Professor Jonathan Blackburn

Applied Proteomics & Chemical Biology Group

Professor Jonathan Blackburn PhD MASSAf

South African Research Chair in Applied Proteomics & Chemical Biology; Deputy Director, Institute of Infectious Disease and Molecular Medicine (IDM); Head of Division Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences; Head, D-CYPHR Molecular Phenotyping Hub, IDM. Jonathan Blackburn is an elected member of the Academy of Science of South Africa, of the Council of the Human Proteome Organisation, a University of Cape Town Fellow.

Jonathan applies expertise has gained in academia and in a United Kingdom start-up biotech environment to drive interdisciplinary, collaborative translational research programs in the precision medicine field, aimed at providing a new level of understanding and prediction concerning the individual nature of disease progression and drug response.

His research strategy is to leverage his Research Group's established technological platforms, technical expertise, and clinical collaborations to create internationally leading clinical proteomics research programs that have a strong translational emphasis. Their overarching goal is to combine basic and clinical research to create a pipeline from protein and antibody biomarker discovery, through to validation, and ultimately to application in the human health sector.

Jonathan's academic expertise ranges from mechanistic enzymology, protein biochemistry, molecular biology to protein microarrays and mass spectrometry-based proteomics. He is currently interested in the translational applications of protein microarray technology, as well as mass spectrometry-based proteomics and metabolomics, in diagnostic marker discovery and validation, in unravelling molecular mechanisms of disease, and in predicting patient response to treatment in cancers, autoimmune- and infectious diseases. He has published over 100 peer reviewed papers, nine book chapters and has 32 granted patents.

Current research projects include use of protein microarrays and proteomics for:

  • Discovery and validation of diagnostic protein biomarkers of pancreatic, prostate, lung and colorectal cancers, as well as melamona;
  • Discovery and validation of protein biomarkers that predict patient response to therapy in lung cancer, melamona, and autoimmune diseases;
  • Development of antigen microarrays for systems serological analysis of patient disease status in neurological and autoimmune disorders, as well as infectious diseases;
  • Mass spectrometry-based mechanistic studies on tuberculosis disease, HIV-associated TB immune reconstitution inflammatory syndrome and HIV-associated neurocognitive disorders; 
  • Mass spectrometry-based discovery and validation of diagnostic urinary biomarkers of TB disease, schistosomiasis, Covid-19 and prostate cancer; and
  • Mass spectrometry-based identification of microbial effectors in gut microbiomes of HIV-exposed infants through metaproteomics

Selected publications:

See publications on the NIH National Library of Medicine.

Contact details:

N3.06 Wernher & Beit Building
Institute of Infectious Disease and Molecular Medicine
Faculty of Health Sciences, University of Cape Town
Anzio Road
Observatory, 7925
South Africa
Tel: +27 21 4066071

Alternate site:

Group members:

Member Position
Tariq Ganief   Senior Research Officer
Andrew Nel Senior Research Officer
Muneerah Smith Senior Research Officer
Katie Lennard Chief Scientific Officer
Shaun Garnett Senior Research Officer
Janique Peyper Senior Research Officer
Nicolette Hendricks-Leukes Senior Research Officer
Fezile Khumalo Research Officer
Liam Bell D-CYPHR Hub lead
Michelle Du Plessis Technical Officer
Xolani Nonzinyana Technical Officer
Nyameka Mhlonyelwa-Mona Administrator
Brandon Murugan  PhD student
Risa Bagwandin PhD student
Darien Schell PhD student
John Iradukunda PhD student
Seanantha Baros PhD student
Nina Radzey PhD student
Andrea Abrahams  PhD student
Pamela Maimela MSc student
Michelle Mullins MSc student
Tara Miller MSc student


Jonathan has numerous inter-disciplinary and inter-institutional research collaborations, within UCT, nationally and internationally, underpinned by major international, collaborative grants. Amongst other these currently include:

  • Within UCT: Profs Dheda, Burgers, Ntusi, Horsnell, Mulder, Meintjes, Warner, Mizrahi and Passmore;
  • Nationally: Profs Madhi and Mayne (Wits), Dr Sigal (AHRI);
  • Internationally: Profs Haselton and Wright (Vanderbilt University), Prof Cebon (ONJCRI, Australia), Prof Abimiku (University of Maryland), Dr Masson (Burnet Institute, Australia), Dr Jaspan (Seattle Childrens), Prof Middleton (University of Birmingham), Prof Stensballe (Aalborg University)