publications

162. Northern light reviews – Application of orthology and network biology to infer gene functions in non‐model plants

Klaas Vandepoele, Sander Thierens, Michiel Van Bel

(2024) - Physiologia Plantarum

DOI
161. MINI‐AC: inference of plant gene regulatory networks using bulk or single‐cell accessible chromatin profiles

Nicolás Manosalva Pérez, Camilla Ferrari, Julia Engelhorn, Thomas Depuydt, Hilde Nelissen, Thomas Hartwig, Klaas Vandepoele

(2024) - The Plant Journal

DOI
160. Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction

Sien Audoor, Gust Bilcke, Katerina Pargana, Darja Belišová, Sander Thierens, Michiel Van Bel, Lieven Sterck, Nadine Rijsdijk, Rossella Annunziata, Maria Immacolata Ferrante, Klaas Vandepoele, Wim Vyverman

(2024) - Molecular Ecology

DOI
159. Arabidopsis transcription factor ANAC102 predominantly expresses a nuclear protein and acts as a negative regulator of methyl viologen-induced oxidative stress responses

Xiaopeng Luo, Xinqiang Jiang, Vivian Schmitt, Shubhada R Kulkarni, Huy Cuong Tran, Sylwia M Kacprzak, Frank Van Breusegem, Olivier Van Aken, Klaas Vandepoele, Inge De Clercq, Saijaliisa Kangasjärvi

(2024) - Journal of Experimental Botany

DOI
158. An Improved Chromosome‐scale Genome Assembly and Population Genetics resource for Populus tremula.

Kathryn Megan Robinson, Bastian Schiffthaler, Hui Liu, Sara M. Rydman, Martha Rendón‐Anaya, Teitur Ahlgren Kalman, Vikash Kumar, Camilla Canovi, Carolina Bernhardsson, Nicolas Delhomme, Jerry Jenkins, Jing Wang, Niklas Mähler, Kerstin H. Richau, Victoria Stokes, Stuart A'Hara, Joan Cottrell, Kizi Coeck, Tim Diels, Klaas Vandepoele, Chanaka Mannapperuma, Eung‐Jun Park, Stephane Plaisance, Stefan Jansson, Pär K. Ingvarsson, Nathaniel Street

(2024) - Physiologia Plantarum

DOI
157. Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses

Anikó Meijer, Mohammad Reza Atighi, Kristof Demeestere, Tim De Meyer, Klaas Vandepoele, Tina Kyndt

(2023) - Plant Physiology

DOI
156. Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots

Li Liu, Michel Heidecker, Thomas Depuydt, Nicolas Manosalva Perez, Martin Crespi, Thomas Blein, Klaas Vandepoele

(2023) - Plant Physiology

DOI
155. Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division

Alex Willems, Yuanke Liang, Jefri Heyman, Thomas Depuydt, Thomas Eekhout, Balkan Canher, Hilde Van den Daele, Ilse Vercauteren, Klaas Vandepoele, Lieven De Veylder

(2023) - Plant Physiology

DOI
154. MINI-EX version 2: cell-type-specific gene regulatory network inference using an integrative single-cell transcriptomics approach

Jasper Staut, Nicolás Manosalva Pérez, Thomas Depuydt, Klaas Vandepoele, Svitlana Lukicheva

(2023) -

DOI
153. Charting plant gene functions in the multi-omics and single-cell era

Thomas Depuydt, Bert De Rybel, Klaas Vandepoele

(2023) - Trends in Plant Science

DOI
152. Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation

Jirina Zackova Suchanova, Gust Bilcke, Beata Romanowska, Ali Fatlawi, Martin Pippel, Alastair Skeffington, Michael Schroeder, Wim Vyverman, Klaas Vandepoele, Nils Kröger, Nicole Poulsen

(2023) - New Phytologist

DOI
151. Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types.

Vandepoele K, Kaufmann K

(2023) - Methods in molecular biology (Clifton, N.J.)

DOI
150. Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information.

Manosalva Pérez N, Vandepoele K

(2023) - Methods in molecular biology (Clifton, N.J.)

DOI
149. Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice.

Smet D, Opdebeeck H, Vandepoele K

(2023) - Frontiers in plant science

DOI
148. Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS repressor proteins to reprogram plant immunity and development

Lore Gryffroy, Evi Ceulemans, Nicolás Manosalva Pérez, Jhon Venegas-Molina, Ana Cristina Jaramillo Madrid, Savio Rodrigues, Liesbeth De Milde, Veronique Jonckheere, Marc Van Montagu, Barbara De Coninck, Klaas Vandepoele, Petra Van Damme, Alain Goossens

(2023) - Proceedings of the National Academy of Sciences

DOI
147. A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis

Hieu Nguyen Trang, Louis Thiers, Alex Van Moerkercke, Yuechen Bai, Patricia Fernández Calvo, Max Minne, Thomas Depuydt, Maite Colinas, Kevin Verstaen, Gert Van Isterdael, Hans-Wilhelm Nützmann, Anne Osbourn, Yvan Saeys, Bert De Rybel, Klaas Vandepoele, Andres Ritter, Alain Goossens

(2023) - Nature Plants

DOI
146. Distinctive and complementary roles of E2F transcription factors during plant replication stress responses

Maherun Nisa, Thomas Eekhout, Clara Bergis, Jose-Antonio Pedroza-Garcia, Xiaoning He, Christelle Mazubert, Ilse Vercauteren, Toon Cools, Rim Brik-Chaouche, Jeannine Drouin-Wahbi, Layla Chmaiss, David Latrasse, Catherine Bergounioux, Klaas Vandepoele, Moussa Benhamed, Lieven De Veylder, Cécile Raynaud

(2023) - Molecular Plant

DOI
145. PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

Michiel Van Bel, Francesca Silvestri, Eric M Weitz, Lukasz Kreft, Alexander Botzki, Frederik Coppens, Klaas Vandepoele

(2022) - Nucleic Acids Research

DOI
144. Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues

Anikó Meijer, Tim De Meyer, Klaas Vandepoele, Tina Kyndt

(2022) - BMC Genomics

DOI
143. The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization

Andres Jaramillo-Botero, Julian Colorado, Mauricio Quimbaya, Maria Camila Rebolledo, Mathias Lorieux, Thaura Ghneim-Herrera, Carlos A. Arango, Luis E. Tobón, Jorge Finke, Camilo Rocha, Fernando Muñoz, John J. Riascos, Fernando Silva, Ngonidzashe Chirinda, Mario Caccamo, Klaas Vandepoele, William A. Goddard

(2022) - Frontiers in Plant Science

DOI
142. Chromosome-scale assembly and annotation of the perennial ryegrass genome.

Nagy I, Veeckman E, Liu C, Bel MV, Vandepoele K, Jensen CS, Ruttink T, Asp T

(2022) - BMC genomics

DOI
141. Identification of growth regulators using cross-species network analysis in plants.

Curci PL, Zhang J, Mähler N, Seyfferth C, Mannapperuma C, Diels T, Van Hautegem T, Jonsen D, Street N, Hvidsten TR, Hertzberg M, Nilsson O, Inze D, Vandepoele K

(2022) - Plant physiology

DOI
140. MINI-EX: Integrative inference of single-cell gene regulatory networks in plants

Camilla Ferrari, Nicolás Manosalva Pérez, Klaas Vandepoele

(2022) - Molecular Plant

DOI
139. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

Jaime Abrahan Castro-Mondragon, Rafael Riudavets, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, Jérémy LUCAS, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol Fornés, Tiffany Leung, Alejandro Aguirre, HAMMAL Fayrouz, Daniel Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth Wasserman, Francois Parcy, Anthony Mathelier

(2022) - Nucleic Acids Research

DOI
138. The Quest for Orthologs orthology benchmark service in 2022

Yannis Nevers, Tamsin Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codó, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, Adrian Altenhoff, Elspeth A Bruford, Salvatore Cosentino, Christophe Dessimoz, Ingo Ebersberger, David M Emms, Toni Gabaldón, Natasha Glover, Cristina Guijarro-Clarke, Mark Hickman, Yanhui Hu, Wataru Iwasaki, Tamsin E M Jones, Dushyanth Jyothi, Arnaud Kress, Odile Lecompte, Benjamin Linard, Marina Marcet-Houben, Maria J Martin, Yannis Nevers, Emma Persson, Ivana Piližota, Laetitia Poidevin, David S Roos, Erik Sonhammer, Paul D Thomas, David Thybert, Klaas Vandepoele, Anna Vlasova, Bethan Yates, Salvador Capella-Gutierrez, Laia Codó, Meritxell Ferret, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas

(2022) - Nucleic Acids Research

DOI
137. The gene regulation knowledge commons: the action area of GREEKC

Martin Kuiper, Joseph Bonello, Jesualdo T. Fernández-Breis, Philipp Bucher, Matthias E. Futschik, Pascale Gaudet, Ivan V. Kulakovskiy, Luana Licata, Colin Logie, Ruth C. Lovering, Vsevolod J. Makeev, Sandra Orchard, Simona Panni, Livia Perfetto, David Sant, Stefan Schulz, Steven Vercruysse, Daniel R. Zerbino, Astrid Lægreid, Klaas Vandepoele

(2022) - Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

DOI
136. Comparative genomics reveals new functional insights in uncultured MAST species.

Labarre A, López-Escardó D, Latorre F, Leonard G, Bucchini F, Obiol A, Cruaud C, Sieracki ME, Jaillon O, Wincker P, Vandepoele K, Logares R, Massana R

(2021) - The ISME journal

DOI
135. Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

Benites LF, Bucchini F, Sanchez-Brosseau S, Grimsley N, Vandepoele K, Piganeau G

(2021) - Genome biology and evolution

DOI
134. Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta.

Bilcke G, Van Craenenbroeck L, Castagna A, Osuna-Cruz CM, Vandepoele K, Sabbe K, De Veylder L, Vyverman W

(2021) - Scientific reports

DOI
133. Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

Inge De Clercq, Jan Van de Velde, Xiaopeng Luo, Li Liu, Veronique Storme, Michiel Van Bel, Robin Pottie, Dries Vaneechoutte, Frank Van Breusegem, Klaas Vandepoele

(2021) - Nature Plants

DOI
132. Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle

Gust Bilcke, Cristina Maria Osuna‐Cruz, Marta Santana Silva, Nicole Poulsen, Sofie D’hondt, Petra Bulankova, Wim Vyverman, Lieven De Veylder, Klaas Vandepoele

(2021) - The Plant Journal

DOI
131. A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies

Junha Shin, Harald Marx, Alicia Richards, Dries Vaneechoutte, Dhileepkumar Jayaraman, Junko Maeda, Sanhita Chakraborty, Michael Sussman, Klaas Vandepoele, Jean-Michel Ané, Joshua Coon, Sushmita Roy

(2021) - Nucleic Acids Research

DOI
130. Comment on ‘Hayai-Annotation Plants: an ultrafast and comprehensive functional gene annotation system in plants’: the importance of taking the GO graph structure into account

Michiel Van Bel, Klaas Vandepoele, Alfonso Valencia

(2021) - Bioinformatics

DOI
129. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes

François Bucchini, Andrea Del Cortona, Łukasz Kreft, Alexander Botzki, Michiel Van Bel, Klaas Vandepoele

(2021) - Nucleic Acids Research

DOI
128. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors.

Ding P, Sakai T, Shrestha RK, Perez NM, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG

(2021) - Journal of experimental botany

DOI
127. Multi‐omics network‐based functional annotation of unknown Arabidopsis genes

Thomas Depuydt, Klaas Vandepoele

(2021) - The Plant Journal

DOI
126. Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

Ramon Massana, Aurelie Labarre, David López-Escardó, Aleix Obiol, François Bucchini, Thomas Hackl, Matthias G Fischer, Klaas Vandepoele, Denis V Tikhonenkov, Filip Husnik, Patrick J Keeling

(2021) - The ISME Journal

DOI
125. Subfunctionalization of Paralog Transcription Factors Contributes to Regulation of Alkaloid Pathway Branch Choice in Catharanthus roseus

Maite Colinas, Jacob Pollier, Dries Vaneechoutte, Deniz G. Malat, Fabian Schweizer, Liesbeth De Milde, Rebecca De Clercq, Joana G. Guedes, Teresa Martínez-Cortés, Francisco J. Molina-Hidalgo, Mariana Sottomayor, Klaas Vandepoele, Alain Goossens

(2021) - Frontiers in Plant Science

DOI
124. Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

José Luis Blanco-Pastor, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar‐Gutiérrez, Anna Maria Roschanski, Evelyn Willner, Klaus J. Dehmer, Matthew Hegarty, Hilde Muylle, Elisabeth Veeckman, Klaas Vandepoele, Tom Ruttink, Isabel Roldán‐Ruiz, Stéphanie Manel, Jean‐Paul Sampoux

(2021) - Molecular Ecology Resources

DOI
123. Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms

Petra Bulankova, Mirna Sekulić, Denis Jallet, Charlotte Nef, Cock van Oosterhout, Tom O. Delmont, Ilse Vercauteren, Cristina Maria Osuna-Cruz, Emmelien Vancaester, Thomas Mock, Koen Sabbe, Fayza Daboussi, Chris Bowler, Wim Vyverman, Klaas Vandepoele, Lieven De Veylder

(2021) - Current Biology

DOI
122. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds.

Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F

(2020) - Proceedings of the National Academy of Sciences of the United States of America

DOI
121. The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies.

Bousquet L, Hemon C, Malburet P, Bucchini F, Vandepoele K, Grimsley N, Moreau H, Echeverria M

(2020) - NAR genomics and bioinformatics

DOI
120. Identification and evolution of gene regulatory networks: insights from comparative studies in plants

D. Marc Jones, Klaas Vandepoele

(2020) - Current Opinion in Plant Biology

DOI
119. Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms

Emmelien Vancaester, Thomas Depuydt, Cristina Maria Osuna-Cruz, Klaas Vandepoele, Fabia Ursula Battistuzzi

(2020) - Molecular Biology and Evolution

DOI
118. The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms.

Osuna-Cruz CM, Bilcke G, Vancaester E, De Decker S, Bones AM, Winge P, Poulsen N, Bulankova P, Verhelst B, Audoor S, Belisova D, Pargana A, Russo M, Vandepoele K

(2020) - Nature communications

DOI
117. Distinctive Growth and Transcriptional Changes of the Diatom Seminavis robusta in Response to Quorum Sensing Related Compounds.

Stock F, Bilcke G, De Decker S, Osuna-Cruz CM, Van den Berge K, Vancaester E, De Veylder L, Vandepoele K, Mangelinckx S, Vyverman W

(2020) - Frontiers in microbiology

DOI
116. Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta.

Bilcke G, Van den Berge K, De Decker S, Bonneure E, Poulsen N, Bulankova P, Osuna-Cruz CM, Dickenson J, Sabbe K, Pohnert G, Vandepoele K, Vyverman W

(2020) - The ISME journal

DOI
115. Virus-host coexistence in phytoplankton through the genomic lens

Sheree Yau, Marc Krasovec, L. Felipe Benites, Stephane Rombauts, Mathieu Groussin, Emmelien Vancaester, Jean-Marc AURY, Evelyne Derelle, Yves Desdevises, Marie-Line Escande, Nigel Grimsley, Julie Guy, HERVE MOREAU, Sophie Sanchez, Yves Van de Peer, Klaas Vandepoele, Sebastien Gourbiere, Gwenael Piganeau

(2020) - Science Advances

DOI
114. Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data

Shubhada R. Kulkarni, D. Marc Jones, Klaas Vandepoele

(2019) - Plant Physiology

DOI
113. Evolution of vascular plants through redeployment of ancient developmental regulators.

Lu KJ, van 't Wout Hofland N, Mor E, Mutte S, Abrahams P, Kato H, Vandepoele K, Weijers D, De Rybel B

(2019) - Proceedings of the National Academy of Sciences of the United States of America

DOI
112. Gene space completeness in complex plant genomes

Michiel Van Bel, François Bucchini, Klaas Vandepoele

(2019) - Current Opinion in Plant Biology

DOI
111. Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants.

Lama S, Broda M, Abbas Z, Vaneechoutte D, Belt K, Säll T, Vandepoele K, Van Aken O

(2019) - Molecular biology and evolution

DOI
110. Inference of plant gene regulatory networks using data-driven methods: A practical overview.

Kulkarni SR, Vandepoele K

(2019) - Biochimica et biophysica acta. Gene regulatory mechanisms

DOI
109. Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom.

Cirri E, De Decker S, Bilcke G, Werner M, Osuna-Cruz CM, De Veylder L, Vandepoele K, Werz O, Vyverman W, Pohnert G

(2019) - Frontiers in microbiology

DOI
108. A new evolutionary model for the vertebrate actin family including two novel groups.

Witjes L, Van Troys M, Vandekerckhove J, Vandepoele K, Ampe C

(2019) - Molecular phylogenetics and evolution

DOI
107. Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth.

Vercruysse J, Van Bel M, Osuna-Cruz CM, Kulkarni SR, Storme V, Nelissen H, Gonzalez N, Inzé D, Vandepoele K

(2019) - Plant biotechnology journal

DOI
106. Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase

Jelle Van Leene, Chao Han, Astrid Gadeyne, Dominique Eeckhout, Caroline Matthijs, Bernard Cannoot, Nancy De Winne, Geert Persiau, Eveline Van De Slijke, Brigitte Van de Cotte, Elisabeth Stes, Michiel Van Bel, Veronique Storme, Francis Impens, Kris Gevaert, Klaas Vandepoele, Ive De Smet, Geert De Jaeger

(2019) - Nature Plants

DOI
105. Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number.

Prince SJ, Valliyodan B, Ye H, Yang M, Tai S, Hu W, Murphy M, Durnell LA, Song L, Joshi T, Liu Y, Van de Velde J, Vandepoele K, Grover Shannon J, Nguyen HT

(2018) - Plant, cell & environment

DOI
104. Genome analyses of the microalga Picochlorum provide insights into the evolution of thermotolerance in the green lineage.

Krasovec M, Vancaester E, Rombauts S, Bucchini F, Yau S, Hemon C, Lebredonchel H, Grimsley N, Moreau H, Sanchez-Brosseau S, Vandepoele K, Piganeau G

(2018) - Genome biology and evolution

DOI
103. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis.

Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van de Velde J, Vandepoele K, Van de Walle D, Nowack MK

(2018) - Nature plants

DOI
102. Curse: Building expression atlases and co-expression networks from public RNA-Seq data.

Vaneechoutte D, Vandepoele K

(2018) - Bioinformatics (Oxford, England)

DOI
101. A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis.

Pollier J, Vancaester E, Kuzhiumparambil U, Vickers CE, Vandepoele K, Goossens A, Fabris M

(2018) - Nature microbiology

DOI
100. Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).

Veeckman E, Van Glabeke S, Haegeman A, Muylle H, van Parijs FRD, Byrne SL, Asp T, Studer B, Rohde A, Roldán-Ruiz I, Vandepoele K, Ruttink T

(2018) - DNA research : an international journal for rapid publication of reports on genes and genomes

DOI
99. GS^yellow, a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants

Nienke Besbrugge, Jelle Van Leene, Dominique Eeckhout, Bernard Cannoot, Shubhada R. Kulkarni, Nancy De Winne, Geert Persiau, Eveline Van De Slijke, Michiel Bontinck, Stijn Aesaert, Francis Impens, Kris Gevaert, daniel van damme, Mieke Van Lijsebettens, Dirk Inzé, Klaas Vandepoele, Hilde Nelissen, Geert De Jaeger

(2018) - Plant Physiology

DOI
98. Insights into the Evolution of Multicellularity from the Sea Lettuce Genome

Olivier De Clerck, Shu-Min Kao, Kenny A. Bogaert, Jonas Blomme, Fatima Foflonker, Michiel Kwantes, Emmelien Vancaester, Lisa Vanderstraeten, Eylem Aydogdu, Jens Boesger, Gianmaria Califano, Benedicte Charrier, Rachel Clewes, Andrea Del Cortona, Sofie D’Hondt, Noe Fernandez-Pozo, Claire M. Gachon, Marc Hanikenne, Linda Lattermann, Frederik Leliaert, Xiaojie Liu, Christine A. Maggs, Zoë A. Popper, John A. Raven, Michiel Van Bel, Per K.I. Wilhelmsson, Debashish Bhattacharya, Juliet C. Coates, Stefan A. Rensing, Dominique Van Der Straeten, Assaf Vardi, Lieven Sterck, Klaas Vandepoele, Yves Van de Peer, Thomas Wichard, John H. Bothwell

(2018) - Current Biology

DOI
97. Gearing up to handle the mosaic nature of life in the quest for orthologs

Sofia K Forslund, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith Blake, Jesualdo Tomás Fernández Breis, Brigitte Boeckmann, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz, Suzanna Lewis, Adrian Altenhoff, Carla Bello, Judith Blake, Brigitte Boeckmann, Sébastien Briois, Salvador Capella-Gutierrez, Edward Chalstrey, Hirokazu Chiba, Oscar Conchillo-Solé, Vincent Daubin, Todd DeLuca, Christophe Dessimoz, Jean-Francois Dufayard, Dannie Durand, Ingo Ebersberger, Jesualdo Tomás Fernández-Breis, Kristoffer Forslund, Natasha Glover, Alexander Hauser, Davide Heller, Jaime Huerta-Cepas, Mateusz Kaduk, Jan Koch, Eugene V Koonin, Evgenia Kriventseva, Shigehiro Kuraku, Odile Lecompte, Olivier Lespinet, Jeremy Levy, Suzanna Lewis, Benjamin Liebeskind, Benjamin Linard, Marina Marcet-Houben, Maria Martin

(2018) - Bioinformatics

DOI
96. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Michiel Van Bel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, Klaas Vandepoele

(2018) - Nucleic Acids Research

DOI
95. The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution

Daniel Lang, Kristian Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, Fabian B. Haas, Mathieu Piednoel, Heidrun Gundlach, Michiel Van Bel, Rabea Meyberg, Cristina Vives, Jordi Morata, Aikaterini Symeonidi, Manuel Hiss, Wellington Muchero, Yasuko Kamisugi, Omar Saleh, Guillaume Blanc, Eva L. Decker, Nico van Gessel, Jane Grimwood, Richard D. Hayes, Sean W. Graham, Lee E. Gunter, Stuart F. McDaniel, Sebastian N.W. Hoernstein, Anders Larsson, Fay‐Wei Li, Pierre-François Perroud, Jeremy Phillips, Priya Ranjan, Daniel S. Rokshar, Carl J. Rothfels, Lucas Schneider, Shengqiang Shu, Dennis W. Stevenson, Fritz Thümmler, Michael Tillich, Juan C. Villarreal Aguilar, Thomas Widiez, Gane Ka‐Shu Wong, Ann Wymore, Yong Zhang, Andreas D. Zimmer, Ralph S. Quatrano, Klaus F.X. Mayer, David Goodstein, Josep M. Casacuberta, Klaas Vandepoele, Ralf Reski, Andrew Cuming

(2018) - The Plant Journal

DOI
94. Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana

Bjoern Oest Hansen, Etienne H. Meyer, Camilla Ferrari, Neha Vaid, Sara Movahedi, Klaas Vandepoele, Zoran Nikoloski, Marek Mutwil

(2018) - New Phytologist

DOI
93. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R Kulkarni, Ge Tan, Damir Baranasic, David J Arenillas, Albin Sandelin, Klaas Vandepoele, Boris Lenhard, Benoît Ballester, Wyeth W Wasserman, François Parcy, Anthony Mathelier

(2018) - Nucleic Acids Research

DOI
92. The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes

Andrea Del Cortona, Frederik Leliaert, Kenny A. Bogaert, Monique Turmel, Christian Boedeker, Jan Janouškovec, Juan M. Lopez-Bautista, Heroen Verbruggen, Klaas Vandepoele, Olivier De Clerck

(2017) - Current Biology

DOI
91. Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)

Kristof De Schutter, Mariya Tsaneva, Shubhada R. Kulkarni, Pierre Rougé, Klaas Vandepoele, Els J. M. Van Damme

(2017) - Rice

DOI
90. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

Łukasz Kreft, Alexander Botzki, Frederik Coppens, Klaas Vandepoele, Michiel Van Bel

(2017) - Bioinformatics

DOI
89. The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a

Xinhua Zhang, Aneta Ivanova, Klaas Vandepoele, Jordan Radomiljac, Jan Van de Velde, Oliver Berkowitz, Patrick Willems, Yue Xu, Sophia Ng, Olivier Van Aken, Owen Duncan, Botao Zhang, Veronique Storme, Kai Xun Chan, Dries Vaneechoutte, Barry James Pogson, Frank Van Breusegem, James Whelan, Inge De Clercq

(2017) - Plant Physiology

DOI
88. TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information.

Kulkarni SR, Vaneechoutte D, Van de Velde J, Vandepoele K

(2017) - Nucleic Acids Research

DOI
87. Genome‐wide characterization of differential transcript usage in Arabidopsis thaliana

Dries Vaneechoutte, April R. Estrada, Ying‐Chen Lin, Ann E. Loraine, Klaas Vandepoele

(2017) - The Plant Journal

DOI
86. A Guide to the PLAZA 3.0 Plant Comparative Genomic Database

Klaas Vandepoele

(2017) - Methods in Molecular Biology

DOI
85. The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis

Andrés Ritter, Sabrina Iñigo, Patricia Fernández-Calvo, Ken S. Heyndrickx, Stijn Dhondt, Hua Shi, Liesbeth De Milde, Robin Vanden Bossche, Rebecca De Clercq, Dominique Eeckhout, Mily Ron, David E. Somers, Dirk Inzé, Kris Gevaert, Geert De Jaeger, Klaas Vandepoele, Laurens Pauwels, Alain Goossens

(2017) - Nature Communications

DOI
84. The mutation nrpb1‐A325V in the largest subunit of RNA polymerase II suppresses compromised growth of Arabidopsis plants deficient in a function of the general transcription factor IIF

Elena Babiychuk, Khai Trinh Hoang, Klaas Vandepoele, Eveline Van De Slijke, Danny Geelen, Geert De Jaeger, Junichi Obokata, Sergei Kushnir

(2017) - The Plant Journal

DOI
83. Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

Colin Ruprecht, Sebastian Proost, Marcela Hernandez‐Coronado, Carlos Ortiz‐Ramirez, Daniel Lang, Stefan A. Rensing, Jörg D. Becker, Klaas Vandepoele, Marek Mutwil

(2017) - The Plant Journal

DOI
82. CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool

Oren Tzfadia, Tim Diels, Sam De Meyer, Klaas Vandepoele, Asaph Aharoni, Yves Van de Peer

(2016) - Frontiers in Plant Science

DOI
81. Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

Elisabeth Veeckman, Tom Ruttink, Klaas Vandepoele

(2016) - The Plant Cell

DOI
80. Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development

Jelle Van Leene, Jonas Blomme, Shubhada R Kulkarni, Bernard Cannoot, Nancy De Winne, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Leen Vercruysse, Robin Vanden Bossche, Ken S Heyndrickx, Steffen Vanneste, Alain Goossens, Kris Gevaert, Klaas Vandepoele, Nathalie Gonzalez, Dirk Inzé, Geert De Jaeger

(2016) - Journal of Experimental Botany

DOI
79. A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants

Jan Van de Velde, Michiel Van Bel, Dries Vaneechoutte, Klaas Vandepoele

(2016) - Plant Physiology

DOI
78. Functional Analysis of Arabidopsis TETRASPANIN Gene Family in Plant Growth and Development

Feng Wang, Antonella Muto, Jan Van de Velde, Pia Neyt, Kristiina Himanen, Klaas Vandepoele, Mieke Van Lijsebettens

(2015) - Plant Physiology

DOI
77. An update on LNCipedia: a database for annotated human lncRNA sequences

Pieter-Jan Volders, Kenneth Verheggen, Gerben Menschaert, Klaas Vandepoele, Lennart Martens, Jo Vandesompele, Pieter Mestdagh

(2015) - Nucleic Acids Research

DOI
76. A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis

Nathalie Gonzalez, Laurens Pauwels, Alexandra Baekelandt, Liesbeth De Milde, Jelle Van Leene, Nienke Besbrugge, Ken Heyndrickx, Amparo Cuéllar Pérez, Astrid Nagels Durand, Rebecca De Clercq, Eveline Van De Slijke, robin Vanden Bossche, Dominique Eeckhout, Kris Gevaert, Klaas Vandepoele, Geert De Jaeger, Alain Goossens, Dirk Inzé

(2015) - The Plant Cell

DOI
75. Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B

Natasha M. Glover, Josquin Daron, Lise Pingault, Klaas Vandepoele, Etienne Paux, Catherine Feuillet, Frédéric Choulet

(2015) - Genome Biology

DOI
74. PLAZA 3.0: an access point for plant comparative genomics

Sebastian Proost, Michiel Van Bel, Dries Vaneechoutte, Yves Van de Peer, Dirk Inzé, Bernd Mueller-Roeber, Klaas Vandepoele

(2015) - Nucleic Acids Research

DOI
73. BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements

Dieter De Witte, Jan Van de Velde, Dries Decap, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier

(2015) - Bioinformatics

DOI
72. Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes

Aurine Verkest, Marina Byzova, Cindy Martens, Patrick Willems, Tom Verwulgen, Bram Slabbinck, Debbie Rombaut, Jan Van de Velde, Klaas Vandepoele, Evi Standaert, Marrit Peeters, Mieke Van Lijsebettens, Frank Van Breusegem, Marc De Block

(2015) - Plant Physiology

DOI
71. An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

Jelle Van Leene, Dominique Eeckhout, Bernard Cannoot, Nancy De Winne, Geert Persiau, Eveline Van De Slijke, Leen Vercruysse, Maarten Dedecker, Aurine Verkest, Klaas Vandepoele, Lennart Martens, Erwin Witters, Kris Gevaert, Geert De Jaeger

(2015) - Nature Protocols

DOI
70. Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf

Hilde Nelissen, Dominique Eeckhout, Kirin Demuynck, Geert Persiau, Alan Walton, Michiel van Bel, Marieke Vervoort, Jasper Candaele, Jolien De Block, Stijn Aesaert, Mieke Van Lijsebettens, Sofie Goormachtig, Klaas Vandepoele, Jelle Van Leene, Michael Muszynski, Kris Gevaert, Dirk Inzé, Geert De Jaeger

(2015) - The Plant Cell

DOI
69. Evolutionary trails of plant steroid genes

Cécile Vriet, Karen Lemmens, Klaas Vandepoele, Christophe Reuzeau, Eugenia Russinova

(2015) - Trends in Plant Science

DOI
68. Big data and other challenges in the quest for orthologs

Erik L.L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, the Quest for Orthologs consortium

(2014) - Bioinformatics

DOI
67. Structural and functional partitioning of bread wheat chromosome 3B

Frédéric Choulet, Adriana Alberti, Sébastien Theil, Natasha Glover, Valérie Barbe, Josquin Daron, Lise Pingault, Pierre Sourdille, Arnaud Couloux, Etienne Paux, Philippe Leroy, Sophie Mangenot, Nicolas Guilhot, Jacques Le Gouis, Francois Balfourier, Michael Alaux, Véronique Jamilloux, Julie Poulain, Céline Durand, Arnaud Bellec, Christine Gaspin, Jan Safar, Jaroslav Dolezel, Jane Rogers, Klaas Vandepoele, Jean-Marc Aury, Klaus Mayer, Hélène Berges, Hadi Quesneville, Patrick Wincker, Catherine Feuillet

(2014) - Science

DOI
66. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors inArabidopsis thaliana

Søren Lindemose, Michael K. Jensen, Jan Van de Velde, Charlotte O'Shea, Ken S. Heyndrickx, Christopher T. Workman, Klaas Vandepoele, Karen Skriver, Federico De Masi

(2014) - Nucleic Acids Research

DOI
65. Drought Tolerance Conferred to Sugarcane by Association with Gluconacetobacter diazotrophicus: A Transcriptomic View of Hormone Pathways

Lívia Vargas, Ailton B. Santa Brígida, José P. Mota Filho, Thais G. de Carvalho, Cristian A. Rojas, Dries Vaneechoutte, Michiel Van Bel, Laurent Farrinelli, Paulo C. G. Ferreira, Klaas Vandepoele, Adriana S. Hemerly

(2014) - PLoS ONE

DOI
64. A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana

Ken Heyndrickx, Jan Van de Velde, Congmao Wang, Detlef Weigel, Klaas Vandepoele

(2014) - The Plant Cell

DOI
63. ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development

Liesbeth Vercruyssen, Aurine Verkest, Nathalie Gonzalez, Ken S. Heyndrickx, Dominique Eeckhout, Soon-Ki Han, Teddy Jégu, Rafal Archacki, Jelle Van Leene, Megan Andriankaja, Stefanie De Bodt, Thomas Abeel, Frederik Coppens, Stijn Dhondt, Liesbeth De Milde, Mattias Vermeersch, Katrien Maleux, Kris Gevaert, Andrzej Jerzmanowski, Moussa Benhamed, Doris Wagner, Klaas Vandepoele, Geert De Jaeger, Dirk Inzé

(2014) - The Plant Cell

DOI
62. A Generic Tool for Transcription Factor Target Gene Discovery in Arabidopsis Cell Suspension Cultures Based on Tandem Chromatin Affinity Purification

Aurine Verkest, Thomas Abeel, Ken S. Heyndrickx, Jelle Van Leene, Christa Lanz, Eveline Van De Slijke, Nancy De Winne, Dominique Eeckhout, Geert Persiau, Frank Van Breusegem, Dirk Inzé, Klaas Vandepoele, Geert De Jaeger

(2014) - Plant Physiology

DOI
61. MAGIC: access portal to a cross-platform gene expression compendium for maize

Qiang Fu, Ana Carolina Fierro, Pieter Meysman, Aminael Sanchez-Rodriguez, Klaas Vandepoele, Kathleen Marchal, Kristof Engelen

(2014) - Bioinformatics

DOI
60. Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis

Jan Van de Velde, Ken Heyndrickx, Klaas Vandepoele

(2014) - The Plant Cell

DOI
59. pico-PLAZA, a genome database of microbial photosynthetic eukaryotes

Vandepoele, Klaas, Van Bel, Michiel, Richard, Guilhem, Van Landeghem, Sofie, Verhelst, Bram, Moreau, Herve, Van de Peer, Yves, Grimsley, Nigel, Piganeau, Gwenael

(2013) - Environmental Microbiology

DOI
58. The Membrane-Bound NAC Transcription Factor ANAC013 Functions in Mitochondrial Retrograde Regulation of the Oxidative Stress Response in Arabidopsis

Inge De Clercq, Vanessa Vermeirssen, Olivier Van Aken, Klaas Vandepoele, Monika W. Murcha, Simon R. Law, Annelies Inzé, Sophia Ng, Aneta Ivanova, Debbie Rombaut, Brigitte van de Cotte, Pinja Jaspers, Yves Van de Peer, Jaakko Kangasjärvi, James Whelan, Frank Van Breusegem

(2013) - The Plant Cell

DOI
57. ERF115 Controls Root Quiescent Center Cell Division and Stem Cell Replenishment

Jefri Heyman, Toon Cools, Filip Vandenbussche, Ken S. Heyndrickx, Jelle Van Leene, Ilse Vercauteren, Sandy Vanderauwera, Klaas Vandepoele, Geert De Jaeger, Dominique Van Der Straeten, Lieven De Veylder

(2013) - Science

DOI
56. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Riet De Smet, Keith L. Adams, Klaas Vandepoele, Marc C. E. Van Montagu, Steven Maere, Yves Van de Peer

(2013) - Proceedings of the National Academy of Sciences

DOI
55. TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Michiel Van Bel, Sebastian Proost, Christophe Van Neste, Dieter Deforce, Yves Van de Peer, Klaas Vandepoele

(2013) - Genome Biology

DOI
54. Molecular and Physiological Analysis of Growth-Limiting Drought Stress in Brachypodium distachyon Leaves

Wim Verelst, Edoardo Bertolini, Stefanie De Bodt, Klaas Vandepoele, Marlies Demeulenaere, Mario Enrico Pè, Dirk Inzé

(2013) - Molecular Plant

DOI
53. Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana.

Petrov, V., Vermeirssen, V., De Clercq, I., Van Breusegem, F., Minkov, I., Vandepoele, K., Gechev, T. S.

(2012) - Gene

DOI
52. i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

Sebastian Proost, Jan Fostier, Dieter De Witte, Bart Dhoedt, Piet Demeester, Yves Van de Peer, Klaas Vandepoele

(2012) - Nucleic Acids Research

DOI
51. Comparative co‐expression analysis in plant biology

SARA MOVAHEDI, MICHIEL VAN BEL, KEN S. HEYNDRICKX, KLAAS VANDEPOELE

(2012) - Plant, Cell & Environment

DOI
50. Tetraspanin genes in plants

Feng Wang, Klaas Vandepoele, Mieke Van Lijsebettens

(2012) - Plant Science

DOI
49. Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

Michiel Van Bel, Sebastian Proost, Elisabeth Wischnitzki, Sara Movahedi, Christopher Scheerlinck, Yves Van de Peer, Klaas Vandepoele

(2012) - Plant Physiology

DOI
48. Identification of putative cancer genes through data integration and comparative genomics between plants and humans

Mauricio Quimbaya, Klaas Vandepoele, Eric Raspé, Michiel Matthijs, Stijn Dhondt, Gerrit T. S. Beemster, Geert Berx, Lieven De Veylder

(2012) - Cellular and Molecular Life Sciences

DOI
47. Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Hervé Moreau, Bram Verhelst, Arnaud Couloux, Evelyne Derelle, Stephane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F Hohmann-Marriott, Gwenael Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele

(2012) - Genome Biology

DOI
46. Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

Daniel Vaulot, Cécile Lepère, Eve Toulza, Rodrigo De la Iglesia, Julie Poulain, Frédéric Gaboyer, Hervé Moreau, Klaas Vandepoele, Osvaldo Ulloa, Frederick Gavory, Gwenael Piganeau

(2012) - PLoS ONE

DOI
45. Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

Ken S. Heyndrickx, Klaas Vandepoele

(2012) - Plant Physiology

DOI
44. Toward community standards in the quest for orthologs

Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero, the Quest for Orthologs Consortium, Klaas Vandepoele

(2012) - Bioinformatics

DOI
43. Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

Sara Movahedi, Yves Van de Peer, Klaas Vandepoele

(2011) - Plant Physiology

DOI
42. Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

Elena Babiychuk, Klaas Vandepoele, Josef Wissing, Miguel Garcia-Diaz, Riet De Rycke, Hana Akbari, Jérôme Joubès, Tom Beeckman, Lothar Jänsch, Margrit Frentzen, Marc C. E. Van Montagu, Sergei Kushnir

(2011) - Proceedings of the National Academy of Sciences

DOI
41. A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele

(2011) - Bioinformatics

DOI
40. ROS signaling: the new wave?

Ron Mittler, Sandy Vanderauwera, Nobuhiro Suzuki, Gad Miller, Vanesa B. Tognetti, Klaas Vandepoele, Marty Gollery, Vladimir Shulaev, Frank Van Breusegem

(2011) - Trends in Plant Science

DOI
39. Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling

Marie JJ Huysman, Cindy Martens, Klaas Vandepoele, Jeroen Gillard, Edda Rayko, Marc Heijde, Chris Bowler, Dirk Inzé, Yves Peer, Lieven De Veylder, Wim Vyverman

(2010) - Genome Biology

DOI
38. The MCM-Binding Protein ETG1 Aids Sister Chromatid Cohesion Required for Postreplicative Homologous Recombination Repair

Naoki Takahashi, Mauricio Quimbaya, Veit Schubert, Tim Lammens, Klaas Vandepoele, Ingo Schubert, Minami Matsui, Dirk Inzé, Geert Berx, Lieven De Veylder

(2010) - PLoS Genetics

DOI
37. Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus

Gwenael Piganeau, Klaas Vandepoele, Sébastien Gourbière, Yves Van de Peer, Hervé Moreau

(2009) - Journal of Molecular Evolution

DOI
36. Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

Klaas Vandepoele, Mauricio Quimbaya, Tine Casneuf, Lieven De Veylder, Yves Van de Peer

(2009) - Plant Physiology

DOI
35. The Mouse Thymosin Beta15 Gene Family Displays Unique Complexity and Encodes A Functional Thymosin Repeat

Stien Dhaese, Klaas Vandepoele, Davy Waterschoot, Berlinda Vanloo, Joël Vandekerckhove, Christophe Ampe, Marleen Van Troys

(2009) - Journal of Molecular Biology

DOI
34. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouzé, Yves Van de Peer

(2009) - BMC Genomics

DOI
33. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes

Naïra Naouar, Klaas Vandepoele, Tim Lammens, Tineke Casneuf, Georg Zeller, Paul Van Hummelen, Detlef Weigel, Gunnar Rätsch, Dirk Inzé, Martin Kuiper, Lieven De Veylder, Marnik Vuylsteke

(2009) - The Plant Journal

DOI
32. The flowering world: a tale of duplications

Yves Van de Peer, Jeffrey A. Fawcett, Sebastian Proost, Lieven Sterck, Klaas Vandepoele

(2009) - Trends in Plant Science

DOI
31. PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

Sebastian Proost, Michiel Van Bel, Lieven Sterck, Kenny Billiau, Thomas Van Parys, Yves Van de Peer, Klaas Vandepoele

(2009) - The Plant Cell

DOI
30. Hydrogen Peroxide-Induced Gene Expression across Kingdoms: A Comparative Analysis

K. Vandenbroucke, S. Robbens, K. Vandepoele, D. Inze, Y. Van de Peer, F. Van Breusegem

(2008) - Molecular Biology and Evolution

DOI
29. ThePRA1Gene Family in Arabidopsis

Claire Lessa Alvim Kamei, Joanna Boruc, Klaas Vandepoele, Hilde Van den Daele, Sara Maes, Eugenia Russinova, Dirk Inzé, Lieven De Veylder

(2008) - Plant Physiology

DOI
28. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Chris Bowler, Andrew E. Allen, Jonathan H. Badger, Jane Grimwood, Kamel Jabbari, Alan Kuo, Uma Maheswari, Cindy Martens, Florian Maumus, Robert P. Otillar, Edda Rayko, Asaf Salamov, Klaas Vandepoele, Bank Beszteri, Ansgar Gruber, Marc Heijde, Michael Katinka, Thomas Mock, Klaus Valentin, Fréderic Verret, John A. Berges, Colin Brownlee, Jean-Paul Cadoret, Anthony Chiovitti, Chang Jae Choi, Sacha Coesel, Alessandra De Martino, J. Chris Detter, Colleen Durkin, Angela Falciatore, Jérome Fournet, Miyoshi Haruta, Marie J. J. Huysman, Bethany D. Jenkins, Katerina Jiroutova, Richard E. Jorgensen, Yolaine Joubert, Aaron Kaplan, Nils Kröger, Peter G. Kroth, Julie La Roche, Erica Lindquist, Markus Lommer, Véronique Martin–Jézéquel, Pascal J. Lopez, Susan Lucas, Manuela Mangogna, Karen McGinnis, Linda K. Medlin, Anton Montsant, Marie-Pierre Oudot–Le Secq

(2008) - Nature

DOI
27. Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Cindy Martens, Klaas Vandepoele, Yves Van de Peer

(2008) - Proceedings of the National Academy of Sciences

DOI
26. On the origin and evolution of vertebrate and viral profilins

Debby Polet, Anja Lambrechts, Klaas Vandepoele, Joël Vandekerckhove, Christophe Ampe

(2007) - FEBS Letters

DOI
25. Novel Plant-specific Cyclin-dependent Kinase Inhibitors Induced by Biotic and Abiotic Stresses

Adrian Peres, Michelle L. Churchman, Srivaidehirani Hariharan, Kristiina Himanen, Aurine Verkest, Klaas Vandepoele, Zoltan Magyar, Yves Hatzfeld, Els Van Der Schueren, Gerrit T.S. Beemster, Valerie Frankard, John C. Larkin, Dirk Inzé, Lieven De Veylder

(2007) - Journal of Biological Chemistry

DOI
24. Cold Nights Impair Leaf Growth and Cell Cycle Progression in Maize through Transcriptional Changes of Cell Cycle Genes

Bart Rymen, Fabio Fiorani, Fatma Kartal, Klaas Vandepoele, Dirk Inzé, Gerrit T.S. Beemster

(2007) - Plant Physiology

DOI
23. How many genes are there in plants (… and why are they there)?

L STERCK, S ROMBAUTS, K VANDEPOELE, P ROUZE, Y VANDEPEER

(2007) - Current Opinion in Plant Biology

DOI
22. A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety

Riccardo Velasco, Andrey Zharkikh, Michela Troggio, Dustin A. Cartwright, Alessandro Cestaro, Dmitry Pruss, Massimo Pindo, Lisa M. FitzGerald, Silvia Vezzulli, Julia Reid, Giulia Malacarne, Diana Iliev, Giuseppina Coppola, Bryan Wardell, Diego Micheletti, Teresita Macalma, Marco Facci, Jeff T. Mitchell, Michele Perazzolli, Glenn Eldredge, Pamela Gatto, Rozan Oyzerski, Marco Moretto, Natalia Gutin, Marco Stefanini, Yang Chen, Cinzia Segala, Christine Davenport, Lorenzo Demattè, Amy Mraz, Juri Battilana, Keith Stormo, Fabrizio Costa, Quanzhou Tao, Azeddine Si-Ammour, Tim Harkins, Angie Lackey, Clotilde Perbost, Bruce Taillon, Alessandra Stella, Victor Solovyev, Jeffrey A. Fawcett, Lieven Sterck, Klaas Vandepoele, Stella M. Grando, Stefano Toppo, Claudio Moser, Jerry Lanchbury, Robert Bogden, Mark Skolnick, Vittorio Sgaramella

(2007) - PLoS ONE

DOI
21. The gain and loss of genes during 600 million years of vertebrate evolution

Tine Blomme, Klaas Vandepoele, Stefanie De Bodt, Cedric Simillion, Steven Maere, Yves Van de Peer

(2006) - Genome Biology

DOI
20. Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

Klaas Vandepoele, Tineke Casneuf, Yves Van de Peer

(2006) - Genome Biology

DOI
19. Exploring the Plant Transcriptome through Phylogenetic Profiling

Klaas Vandepoele, Yves Van de Peer

(2005) - Plant Physiology

DOI
18. Ancient duplication of cereal genomes

Andrew H. Paterson, John E. Bowers, Yves Van de Peer, Klaas Vandepoele

(2005) - New Phytologist

DOI
17. Genome-Wide Identification of Potential Plant E2F Target Genes

Klaas Vandepoele, Kobe Vlieghe, Kobe Florquin, Lars Hennig, Gerrit T.S. Beemster, Wilhelm Gruissem, Yves Van de Peer, Dirk Inzé, Lieven De Veylder

(2005) - Plant Physiology

DOI
16. A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana

Isabelle Landrieu, Marco da Costa, Lieven De Veylder, Frédérique Dewitte, Klaas Vandepoele, Sahar Hassan, Jean-Michel Wieruszeski, Jean-Denis Faure, Marc Van Montagu, Dirk Inzé, Guy Lippens

(2004) - Proceedings of the National Academy of Sciences

DOI
15. Type II Metacaspases Atmc4 and Atmc9 of Arabidopsis thaliana Cleave Substrates after Arginine and Lysine

Dominique Vercammen, Brigitte van de Cotte, Geert De Jaeger, Dominique Eeckhout, Peter Casteels, Klaas Vandepoele, Isabel Vandenberghe, Jozef Van Beeumen, Dirk Inzé, Frank Van Breusegem

(2004) - Journal of Biological Chemistry

DOI
14. Recent developments in computational approaches for uncovering genomic homology

Cedric Simillion, Klaas Vandepoele, Yves Van de Peer

(2004) - BioEssays

DOI
13. Gene duplication and biased functional retention of paralogs in bacterial genomes

Dirk Gevers, Klaas Vandepoele, Cedric Simillion, Yves Van de Peer

(2004) - Trends in Microbiology

DOI
12. The Quest for Genomic Homology

Klaas Vandepoele, Cedric Simillion, Yves Peer

(2004) - Current Genomics

DOI
11. Building Genomic Profiles for Uncovering Segmental Homology in the Twilight Zone

Cedric Simillion, Klaas Vandepoele, Yvan Saeys, Yves Van de Peer

(2004) - Genome Research

DOI
10. Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates

Klaas Vandepoele, Wouter De Vos, John S. Taylor, Axel Meyer, Yves Van de Peer

(2004) - Proceedings of the National Academy of Sciences

DOI
9. Quantitative cDNA-AFLP analysis for genome-wide expression studies

P. Breyne, R. Dreesen, B. Cannoot, D. Rombaut, K. Vandepoele, S. Rombauts, R. Vanderhaeghen, D. Inzé, M. Zabeau

(2003) - Molecular Genetics and Genomics

DOI
8. Investigating ancient duplication events in the Arabidopsis genome

Jeroen Raes, Klaas Vandepoele, Cedric Simillion, Yvan Saeys, Yves Van de Peer

(2003) - Genome Evolution

DOI
7. Investigating ancient duplication events in the Arabidopsis genome

Jeroen Raes, Klaas Vandepoele, Cedric Simillion, Yvan Saeys, Yves Van de Peer

(2003) - Journal of Structural and Functional Genomics

DOI
6. Evidence That Rice and Other Cereals Are Ancient Aneuploids

Klaas Vandepoele, Cedric Simillion, Yves Van de Peer

(2003) - The Plant Cell

DOI
5. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice

Klaas Vandepoele, Cedric Simillion, Yves Van de Peer

(2002) - Trends in Genetics

DOI
4. Transcriptome analysis during cell division in plants

Peter Breyne, Rozemarijn Dreesen, Klaas Vandepoele, Lieven De Veylder, Frank Van Breusegem, Lindy Callewaert, Stephane Rombauts, Jeroen Raes, Bernard Cannoot, Gilbert Engler, Dirk Inzé, Marc Zabeau

(2002) - Proceedings of the National Academy of Sciences

DOI
3. The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice

Klaas Vandepoele, Yvan Saeys, Cedric Simillion, Jeroen Raes, Yves Van de Peer

(2002) - Genome Research

DOI
2. The hidden duplication past of Arabidopsis thaliana

Cedric Simillion, Klaas Vandepoele, Marc C. E. Van Montagu, Marc Zabeau, Yves Van de Peer

(2002) - Proceedings of the National Academy of Sciences

DOI
1. Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis

Klaas Vandepoele, Jeroen Raes, Lieven De Veylder, Pierre Rouzé, Stephane Rombauts, Dirk Inzé

(2002) - The Plant Cell

DOI