publications

60. Seasonal Metabolic Dynamics of Microeukaryotic Plankton: A Year-long Metatranscriptomic Study in a Temperate Sea

Michiel Perneel, Rune Lagaisse, Jonas Mortelmans, Steven Maere, Pascal I. Hablützel

(2024) -

DOI
59. Out-of-Sample R 2 : Estimation and Inference

Stijn Hawinkel, Willem Waegeman, Steven Maere

(2024) - The American Statistician

DOI
58. Citizen science boosts fundamental and applied research for sustainable soybean cultivation in North‐Western Europe

Lena Vlaminck, Birgit Vanden Berghen, Stien Mertens, Jurgen Wuyts, Liesbeth Aerts, Judith Van Dingenen, Sofie Bekaert, Steven Maere, Liesbet Vranken, Sofie Goormachtig

(2024) - PLANTS, PEOPLE, PLANET

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57. SMAP design: a multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation

Ward Develtere, Evelien Waegneer, Kevin Debray, Jonas De Saeger, Sabine Van Glabeke, Steven Maere, Tom Ruttink, Thomas B. Jacobs

(2023) - Nucleic Acids Research

DOI
56. Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression

Sam De Meyer, Daniel Felipe Cruz Galvis, Tom De Swaef, Peter Lootens, Jolien De Block, Kevin Bird, Heike Sprenger, Michael Van de Voorde, Stijn Hawinkel, Tom Van Hautegem, Dirk Inzé, Hilde Nelissen, Isabel Roldán-Ruiz, Steven Maere, Kiran Raosaheb Patil

(2023) - PLOS Computational Biology

DOI
55. Monitoring of drought stress and transpiration rate using proximal thermal and hyperspectral imaging in an indoor automated plant phenotyping platform

Stien Mertens, Lennart Verbraeken, Heike Sprenger, Sam De Meyer, Kirin Demuynck, Bernard Cannoot, Julie Merchie, Jolien De Block, Jonathan T. Vogel, Wesley Bruce, Hilde Nelissen, Steven Maere, Dirk Inzé, Nathalie Wuyts

(2023) - Plant Methods

DOI
54. Interspecies co‐expression analysis of lateral root development using inducible systems in rice, Medicago, and Arabidopsis

Hans Motte, Boris Parizot, Wei Xuan, Qian Chen, Steven Maere, Sandra Bensmihen, Tom Beeckman

(2023) - The Plant Journal

DOI
53. The winner’s curse under dependence: repairing empirical Bayes using convoluted densities

Stijn Hawinkel, Olivier Thas, Steven Maere

(2023) -

DOI
52. ksrates: positioning whole-genome duplications relative to speciation events in KS distributions

Cecilia Sensalari, Steven Maere, Rolf Lohaus, Peter Robinson

(2022) - Bioinformatics

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51. Spatial Regression Models for Field Trials: A Comparative Study and New Ideas

Stijn Hawinkel, Sam De Meyer, Steven Maere

(2022) - Frontiers in Plant Science

DOI
50. Proximal Hyperspectral Imaging Detects Diurnal and Drought-Induced Changes in Maize Physiology

Stien Mertens, Lennart Verbraeken, Heike Sprenger, Kirin Demuynck, Katrien Maleux, Bernard Cannoot, Jolien De Block, Steven Maere, Hilde Nelissen, Gustavo Bonaventure, Steven J. Crafts-Brandner, Jonathan T. Vogel, Wesley Bruce, Dirk Inzé, Nathalie Wuyts

(2021) - Frontiers in Plant Science

DOI
49. Drought affects the rate and duration of organ growth but not inter-organ growth coordination

Lennart Verbraeken, Nathalie Wuyts, Stien Mertens, Bernard Cannoot, Katrien Maleux, Kirin Demuynck, Jolien De Block, Julie Merchie, Stijn Dhondt, Gustavo Bonaventure, Steven Crafts-Brandner, Jonathan T. Vogel, Wesley Bruce, Dirk Inzé, Steven Maere, Hilde Nelissen

(2021) - Plant Physiology

DOI
48. Current status of the multinational Arabidopsis community

Geraint Parry, Nicholas J. Provart, Siobhan M. Brady, Baris Uzilday, The Multinational Arabidopsis Steering Committee

(2020) - Plant Direct

DOI
47. Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

Jos Wendrich, Yang Baojun, Niels Vandamme, Kevin Verstaen, Wouter Smet, Celien Van de Velde, Max Minne, Brecht Wybouw, Eliana Mor, Helena E. Arents, Jonah Nolf, Julie Van Duyse, Gert Van Isterdael, Steven Maere, Yvan Saeys, Bert De Rybel

(2020) - Science

DOI
46. Using single‐plant‐omics in the field to link maize genes to functions and phenotypes

Daniel Felipe Cruz, Sam De Meyer, Joke Ampe, Heike Sprenger, Dorota Herman, Tom Van Hautegem, Jolien De Block, Dirk Inzé, Hilde Nelissen, Steven Maere

(2020) - Molecular Systems Biology

DOI
45. Endoreplication as a potential driver of cell wall modifications

Rahul Bhosale, Steven Maere, Lieven De Veylder

(2019) - Current Opinion in Plant Biology

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44. Interspecific hybridization facilitates niche adaptation in beer yeast

Brigida Gallone, Jan Steensels, Stijn Mertens, Maria C. Dzialo, Jonathan L. Gordon, Ruben Wauters, Florian A. Theßeling, Francesca Bellinazzo, Veerle Saels, Beatriz Herrera-Malaver, Troels Prahl, Christopher White, Mathias Hutzler, Franz Meußdoerffer, Philippe Malcorps, Ben Souffriau, Luk Daenen, Guy Baele, Steven Maere, Kevin J. Verstrepen

(2019) - Nature Ecology & Evolution

DOI
43. The Apicomplexa-specific glucosamine-6-phosphate N-acetyltransferase gene family encodes a key enzyme for glycoconjugate synthesis with potential as therapeutic target

Marta Cova, Borja López-Gutiérrez, Sara Artigas-Jerónimo, Aida González-Díaz, Giulia Bandini, Steven Maere, Lorenzo Carretero-Paulet, Luis Izquierdo

(2018) - Scientific Reports

DOI
42. A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation

Dr. Rahul Bhosale, Veronique Boudolf, Fabiola Nathaly Cuevas Bustamante, RAN LU, Thomas Eekhout, Zhubing Hu, Gert Van Isterdael, GEORGINA LAMBERT, Fan Xu, Moritz Nowack, Richard S. Smith, Ilse Vercauteren, Riet De Rycke, Veronique Storme, Tom Beeckman, John Larkin, Anna Kremer, Herman Hofte, David Galbraith, Robert P. Kumpf, Steven Maere, Lieven De Veylder

(2018) - The Plant Cell

DOI
41. Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Fay-Wei Li, Paul Brouwer, Lorenzo Carretero-Paulet, Shifeng Cheng, Jan de Vries, Pierre-Marc Delaux, Ariana Eily, Nils Koppers, Li-Yaung Kuo, Zheng Li, Mathew Simenc, Ian Small, Eric Wafula, Stephany Angarita, Michael Barker, Andrea Bräutigam, Claude dePamphilis, Sven B. Gould, Prashant S. Hosmani, Yao-Moan Huang, Bruno Huettel, Yoichiro Kato, Xin Liu, Steven Maere, Rose McDowell, Lukas A. Mueller, Klaas G. J. Nierop, Stefan A Rensing, Tanner Robison, Carl Rothfels, Erin M. Sigel, Yue Song, Prakash R. Timilsena, Yves Van de Peer, Hongli Wang, Per K. I. Wilhelmsson, Paul G. Wolf, Xun Xu, Joshua Der, Henriette Schluepmann, Gane Ka-Shu Wong, Kathleen M. Pryer

(2018) - Nature Plants

DOI
40. Origins, evolution, domestication and diversity of Saccharomyces beer yeasts

Brigida Gallone, Stijn Mertens, Jonathan L Gordon, Steven Maere, Kevin J Verstrepen, Jan Steensels

(2018) - Current Opinion in Biotechnology

DOI
39. The Origin of Floral Organ Identity Quartets

Philip Ruelens, Zhicheng Zhang, Hilda van Mourik, Steven Maere, Kerstin Kaufmann, Koen Geuten

(2017) - The Plant Cell

DOI
38. Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance Sensitivity

Setareh Tasdighian, Michiel Van Bel, Zhen Li, Yves Van de Peer, Lorenzo Carretero-Paulet, Steven Maere

(2017) - The Plant Cell

DOI
37. Evolutionary Context Improves Regulatory Network Predictions

Jonathan L. Gordon, Brigida Gallone, Steven Maere, Kevin J. Verstrepen

(2017) - Cell Systems

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36. The reduction in maize leaf growth under mild drought affects the transition between cell division and cell expansion and cannot be restored by elevated gibberellic acid levels

Hilde Nelissen, Xiao‐Huan Sun, Bart Rymen, Yusuke Jikumaru, Mikko Kojima, Yumiko Takebayashi, Rafael Abbeloos, Kirin Demuynck, Veronique Storme, Marnik Vuylsteke, Jolien De Block, Dorota Herman, Frederik Coppens, Steven Maere, Yuji Kamiya, Hitoshi Sakakibara, Gerrit T.S. Beemster, Dirk Inzé

(2017) - Plant Biotechnology Journal

DOI
35. Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture

Pieter Clauw, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, Liesbeth De Milde, Mattias Vermeersch, Katrien Maleux, Steven Maere, Nathalie Gonzalez, Dirk Inzé

(2016) - The Plant Cell

DOI
34. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

Brigida Gallone, Jan Steensels, Troels Prahl, Leah Soriaga, Veerle Saels, Beatriz Herrera-Malaver, Adriaan Merlevede, Miguel Roncoroni, Karin Voordeckers, Loren Miraglia, Clotilde Teiling, Brian Steffy, Maryann Taylor, Ariel Schwartz, Toby Richardson, Christopher White, Guy Baele, Steven Maere, Kevin J. Verstrepen

(2016) - Cell

DOI
33. Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

Zhen Li, Jonas Defoort, Setareh Tasdighian, Steven Maere, Yves Van de Peer, Riet De Smet

(2016) - The Plant Cell

DOI
32. Combined large-scale phenotyping and transcriptomics in maize reveals a robust growth regulatory network

Joke Baute, Dorota Herman, Frederik Coppens, Jolien De Block, Bram Slabbinck, Matteo Dell'Aqcua, Mario Enrico Pè, Steven Maere, Hilde Nelissen, Dirk Inzé

(2016) - Plant Physiol.

DOI
31. Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

Joke Baute, Dorota Herman, Frederik Coppens, Jolien De Block, Bram Slabbinck, Matteo Dell’Acqua, Mario Enrico Pè, Steven Maere, Hilde Nelissen, Dirk Inzé

(2015) - Genome Biol

DOI
30. A conserved core of PCD indicator genes discriminates developmentally and environmentally induced programmed cell death in plants

Yadira Olvera-Carrillo, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Matthias Van Durme, Marlies Huysmans, Mária Šimášková, Pierre Buscaill, Susana Rivas, Nuria S. Coll, Steven Maere, Frederik Coppens, Moritz K Nowack

(2015) - Plant Physiol.

DOI
29. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development

Qian Chen, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, Jessica Lucas, Valya Vassileva, Saeko Kitakura, Peter Marhavý, Krzysztof Wabnik, Niko Geldner, Eva Benková, Jie Le, Hidehiro Fukaki, Erich Grotewold, Chuanyou Li, Jiří Friml, Fred Sack, Tom Beeckman, Steffen Vanneste

(2015) - Nat Comms

DOI
28. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary

Vanneste, Kevin, Baele, Guy, Maere, Steven, Van de Peer, Yves

(2014) - Genome Research

DOI
27. Interview with Steven Maere

Maere, Steven

(2014) - Trends in Plant Science

DOI
26. Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

Vanneste, Kevin, Maere, Steven, Van de Peer, Yves

(2014) - Philosophical Transactions of the Royal Society B-Biological Sciences

DOI
25. Modeling the evolution of molecular systems from a mechanistic perspective

Gutierrez, Jayson, Maere, Steven

(2014) - Trends in Plant Science

DOI
24. The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants

Gadeyne, Astrid, Sanchez-Rodriguez, Clara, Vanneste, Steffen, Di Rubbo, Simone, Zauber, Henrik, Vanneste, Kevin, Van Leene, Jelle, De Winne, Nancy, Eeckhout, Dominique, Persiau, Geert, De Slijke, Eveline Van, Cannoot, Bernard, Vercruysse, Leen, Mayers, Jonathan R., Adamowski, Maciek, Kania, Urszula, Ehrlich, Matthias, Schweighofer, Alois, Ketelaar, Tijs, Maere, Steven, Bednarek, Sebastian Y., Friml, Jiri, Gevaert, Kris, Witters, Erwin, Russinova, Eugenia, Persson, Staffan, De Jaeger, Geert, Van Damme, Daniel

(2014) - Cell

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

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

(2013) - Proceedings of the National Academy of Sciences of the United States of America

DOI
22. Inference of Genome Duplications from Age Distributions Revisited

Vanneste, Kevin, Van de Peer, Yves, Maere, Steven

(2013) - Molecular Biology and Evolution

DOI
21. Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants

Bhosale, Rahul, Jewell, Jeremy B., Hollunder, Jens, Koo, Abraham J. K., Vuylsteke, Marnik, Michoel, Tom, Hilson, Pierre, Goossens, Alain, Howe, Gregg A., Browse, John, Maere, Steven

(2013) - Plant Cell

DOI
20. Expansive Evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE Gene Family in Arabidopsis

Vandesteene, Lies, Lopez-Galvis, Lorena, Vanneste, Kevin, Feil, Regina, Maere, Steven, Lammens, Willem, Rolland, Filip, Lunn, John E., Avonce, Nelson, Beeckman, Tom, Van Dijck, Patrick

(2012) - Plant Physiology

DOI
19. Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification

Vekemans, Dries, Proost, Sebastian, Vanneste, Kevin, Coenen, Heleen, Viaene, Tom, Ruelens, Philip, Maere, Steven, Van de Peer, Yves, Geuten, Koen

(2012) - Molecular Biology and Evolution

DOI
18. Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

Voordeckers, Karin, Brown, Chris A., Vanneste, Kevin, van der Zande, Elisa, Voet, Arnout, Maere, Steven, Verstrepen, Kevin J.

(2012) - Plos Biology

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17. Significance and Biological Consequences of Polyploidization in Land Plant Evolution

Jeffrey A. Fawcett, Yves Van de Peer, Steven Maere

(2012) - Plant Genome Diversity Volume 2

DOI
16. PiNGO: a Cytoscape plugin to find candidate genes in biological networks

Smoot, Michael, Ono, Keiichiro, Ideker, Trey, Maere, Steven

(2011) - Bioinformatics

DOI
15. Duplicate Retention After Small- and Large-Scale Duplications

Steven Maere, Yves Van de Peer

(2011) - Evolution after Gene Duplication

DOI
14. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Van Leene, Jelle, Hollunder, Jens, Eeckhout, Dominique, Persiau, Geert, Van De Slijke, Eveline, Stals, Hilde, Van Isterdael, Gert, Verkest, Aurine, Neirynck, Sandy, Buffel, Yelle, De Bodt, Stefanie, Maere, Steven, Laukens, Kris, Pharazyn, Anne, Ferreira, Paulo C. G., Eloy, Nubia, Renne, Charlotte, Meyer, Christian, Faure, Jean-Denis, Steinbrenner, Jens, Beynon, Jim, Larkin, John C., Van de Peer, Yves, Hilson, Pierre, Kuiper, Martin, De Veylder, Lieven, Van Onckelen, Harry, Inze, Dirk, Witters, Erwin, De Jaeger, Geert

(2010) - Molecular Systems Biology

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13. 2R or not 2R is not the question anymore

Van de Peer, Yves, Maere, Steven, Meyer, Axel

(2010) - Nature Reviews Genetics

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12. Open-ended On-board Evolutionary Robotics for Robot Swarms

Baele, Guy, Bredeche, Nicolas, Haasdijk, Evert, Maere, Steven, Michiels, Nico, Van de Peer, Yves, Schmickl, Thomas, Schwarzer, Christopher, Thenius, Ronald, IEEE

(2009) - 2009 Ieee Congress on Evolutionary Computation, Vols 1-5

DOI
11. OPINION The evolutionary significance of ancient genome duplications

Van de Peer, Yves, Maere, Steven, Meyer, Axel

(2009) - Nature Reviews Genetics

DOI
10. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

Fawcett, Jeffrey A., Maere, Steven, Van de Peer, Yves

(2009) - Proceedings of the National Academy of Sciences of the United States of America

DOI
9. Extracting expression modules from perturbational gene expression compendia

Maere, Steven, Van Dijck, Patrick, Kuiper, Martin

(2008) - Bmc Systems Biology

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8. Integration of biological networks and gene expression data using Cytoscape

Cline, Melissa S., Smoot, Michael, Cerami, Ethan, Kuchinsky, Allan, Landys, Nerius, Workman, Chris, Christmas, Rowan, Avila-Campilo, Iliana, Creech, Michael, Gross, Benjamin, Hanspers, Kristina, Isserlin, Ruth, Kelley, Ryan, Killcoyne, Sarah, Lotia, Samad, Maere, Steven, Morris, John, Ono, Keiichiro, Pavlovic, Vuk, Pico, Alexander R., Vailaya, Aditya, Wang, Peng-Liang, Adler, Annette, Conklin, Bruce R., Hood, Leroy, Kuiper, Martin, Sander, Chris, Schmulevich, Ilya, Schwikowski, Benno, Warner, Guy J., Ideker, Trey, Bader, Gary D.

(2007) - Nature Protocols

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7. The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth

Fleury, Delphine, Himanen, Kristiina, Cnops, Gerda, Nelissen, Hilde, Boccardi, Tommaso Matteo, Maere, Steven, Beemster, Gerrit T. S., Neyt, Pia, Anami, Sylvester, Robles, Pedro, Micol, Jose Luis, Inze, Dirk, Van Lijsebettens, Mieke

(2007) - Plant Cell

DOI
6. Validating module network learning algorithms using simulated data

Michoel, Tom, Maere, Steven, Bonnet, Eric, Joshi, Anagha, Saeys, Yvan, Van den Bulcke, Tim, Van Leemput, Koenraad, van Remortel, Piet, Kuiper, Martin, Marchal, Kathleen, de Peer, Yves Van

(2007) - Bmc Bioinformatics

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5. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana

Casneuf, T, De Bodt, S, Raes, J, Maere, S, Van de Peer, Y

(2006) - Genome Biology

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

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

(2006) - Genome Biology

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3. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Maere, S, Heymans, K, Kuiper, M

(2005) - Bioinformatics

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2. Genome duplication and the origin of angiosperms

De Bodt, S, Maere, S, Van de Peer, Y

(2005) - Trends in Ecology & Evolution

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1. Modeling gene and genome duplications in eukaryotes

Maere, S, De Bodt, S, Raes, J, Casneuf, T, Van Montagu, M, Kuiper, M, Van de Peer, Y

(2005) - Proceedings of the National Academy of Sciences of the United States of America

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