PhD fellow job at Infectious Diseases Institute (IDI)

General Summary

The African Centre of Excellence in Bioinformatics and Data-Intensive Sciences (ACE) at the Infectious Diseases Institute, Makerere University, invites applications for two (2) PhD fellowship positions under the AIMAR project, funded by the Google.

AIMaR is a multidisciplinary research project that applies advanced artificial intelligence tools, including the EVE (Evolutionary model of Variant Effect) framework and AlphaFold 3, to predict and characterize mutations across the Plasmodium falciparum proteome. The project aims to identify mutations relevant to malaria surveillance, drug resistance, and vaccine design, and to associate these with epidemiological and clinical parameters using a decade's worth of annotated samples collected from multiple sites across Uganda.

The PhD fellows will be embedded within the AIMAR research team and will develop and lead independent doctoral research in line with the project's aims. Fellows are expected to produce at least two first-authored peer-reviewed publications during their doctoral training, benefiting from mentorship by experienced researchers across bioinformatics, structural biology, epidemiology, and malaria science.

Benefits of the Project

• Tuition support and a stipend for a 3-year full-time PhD programme.
• Coverage of research ethics approval fees for the PhD research project.
• Access to a high-performance computing platform.
• Mentorship from experts in the fields of malaria and artificial intelligence (AI).

Key Responsibilities

• Develop an independent doctoral research proposal in malaria bioinformatics or computational biology, aligned with the aims and scope of the AIMaR project, in consultation with the project's principal investigators.
• Design and execute the doctoral project from conceptualization through to data analysis, interpretation, and dissemination.
• Prepare and defend a PhD thesis meeting all requirements of Graduate Studies.
• Write a minimum of two first-authored peer-reviewed publications arising from the doctoral research.
• Attend and present research findings at AIMAR team meetings, institutional seminars, and at national and international scientific conferences.
• Where relevant, provide research mentorship and guidance to MSc students engaged in the AIMAR project.
• Contribute to project reports and deliverables as required by the project team and the funder.
• Maintain thorough documentation of research activities, datasets, and analytical workflows.
• Adhere to all ethical standards governing the conduct of research involving human biological samples and associated clinical and epidemiological data.

Academic Qualifications

• Masters of Science in Bioinformatics
• Master's of Science in Computational Biology
• Masters of Science in Structural Biology
• Master of Science in Molecular Biology

Person Specification

Eligibility

• A master's degree in bioinformatics, computational biology, structural biology, molecular biology or a closely related field with a strong quantitative component.
• Applicants should provide proof of admission to a PhD programme.
• Applicants should be available on a full-time basis.

Experience

• Demonstrated research experience in bioinformatics, computational biology, structural biology, or a closely related area, as evidenced by an MSc thesis, publications, or equivalent research work.
• Proficiency in Python and/or R for biological data analysis, with a portfolio of applied work.
• Working knowledge of Linux/Unix environments and High Performance Computing (HPC) systems.
• Experience with biological sequence or structural databases (e.g., NCBI, UniProt, PlasmoDB, PDB, AlphaFold DB).
• Experience with AI or machine learning tools applied to biological data, including variant effect prediction, protein structure modeling, or related applications.
• Understanding of malaria biology, P. falciparum genomics, antimalarial drug resistance mechanisms, or vaccine antigen biology.
• Experience contributing to collaborative, multidisciplinary research teams.

• Develop an independent doctoral research proposal in malaria bioinformatics or computational biology, aligned with the aims and scope of the AIMaR project, in consultation with the project's principal investigators.
• Design and execute the doctoral project from conceptualization through to data analysis, interpretation, and dissemination.
• Prepare and defend a PhD thesis meeting all requirements of Graduate Studies.
• Write a minimum of two first-authored peer-reviewed publications arising from the doctoral research.
• Attend and present research findings at AIMAR team meetings, institutional seminars, and at national and international scientific conferences.
• Where relevant, provide research mentorship and guidance to MSc students engaged in the AIMAR project.
• Contribute to project reports and deliverables as required by the project team and the funder.
• Maintain thorough documentation of research activities, datasets, and analytical workflows.
• Adhere to all ethical standards governing the conduct of research involving human biological samples and associated clinical and epidemiological data.

• Proficiency in Python and/or R for biological data analysis, with a portfolio of applied work.
• Working knowledge of Linux/Unix environments and High Performance Computing (HPC) systems.
• Experience with biological sequence or structural databases (e.g., NCBI, UniProt, PlasmoDB, PDB, AlphaFold DB).
• Experience with AI or machine learning tools applied to biological data, including variant effect prediction, protein structure modeling, or related applications.
• Understanding of malaria biology, P. falciparum genomics, antimalarial drug resistance mechanisms, or vaccine antigen biology.
• Experience contributing to collaborative, multidisciplinary research teams.

• Masters of Science in Bioinformatics
• Master's of Science in Computational Biology
• Masters of Science in Structural Biology
• Master of Science in Molecular Biology
• A master's degree in bioinformatics, computational biology, structural biology, molecular biology or a closely related field with a strong quantitative component.
• Proof of admission to a PhD programme.
• Availability on a full-time basis.
• Demonstrated research experience in bioinformatics, computational biology, structural biology, or a closely related area, as evidenced by an MSc thesis, publications, or equivalent research work.