Our HI research and innovation activities are organised around four broad themes, applicable to clinical medicine, biomedical sciences, public health, and global health. Each theme is anchored at Makerere University, co-designed with the people who'll use the results, and translated into the systems, policies, and practice that improve health outcomes. Our immediate focus is infectious diseases (viral pathogens, bacterial superbugs/AMR, and Neglected Tropical Diseases), with an explicit expansion roadmap into Non-Communicable Diseases (NCDs).
Research and Innovation Themes
Our Research
Four research and innovation themes, across clinical medicine, biomedical sciences, public health, and global health
Research themes
From data architecture and genomics to surveillance, AI, software and evaluation
HIRI's portfolio spans the full health informatics value chain. Use the cards below to jump to any theme; full descriptions follow.
01 — Interoperability and Data Architecture
Data exchange, standards and data governance
02 — Translational Genomics and Health AI
Sequence data, machine learning and prediction
03 — Digital Health Surveillance, Clinical and Field Informatics
Outbreak prediction, clinical and field informatics
04 — Digital Innovation, Software Engineering and Evaluation
Software, scalability costing and impact evaluation
Theme 01
Interoperability and Data Architecture
This theme builds and maintains the secure, open-source data exchange middleware (e.g., HL7 FHIR). It scales HIRI’s research pilots such as the NIHS and NIAMR into permanent, production-grade APIs. It integrates disparate systems by establishing real-time data syncs between public sector EMRs, private-sector hospital systems, NGO/faith-based facilities systems, and pharmacy, laboratory and billing information systems, securely normalising this data for national clinical reporting architectures. It maps clinical records to global medical terminologies (e.g., SNOMED-CT, ICD-11, LOINC) and manages the data lifecycle, access rights, and data provenance to guarantee full compliance with the health data regulations and data privacy guidelines.
Data exchange middleware
Secure, open-source middleware (e.g., HL7 FHIR), with research pilots scaled into production-grade APIs.
System integration
Real-time data syncs between public sector EMRs, private-sector hospital systems, NGO/faith-based facilities systems, and pharmacy, laboratory and billing information systems.
Terminology and data governance
Clinical records mapped to global medical terminologies, with the data lifecycle, access rights and provenance managed for compliance.
Theme 02
Translational Genomics and Health AI
This theme operates as a pure data consumer and modeler. Working from the standardised clinical records produced under Theme 01, our Bioinformaticians cleanly ingest raw digital sequence files (FASTQ / VCF) and map them against patient clinical outcomes. We run machine learning models, Nextflow workflows, and statistical genomics to automate phenotypic predictions, map plasmid-mediated antibiotic resistance, and trace viral mutation paths. Our computer science and information systems researchers also apply machine learning to disease diagnosis and prediction, personalised medicine and treatment plans, and predictive analytics for patient outcomes.
Genomic data and outcomes
Raw digital sequence files (FASTQ / VCF) mapped against patient clinical outcomes.
Resistance and mutation tracking
Machine learning models, Nextflow workflows and statistical genomics to map plasmid-mediated antibiotic resistance and trace viral mutation paths.
Health AI
Machine learning for phenotypic prediction, disease diagnosis, personalised medicine and patient outcomes.
Theme 03
Digital Health Surveillance, Clinical and Field Informatics
This theme brings together clinical informatics and field informatics to predict, detect and mitigate infectious disease outbreaks. It joins data from hospitals and health centres with spatial, environmental and community-level data, such as Geographic Information Systems (GIS), satellite climate maps and ecological vectors, to predict outbreak expansions and trace transmission networks. This covers passive, active, syndromic, and One Health surveillance for disease control, epidemic preparedness and response. The aim is to turn fragmented data streams into actionable, real-time intelligence for clinicians, epidemiologists and public health decision-makers.
Passive, active, syndromic & One Health surveillance
Detecting and tracking endemic and emerging diseases through routine, sentinel, and event-based systems.
Clinical informatics
Automated syndromic surveillance pipelines within health facilities, using NLP to screen unstructured clinical notes in EHRs, HL7 FHIR standards for real-time laboratory data extraction, and Clinical Decision Support (CDS) alerts to guide frontline triage during active threats.
Field informatics
Methods to capture disease signals before and outside health facilities, including wastewater-based epidemiology (WBE), GIS mapping of population mobility and transmission corridors, and monitoring of ecological or climatic triggers that accelerate vector-borne and zoonotic spillovers, in the districts and communities where outbreaks are first detected.
Theme 04
Digital Innovation, Software Engineering and Evaluation
This theme is the production and evaluation engine of HIRI. Our computer science and information systems researchers take the analytical scripts, models, and pipelines built by the peer themes and harden them into user-friendly software like secure UI/UX web dashboards for the MoH National Task Force. We build offline-first mobile applications optimised for community health workers operating in low-bandwidth rural districts, while our Health Economists calculate the return on investment (ROI) and cost-effectiveness of scaling the digital interventions nationally and evaluate their impact on health outcomes. We translate this work into evidence for policy- and decision-making, programmatic planning and improved health service delivery.
Software engineering
Analytical scripts, models and pipelines hardened into user-friendly software such as secure web dashboards for the MoH National Task Force.
Offline-first mobile applications
Optimised for community health workers and village health teams operating in low-bandwidth rural districts.
Scalability costing and impact evaluation
The cost, return on investment and cost-effectiveness of scaling digital interventions nationally, and evaluation of their impact on health outcomes, translated into evidence for policy- and decision-making.
Integrated across every theme
Co-design, capacity, and change management
Co-designing with users, capacity development and training, and change management are integrated across all research-project themes — for policy- and decision-makers, healthcare professionals and workers, scientists and researchers, patients, and the community.
Research projects
See HIRI's active and completed research projects
Each project sits within one or more of the four themes — from interoperable AMR surveillance to costing studies of national digital health platforms. Browse the full portfolio to see what we're working on right now and what we've delivered.