Maere Lab | Evolutionary Systems Biology
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*co-first or co-last author
2020
(47) Wendrich, J.R. *, Yang, B. *, Vandamme, N. *, Verstaen, K. *, Smet, W., Van de Velde, C., Minne, M., Wybouw, B., Mor, E., Arents, H.E., Nolf, J., Van Duyse, J., Van Isterdael, G., Maere, S., Saeys, Y. *, De Rybel, B. * (2020) Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions. Science 370: eaay4970.
(46) Parry, G., Provart. N.J., Brady. S.M., Uzilday, B.; Multinational Arabidopsis Steering Committee (2020) Current status of the multinational Arabidopsis community. Plant Direct 4:e00248.
2019
(45) Gallone, B. *, Steensels, J. *, Mertens, S., Dzialo, M.C., Gordon, J.L., Wauters, R., Theßeling, F.A., Bellinazzo, F., Saels, V., Herrera-Malaver, B., Prahl, T., White, C., Hutzler, M., Meußdoerffer, F., Malcorps, P., Souffriau, B., Daenen, L., Baele, G., Maere, S. *,Verstrepen, K.J. * (2019) Interspecific hybridisation facilitates niche adaptation in beer yeast. Nat Ecol Evol. 3:1562–1575.
(44) Bhosale, R., Maere, S., De Veylder, L. (2019) Endoreplication as a potential driver of cell wall modifications. Curr Opin Plant Biol. 51:58-65.
2018
(43) Bhosale, R. *, Boudolf, V. *, Cuevas, F. *, Lua, R., Eekhout, T., Hua, Z., Van Isterdael, G., Lambert, G.M., Nowack, M.K., Smith, R.S., Vercauteren, I., De Rycke, R., Storme, V., Beeckman, T., Larkin, J.C., Kremer, A., Höfte, H., Galbraith, D.W., Kumpf, R.P., Maere, S. *, De Veylder, L. * (2018) A spatiotemporal DNA endoploidy map of the Arabidopsis root reveals roles for the endocycle in root development and stress adaptation. Plant Cell 30: 2330-2351.
(42) Li, F.-W., Brouwer, P., Carretero-Paulet, L., Cheng, S., de Vries, J., Delaux, P.-M., Eily, A., Koppers, N., Kuo, L.-Y., Li, Z., Simenc, M., Small, I., Wafula, E., Angarita, S., Barker, M.S., Bräutigam, A., dePamphilis, C., Gould, S., Hosmani, P.S., Huang, Y.-M., Huettel, B., Kato, Y., Liu, X., Maere, S., McDowell, R., Mueller, L.A., Nierop, K.G.J., Rensing, S.A., Robison, T., Rothfels, C.J., Sigel, E.M., Song, Y., Timilsena, P.R., Van de Peer, Y., Wang, H., Wilhelmsson, P.K.I., Wolf, P.G., Xu, X., Der, J.P., Schluepmann, H., Wong, G.K.-S., Pryer, K.M.(2018) Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants 4:460-72.
(41) Cova, M., López-Gutiérrez, B., Artigas-Jerónimo, S., González-Díaz, A., Bandini, G., Maere, S., Carretero-Paulet, L. *, Izquierdo, L. * (2018) The Apicomplexa-specific glucosamine-6-phosphate N-acetyltransferase gene family encodes a key enzyme for glycoconjugate synthesis with potential as therapeutic target. Scientific Reports 8: 4005.
(40) Gallone, B., Mertens, S., Gordon, J.L., Maere, S., Verstrepen, K.J. *, Steensels, J. * (2018) Origins, evolution, domestication and diversity of Saccharomyces beer yeasts. Curr Opin Biotechnol. 49:148-55.
(39) Nelissen, H., Sun, X.H., Rymen, B., Jikumaru, Y., Kojima, M., Takebayashi, Y., Abbeloos, R., Demuynck, K., Storme, V., Vuylsteke, M., De Block, J., Herman, D., Coppens, F., Maere, S., Kamiya, Y., Sakakibara, H., Beemster, G.T.S., Inzé, D. (2018) 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. Plant Biotechnol J. 16: 615-27.
2017
(38) Tasdighian, S., Van Bel, M., Li, Z., Van de Peer, Y., Carretero-Paulet, L., Maere S. (2017) Reciprocally retained genes in the angiosperm lineage show the hallmarks of dosage balance sensitivity. Plant Cell 29: 2766-85.
(37) Gordon, J.L., Gallone, B., Maere, S., Verstrepen, K.J. (2017) Evolutionary context improves regulatory network predictions. Cell Syst. 4: 478-9.
(36) Ruelens, P., Zhang, Z., van Mourik, H., Maere, S., Kaufmann, K., Geuten, K. (2017) The origin of floral organ identity quartets. Plant Cell 29:229-42.
2016
(35) Clauw, P., Coppens, F., Korte, A., Herman, D., Slabbinck, B., Dhondt, S., Van Daele, T., De Milde, L., Vermeersch, M., Maleux, K., Maere, S., Gonzalez, N.* and Inzé, D.* (2016) Leaf growth response to mild drought: natural variation in Arabidopsis sheds light on trait architecture. Plant Cell 28:2417-34.
(34) Gallone, B. *, Steensels, J. *, Prahl, T., Soriaga, L., Saels, V., Herrera-Malaver, 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.J. * (2016) Domestication and divergence of Saccharomyces cerevisiae beer yeasts. Cell 166:1397-1410.
(33) Baute, J., Herman, D., Coppens, F., De Block, J., Slabbinck, B., Dell'Aqcua, M., Pè, M.E., Maere, S., Nelissen, H., Inzé, D. (2016) Combined large-scale phenotyping and transcriptomics in maize reveals a robust growth regulatory network. Plant Physiol. 170:1848-67.
(32) Li, Z. *, Defoort, J. *, Tasdighian, S., Maere, S., Van de Peer, Y., De Smet, R. (2016) Gene duplicability of core genes is highly consistent across all angiosperms. Plant Cell 28:326-44.
2015
(31) Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., Xuan, W., Lucas, J., Vassileva, V., Kitakura, S., Marhavy, P., Wabnik, K., Geldner, N., Benková, E., Le, J., Fukaki, H., Grotewold, E., Li, C., Friml, J., Sack, F., Beeckman, T., Vanneste, S. (2015) A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nat. Commun. 18: 8821.
(30) Olvera-Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Simaskova, M., van Durme, M., Buscaill, P., Rivas, S., Sánchez-Coll, N., Coppens, F., Maere, S., Nowack, M.K. (2015) A conserved core of PCD indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiol. 169:2684-99.
(29) Baute, J., Herman, D., Coppens, F., De Block, J., Slabbinck, B., Dell'Acqua, M., Pè, E., Maere, S., Nelissen, H., Inzé, D. (2015) Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population. Genome Biol. 16:168.
2014
(28) Vanneste, K., Baele, G., Maere, S. *, Van de Peer, Y. * (2014) Analysis of 41 plant genomes supports a wave of successful genome duplications at the Cretaceous-Tertiary boundary. Genome Res. 24:1334-47.
(27) Vanneste, K., Maere, S., Van de Peer, Y. (2014) Tangled up in two: A burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Phil Trans R Soc B 369: 20130353
(26) Gutiérrez, J., Maere, S. (2014) Modeling the evolution of molecular systems from a mechanistic perspective. Trends Plant Sci. 19:292-303.
(25) Maere, S. (2014) Interview with Steven Maere. Trends Plant Sci. 19(5):276-7.
(24) Gadeyne, A., Sánchez-Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H., Vanneste, K., Van Leene, J., De Winne, N., Eeckhout, D., Persiau, G., Van De Slijke, E., Cannoot, B., Vercruysse, L., Mayers, J.R., Adamowski, M., Kania, U., Ehrlich, M., Schweighofer, A., Ketelaar, T., Maere, S., Bednarek, S.Y., Friml, J., Gevaert, K., Witters, E., Russinova, E., Persson, S., De Jaeger, G., Van Damme, D. (2014) The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell 156:691-704.
2013
(23) Bhosale, R.*, Jewell, J.B.*, Hollunder, J., Koo, A.J.K., Vuylsteke, M., Michoel, T., Hilson, P., Goossens, A., Howe, G.A., Browse, J., Maere, S. (2013) Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants. Plant Cell 25:2865-77.
(22) De Smet, R., Adams, K.L., Vandepoele, K., Van Montagu, M.C., Maere, S., Van de Peer, Y. (2013) Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc. Natl. Acad. Sci. U. S. A. 110:2898-903.
(21) Vanneste, K., Van de Peer, Y., Maere, S. (2013) Inference of genome duplications from age distributions revisited. Mol. Biol. Evol. 30:177-90.
(20) Fawcett, J., Van de Peer, Y., Maere, S. (2013) Significance and biological consequences of polyploidization in land plant evolution. In: Plant Genome Diversity, Volume 2, Greilhuber, J., Dolezel, J., Leitch, I. and Wendel, J. (eds) Springer-Verlag (Vienna)
2012
(19) Voordeckers, K.*, Brown, C.A.*, Vanneste, K., van der Zande, E., Voet, A., Maere, S.*, Verstrepen, K.J.* (2012) Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PLoS Biol. 10:e1001446.
(18) Vekemans, D., Proost, S., Vanneste, K., Coenen, H., Viaene, T., Ruelens, P., Maere, S., Van de Peer, Y., Geuten, K. (2012) Gamma paleohexaploidy in the stem-lineage of core eudicots: significance for MADS-box gene and species diversification. Mol. Biol. Evol. 29:3793-806.
(17) Vandesteene, L., Lopez-Galvis, L., Vanneste, K., Feil, R., Maere, S., Lammens, W., Rolland, F., Lunn, J.E., Avonce, N., Beeckman, T., Van Dijck, P. (2012) Expansive evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE gene family in Arabidopsis thaliana. Plant Physiol. 160:884-96.
2011
(16) Smoot, M., Ono, K., Ideker, T., Maere, S. (2011) PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics 27:1030-1.
2010
(15) Van Leene, J., Hollunder, J., Eeckhout, D., Persiau, G., Van De Slijke, E., Stals, H., Van Isterdael, G., Verkest, A., Neirynck, S., Buffel, Y., De Bodt, S., Maere, S., Laukens, K., Pharazyn, A., Ferreira, P.C., Eloy, N., Renne, C., Meyer, C., Faure, J.D., Steinbrenner, J., Beynon, J., Larkin, J.C., Van de Peer, Y., Hilson, P., Kuiper, M., De Veylder, L., Van Onckelen, H., Inzé, D., Witters, E., De Jaeger, G. (2010) Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 10:397.
(14) Van de Peer, Y., Maere, S., Meyer, A. (2010) 2R or not 2R is not the question anymore. Nat Rev Genet doi:10.1038/nrg2600-c2 (Correspondence on Nat. Rev. Genet. 10:725-32)
(13) Maere, S., Van de Peer, Y. (2010) Duplicate retention after small‐ and large‐scale duplications. In: Evolution after gene duplication, Liberles, D.A. and Dittmar, K., eds., Wiley (New York)
2009
(12) Van de Peer, Y., Maere, S., Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10:725-32.
(11) Baele, G., Bredeche, N., Haasdijk, E., Maere, S., Michiels, N., Van de Peer, Y., Schmickl, T., Schwarzer, C., Thenius, R. (2009) Open-ended on-board evolutionary robotics for robot swarms. Proceedings of the 2009 IEEE Congress On Evolutionary Computation (CEC 2009), 1123-30.
(10) * Fawcett, J., * Maere, S., Van de Peer, Y. (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc. Natl. Acad. Sci. U. S. A. 106, 5737-42.
2008
(9) Maere, S., Van Dijck, P., Kuiper, M. (2008) Extracting expression modules from perturbational gene expression compendia. BMC Syst. Biol. 2:33.
2007
(8) * Michoel, T., * Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module networks learning algorithms using simulated data. BMC Bioinformatics 8, S5.
(7) Fleury, D., Himanen, K., Cnops, G., Nelissen, B., Boccardi, T.M., Maere, S., Beemster, G.T.S., Neyt, P., Anami, S., Robles, P., Micol, J.S., Inzé, D., Van Lijsebettens, M. (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19, 417-32.
(6) Cline, M.S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., Hanspers, K., Isserlin, R., Kelley, R., Killcoyne, S., Lotia, S., Maere, S., Morris, J., Ono, K., Pavlovic, V., Pico, A.R., Vailaya, A., Wang, X., Adler, A., Conklin, B.R., Hood, L., Kuiper, M., Sander, C., Schmulevich, I., Schwikowski, B., Warner, G.J., Ideker, T., Bader, G.D. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366 - 2382.
2006
(5) Casneuf, T., De Bodt, S., Raes, J., Maere, S., Van de Peer, Y. (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol. 7, R13.
(4) Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., Van de Peer, Y. (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7, R43.
2005
(3) * De Bodt, S., * Maere, S., Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-7.
(2) Maere, S., Heymans, K., Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-9.
(1) * Maere, S., * De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., Van de Peer, Y. (2005) Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 102, 5454-9.