Johan van Heerden / Assistant professor

I’m currently involved in several research projects, including the study of single bacterial cell (E. coli and B. subtilis) growth rate regulation, quantification of the fitness contribution of every non-essential S. cerevisiae gene in adaptations to oxygen availability fluctuations, and the development and characterization of FRET-based metabolite sensors.

My main focus is on growth rate regulation in single bacterial cells, investigating how the fundamental growth laws derived from population-level measurements relate to the growth behaviour of individual cells. To this end, I employ time-lapse microscopy and an in-house-developed generic pipeline for monitoring, segmenting and tracking of individual cells in dense bacterial cultures.


To view a summary of the pipeline, click here.

Examples of brightfield time-lapse segmentation for different microorganisms

E. coli

Schizosaccharomyces pombe

Bacillus subtilis

Research interests
Non-genetic origins of phenotypic variability
Coordination of growth and metabolism
Dynamic (fast) and adaptive (slow) aspects of metabolic regulation
Metabolic and physiological adaptation strategies
Single-cell measurement techniques
Developing and improving experimental methodologies

About me
I obtained my B.Sc. (2006) and M.Sc. (2009) degrees in molecular cell biology from the University of Cape Town (South Africa). I started my research career by investigating the potential to exploit gene expression profiles of peripheral tissues as non-invasive diagnostic indicators of psychiatric states, which culminated in my M.Sc. dissertation. In 2009, I joined Prof. Bas Teusink as a PhD student, venturing into the world of microbial physiology and metabolism. In this position, I researched the dynamic regulation of glycolysis in baker’s yeast, focusing on the role that trehalose metabolism plays during transitions from low to high glucose environments.

In 2014, I joined Prof. Frank Bruggeman as a post-doctoral research, where I set out to understand how the processes of growth and division impact the stability and variability of phenotypic traits in microbial populations. In this position, I co-developed a pipeline for the automated segmentation and tracking of individual cells in dense bacterial cultures.

Recently, I became a staff member in the Systems Bioinformatics group, where I am involved in several research projects while continuing to pursue a deeper understanding of growth processes at the single cell level.

Contact me
Vrije Universiteit Amsterdam
De Boelelaan 1108, 1081 HZ, Amsterdam
Faculty of Earth and Life Science
Room O|2 01W55
tel: +31 (0)20 598 6993
mail: please click my photo



N Nordholt, J van Heerden, R Kort, FJ Bruggeman (2017). Effects of growth rate and promoter activity on single-cell protein expression. Scientific Reports 7:6229

C van Boxtel, JH van Heerden*, N Nordholt, P Schmidt, FJ Bruggeman (2017). Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments. Journal of The Royal Society Interface 14 (132), 20170141

JH van Heerden*, H Kempe, A Doerr, T Maarleveld, N Nordholt, FJ Bruggeman (2017). Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli. Scientific Reports 7:16094

*Shared first authorship


Iraes Rabbers, Johan H. van Heerden, Niclas Nordholt, Herwig Bachmann, Bas Teusink, Frank J. Bruggeman (2015). Metabolism at evolutionary optimal States. Metabolites (2):3

JH van Heerden, FJ Bruggeman, B Teusink (2015). Multi‐tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic. BioEssays 37 (1), 34-45


Johan H van Heerden, Meike T Wortel, Frank J Bruggeman, Joseph J Heijnen, Yves JM Bollen, Robert Planqué, Josephus Hulshof, Tom G O’Toole, S Aljoscha Wahl, Bas Teusink, (2014). Lost in Transition: Startup of Glycolysis Yields Subpopulations of Nongrowing Cells. Science, 1245114

Johan H van Heerden, Meike T Wortel, Frank J Bruggeman, Joseph J Heijnen, Yves JM Bollen, Robert Planqué, Josephus Hulshof, Tom G O’Toole, S Aljoscha Wahl, Bas Teusink, (2014). Fatal attraction in glycolysis: how Saccharomyces cerevisiae manages sudden transitions to high glucose. Microbial Cell 1 (3), 103-106


JH van Heerden, V Russell, A Korff, DJ Stein, N Illing, (2010). Evaluating the behavioural consequences of early maternal separation in adult C57BL/6 mice; the importance of time. Behavioural brain research 207 (2), 332-342

DS Williamson, KC Dent, BW Weber, A Varsani, J Frederick, RN Thuku, RA Cameron, JH van Heerden, DA Cowan, BT Sewell, (2010). Structural and biochemical characterization of a nitrilase from the thermophilic bacterium,Geobacillus pallidus RAPc8. Appl. Microbiol. Biotechnol. 88:143-153 [DOI] [PubMed]


J van Heerden, A Conesa, D Stein, D Montaner, V Russell, N Illing, (2009). Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse. BMC research notes 2 (1), 195


J van Heerden, SA Walford, A Shen, N Illing, (2007). A framework for the informed normalization of printed microarrays. South African Journal of Science 103 (9-10), 381-390

N. Illing, S. Walford, A. Shen, J. van Heerden, N. Immelman, N. Mulder, DK. Denby, (2007). Molecular tools to study desiccation tolerance in the resurrection plant Xerophyta humilis. South African J. Bot. 73:487-487

Supervision of students (BSc and MSc)

NameCo-supervisor(s)Project titleBSc/MScYear
Mirushe IsakuFrank BruggemanTowards Schizosaccharomyces pombe as an alternative model for eukaryotic metabolismBSc2017
Ioanna ChatzigiannidouFrank BruggemanModulating stress susceptibility in E. coli through environmental conditioningMSc2015
Coco van BoxtelFrank BruggemanImplementing and evaluating Spinach2 for in vivo flourescence based monitoring of intracellular ADP levels in E. coliMSc2015
Joyce LamBas Teusink/Joachim GoedhartIn vitro characterizing of the pH-dependence of FRET-sensors for glycoltyic intermediatesMSc2014
Phillipp SchmidtFrank Bruggeman/Anne SchwabeQuantifying the reciprocal regulation of the PFK/FBP enzyme pair in yeast, using RNA FISHMSc2014
Valentijn JansenBas TeusinkEvaluting the pH dependence of glycolytic enzyme activitiesBSc2013
Wen KorrelBas TeusinkImplementing FRET-sensors for the in vivo quantification of glycolytic metabolites in S. cerevisiaeBSc2013
Sandra WindhorstBas TeusinkIntracellular pH dynamics of tps1- mutantsBSc2011
Bahar RamezanpourBas TeusinkGlucose tolerance of tps1- mutantsBSc2010