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Intrigued by the rapid technological advances is biotechnology, I started my PhD in 2003 mainly focusing on the development of methods to study molecular interactions in plants. My initial interest was to transfer and optimize tandem affinity purification coupled to mass spectrometry to study protein complexes in plants. During my PhD and post-doc, I continuously challenged myself to further improve and fine-tune these methods, enabling investigation of not only stable but also more transient and weak protein interactions from a diverse set of plant tissues/species. This finally led to the development of a streamlined technology platform, which formed the base of the current Plant Interactomics Facility at PSB, delivering internal and external AP-MS service for academia and industry.
In parallel I also invested quite some time in the development of methods to study interactions between proteins and DNA in situ, giving rise to the TChAP-seq technology in cell suspension cultures that provides deep coverage in the mapping of gene regulatory networks. As a complementary approach, I have been exploring methods to study protein-DNA interactions from a gene-centered view, identifying proteins bound to a genomic region of interest.
From a biological perspective, I initially applied these methods to obtain more insight into how plant cells proliferate, studying protein complexes that involve core cell cycle regulators. This allowed me to map a comprehensive cell cycle interactome in plants. In recent years, I switched my interest trying to understand how plants sense energy and nutrients and translate this information into adequate growth responses. Hereto, I am investigating the dynamic signaling networks around the TOR and SnRK1 kinases, integrating interactomics with phosphoproteomics.

Post-doctoral fellow

Judith is a postdoctoral scientist in the group of Prof. Sofie Goormachtig at VIB-UGent Center for Plant Systems Biology (FWO fellowships) since 2019. She obtained her PhD in 2016 in the group of Prof. Dirk Inze, where she focused on the regulation of Arabidopsis leaf growth by sugars. After her PhD, she joined the group of Dr. Vanessa Wahl at the Department of Prof. Mark Stitt in the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany), where she studied the effect of limited nitrogen availability on flowering and tuberization in Arabidopsis and potato. In her current research, she uses this expertise to investigate plant-microbe symbiotic interactions in different plant crops. Her main focus is unraveling the role of sugar signaling during soybean and pea nodulation.

Between 2008 and 2012, I was a PhD student in the group of Yves van de Peer and guided by Klaas Vandepoele, doing research and software development in the fields of comparative and functional genomics. During this time, I developed the PLAZA platform (https://bioinformatics.psb.ugent.be/plaza). After obtaining my PhD in 2012, I joined the Applied Bioinformatics and Biostatistics (ABB) group, which provides support to the PSB Center in a variety of fields: from help with small scripts to large scale project analyzes. Meanwhile, I am still the main developer of the PLAZA platform, which is co-developed with the group of Klaas Vandepoele and ELIXIR Belgium.
 

PhD fellow

Simon Tack obtained his Bachelors in Biochemistry and Biotechnology at the University of Ghent (UGhent, Belgium). He stayed at UGhent to persue a Master in Molecular Plant Biology. During his Master-thesis he joined the VIB-UGhent 'Oxidative Stress Signaling' lab (led by Prof. Dr. F. Van Breusegem) where he focused on showing Metacaspase activity using FRET-based sensors under the guidance of Dr. A.D. Fernandez Fernandez and Prof. Dr. S. Stael. In November 2022 he joined the OSS lab as a PhD fellow and continues his efforts on showing protease activity in plants (Arabidopsis thaliana and Brassica napus) under the direct supervision of Prof. Dr. Van Breusegem.

Naomi obtained her master’s degree in Biochemistry and Biotechnology from Ghent University in 2020. For her master’s thesis she performed an Erasmus exchange to the Sainsbury lab of Cambridge University (SLCU), where she worked on the role MtLSH1 and MtNOOT1/2 during early nodule organogenesis in Medicago truncatula within the group of Prof. Dr. Giles Oldroyd. Currently, Naomi is performing her PhD research (FWO-SB fellowship) at the Rhizosphere group of Prof. Dr. Sofie Goormachtig, this time shifting her focus to another symbiont: arbuscular mycorrhizal fungi (AMF). During her PhD, Naomi uses diverse single cell and -nuclei transcriptomics and proteomics approaches to obtain a better understanding of the immunity-related crosstalk occurring during the tomato-AMF symbiotic interaction.