Steven Maere Lab

Research focus

Modeling the evolution of transcriptional systems in silico 
For the past few decades, the field of molecular evolution has largely focused on the evolution of individual gene families and overall genome structure. Analogous to the transition from reductionist to system-scale approaches in molecular biology, the logical next step in molecular evolution research is to study the evolution of genes in the context of the systems in which they function. One way to study how systems of interacting components evolve is to simulate the evolution of suitably abstracted system models in silico. Given recent developments in the field of high-performance computing, it is now possible to simulate the evolution of molecular systems at an unprecedented level of mechanistic detail. We use mathematical models to map the genotype of artificial transcriptional regulatory systems to their expression phenotype. We then use these models in population-scale evolutionary simulations to investigate how transcriptional systems evolve. One of our major research interests is to study how duplicated transcriptional systems diverge. We are particularly interested in unraveling the mechanisms by which dosage-balance constraints on duplicated transcription factors can be resolved over evolutionary time. Many regulatory genes do not duplicate easily on their own, because duplication upsets their dosage balance with other transcription factors or targets. Whole-genome duplication (WGD) on the other hand is thought to preserve dosage balance, and moreover to lead to selective retention of dosage-balance sensitive genes, since their loss after WGD would create a reverse dosage balance effect. As a consequence, post-WGD organisms are endowed with a 'regulatory spandrel’, a collection of regulatory genes that may not immediately add extra functionality but that cannot be purged easily from the genome. It is thought that under the right circumstances, these non-adaptively preserved genes may be co-opted for adaptive innovations, but this requires that the dosage-balance constraints be lifted, and it is currently not clear how this is accomplished.
 Profiling individual field-grown plants to reverse engineer plant systems and crosstalk between stress pathways
 To develop crops with enhanced yield and tolerance to field stress conditions, we need to fundamentally change our approach to studying stress response pathways in plants. Most stress studies performed under controlled laboratory conditions are of limited predictive value for phenotypes in the field. In lab conditions, stress responses are usually studied in isolation, whereas in the open environment a multitude of stresses operate in synergistic and antagonistic interaction to modulate plant phenotypes. To get a view on the complex interactions between plant stress response pathways and their effect on yield phenotypes, we aim to harness natural gene expression and phenotype variation among genetically identical field-grown plants, based on the premise that each individual plant is subject to subtle deviations of several micro-environmental factors from the field average. We are currently developing methods to use individual plant datasets for reverse engineering stress response pathways, their interaction and their impact on yield-related phenotypes, focusing on maize and rapeseed as model crops.


Interspecific hybridization facilitates niche adaptation in beer yeast.Gallone Brigida* Steensels Jan* Mertens Stijn Dzialo Maria Gordon Jonathan Wauters Ruben Thesseling Florian Bellinazzo Francesca Saels Veerle Herrera-Malaver Beatriz Prahl Troels White Christopher Hutzler Mathias Meußdoerffer Franz Malcorps Philippe Souffriau Ben Daenen Luk Baele Guy Maere Steven@ Verstrepen Kevin@Nature Ecology & Evolution, 3, 1562-1575, 2019* or °: authors contributed equally@: corresponding authors
A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress AdaptationBhosale R* Boudolf V* Cuevas Bustamante F Lu R Eekhout T Hu Z Van Isterdael G Lambert G Xu F Nowack M Smith R Vercauteren I De Rycke R Storme V Beeckman T Larkin J Kremer A Höfte H Galbraith D Kumpf R Maere S* De Veylder L*PLANT CELL, 30, 2330-2351, 2018* or °: authors contributed equally
Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance SensitivityTasdighian Setareh Van Bel Michiel Li Zhen Van de Peer Yves Carretero-Paulet Lorenzo Maere StevenPLANT CELL, 29, 2766-2785, 2017
Domestication and Divergence of Saccharomyces cerevisiae Beer YeastsGallone B* Steensels J* Prahl T Soriaga L Saels V Herrera B Merlevede A Roncoroni M Voordeckers K Miraglia L Teiling C Steffy B Taylor M Schwartz A Richardson T White C Baele G Maere S* Verstrepen K*CELL, 166, 1397-1410, 2016* or °: authors contributed equally
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundaryVanneste K Baele G Maere S* Van De Peer Y*GENOME RESEARCH, 24, 1334-47, 2014* or °: authors contributed equally

Job openings


The secret of classic Belgian beers? Medieval super yeasts!

21/10/2019 - A team of scientists, led by Kevin Verstrepen (VIB-KU-Leuven) & Steven Maere (VIB-UGent), has discovered that some of the most renowned classic Belgian beers, including Gueuze and Trappist ales, are fermented with a rare form of hybrid yeasts.

Beer yeasts are dogs, wine yeasts are cats

08/09/2016 - Researchers from VIB, KU Leuven and Ghent University found that yeasts used for beer and winemaking have been domesticated in the 16th century, around 100 years before the discovery of microbes.

Steven Maere

Steven Maere

Research area(s)

Model organism(s)


​​PhD: VIB-Ghent Univ., Ghent, Belgium, 2006
Visiting Postdoc.: Univ. California, Berkeley, USA, 2008-09
VIB Group leader since October 2009

Contact Info

VIB-UGent Center for Plant Systems BiologyUGent-VIB Research Building FSVMTechnologiepark 71 9052 GENTRoute description