about how these pipelines could fit into their analysis workflow and how future improvements could be tailored to better suit their data.

While the sequencing phase is still in progress, we’ve laid the foundation for a strong collaborative relationship. We’ve scheduled follow-up meetings to continue developing this project, and I’m looking forward to receiving the first batches of data to begin analysis. This partnership holds strong potential for both impactful research and capacity building in genomic epidemiology and pathogen detection in Ghana.

Excited about working with data sequenced in Ghana that is relevant to them out there. This is only the beginning of the collaboration, and I am glad I had this opportunity to establish this collaboration between my alma mater and Rice University. In the next few months, I am hoping to receive the data after sequencing in order to run some analysis which I believe will lead to a collaborative publication.

Accomplishments This Summer

  1. Initiated a collaboration between the Treangen Lab at Rice University and WACCBIP at the University of Ghana.

  2. Engaged in capacity building by mentoring interns and junior researchers in bioinformatics tools, workflows, and graduate school pathways.

  3. Shared computational resources (pipelines, scripts, and documentation) to support local analysis workflows.

Looking Ahead

Although the sequencing data is not yet available, the foundation has been laid for a productive and impactful partnership. In the coming months, I will work with the WACCBIP team to process the first datasets, perform pathogen identification. We anticipate that this work will lead to joint publications and, more importantly, provide actionable insights for public health in Ghana.

What This Experience Meant to Me

Being able to connect with my home country on a scientific level was not just rewarding, it was inspiring. Seeing the depth and quality of research being done at WACCBIP reinforced my belief that African-led science has a powerful role to play in global health. This trip reminded me that research is not just about data and algorithms; it’s about building bridges between countries, institutions, and people to solve problems that matter.

I am deeply grateful to the Expanding Horizons Fellowship for making this experience possible and for supporting scholars like me in pursuing opportunities that strengthen global scientific collaboration.