Klaas Vandepoele Lab

Research focus

The scientific objective of our research group is to extract biological knowledge from large-scale experimental data sets using data integration, comparative sequence and expression analysis, and network biology. Through the development and application of novel bioinformatics methods, new aspects of genome biology, especially in the area of gene function prediction and gene regulation, are identified.

During the last couple of years, we have mapped gene regulatory networks in Arabidopsis using a variety of experimental and computational methods. Apart from developing a transcription factor (TF)-target gene identification workflow based on the integration of novel protein-binding microarray data and multi-species promoter sequence conservation, we have also mapped regulatory interactions using >30 ChIP-Seq data sets. We actively develop new comparative methods to identify conserved non-coding sequences in dicots and monocots and have demonstrated how these show high specificity to map functional TF-target genes in plants. Whereas initial network analysis focused on the model species Arabidopsis, we are in the process of expanding our network portfolio to other dicots (e.g. poplar, soybean) and are exploring new opportunities to perform network-based gene analysis in cereals as well (maize, wheat).

Through the development of the PLAZA comparative genomics platform, we have a strong track record in tool development and plant genomics data analysis. This platform serves as an information hub for comparative, functional and evolutionary plant genomics for a large variety of plants, both in academic and industrial research. To facilitate efficient data analysis for non-model species lacking complete genome sequence information, we have developed efficient methods which offer a rich resource for functional sequence analysis of complete transcriptomes in both uni- and multicellular organisms across the tree of life.

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Publications

The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in ArabidopsisRitter A, Inigo S, Fernández-Calvo P, Heyndrickx K, Dhondt S, Shi H, De Milde L, Vanden Bossche R, De Clercq R, Eeckhout D, Ron M, Somers D, Inzé D, Gevaert K, De Jaeger G, Vandepoele K, Pauwels L, Goossens ANature Communications, 8, 15235, 2017
Structural and functional partitioning of bread wheat chromosome 3BChoulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury J, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet CSCIENCE, 345, 1249721, 2014
A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thalianaHeyndrickx K* Van De Velde J* Wang C Weigel D Vandepoele KPLANT CELL, 26, 3894-910, 2014* These authors contributed equally
PLAZA: a comparative genomics resource to study gene and genome evolution in plantsProost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele KPLANT CELL, 21, 3718-31, 2009

Job openings

Klaas Vandepoele

Klaas Vandepoele

Research area(s)

Model organism(s)

Bio

PhD: Ghent Univ., Ghent, Belgium, 2005
Postdoc: Ghent Univ. - VIB, Ghent, Belgium, 2005-11
Visiting postdoc: Lab Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France, 2006-07
Professor: Ghent Univ., Ghent, Belgium since 2011
VIB group leader as of January 2018

Contact Info

VIB-UGent Center for Plant Systems BiologyUGent-VIB Research Building FSVMTechnologiepark 927 9052 GENTRoute description