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Genome duplication and the origin of angiosperms.
De Bodt S, Maere S, Van de Peer Y. De Bodt S, et al. Trends Ecol Evol. 2005 Nov;20(11):591-7. doi: 10.1016/j.tree.2005.07.008. Epub 2005 Aug 9. Trends Ecol Evol. 2005. PMID: 16701441
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. Maere S, et al. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9. doi: 10.1073/pnas.0501102102. Epub 2005 Mar 30. Proc Natl Acad Sci U S A. 2005. PMID: 15800040 Free PMC article.
The gain and loss of genes during 600 million years of vertebrate evolution.
Blomme T, Vandepoele K, De Bodt S, Simillion C, Maere S, Van de Peer Y. Blomme T, et al. Genome Biol. 2006;7(5):R43. doi: 10.1186/gb-2006-7-5-r43. Epub 2006 May 24. Genome Biol. 2006. PMID: 16723033 Free PMC article.
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event.
Fawcett JA, Maere S, Van de Peer Y. Fawcett JA, et al. Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5737-42. doi: 10.1073/pnas.0900906106. Epub 2009 Mar 26. Proc Natl Acad Sci U S A. 2009. PMID: 19325131 Free PMC article.
The evolutionary significance of ancient genome duplications.
Van de Peer Y, Maere S, Meyer A. Van de Peer Y, et al. Nat Rev Genet. 2009 Oct;10(10):725-32. doi: 10.1038/nrg2600. Epub 2009 Aug 4. Nat Rev Genet. 2009. PMID: 19652647 Review.
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.
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 PC, Eloy N, Renne C, Meyer C, Faure JD, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E, De Jaeger G. Van Leene J, et al. Mol Syst Biol. 2010 Aug 10;6:397. doi: 10.1038/msb.2010.53. Mol Syst Biol. 2010. PMID: 20706207 Free PMC article.
Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. ...
Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and th …
Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification.
Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K. Vekemans D, et al. Mol Biol Evol. 2012 Dec;29(12):3793-806. doi: 10.1093/molbev/mss183. Epub 2012 Jul 20. Mol Biol Evol. 2012. PMID: 22821009
Large-scale phylogenetic and K(S)-based approaches on the inflorescence transcriptomes of Gunnera manicata (Gunnerales) and Pachysandra terminalis (Buxales) provide further support for this placement, enabling us to position the gamma triplication in the stem lineage of th …
Large-scale phylogenetic and K(S)-based approaches on the inflorescence transcriptomes of Gunnera manicata (Gunnerales) and Pachysand …
Expansive evolution of the trehalose-6-phosphate phosphatase gene family in Arabidopsis.
Vandesteene L, López-Galvis L, Vanneste K, Feil R, Maere S, Lammens W, Rolland F, Lunn JE, Avonce N, Beeckman T, Van Dijck P. Vandesteene L, et al. Plant Physiol. 2012 Oct;160(2):884-96. doi: 10.1104/pp.112.201400. Epub 2012 Aug 1. Plant Physiol. 2012. PMID: 22855938 Free PMC article.
Inference of genome duplications from age distributions revisited.
Vanneste K, Van de Peer Y, Maere S. Vanneste K, et al. Mol Biol Evol. 2013 Jan;30(1):177-90. doi: 10.1093/molbev/mss214. Epub 2012 Aug 30. Mol Biol Evol. 2013. PMID: 22936721
K(S) stochasticity is expected to erode the signal of older WGDs, whereas K(S) saturation may lead to artificial peaks in the distribution. ...We show that, although K(S) estimates can be used for WGD inference far beyond the commonly accepted K(S) thr …
K(S) stochasticity is expected to erode the signal of older WGDs, whereas K(S) saturation may lead to artificial peaks in the …
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