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BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.
Maere S, Heymans K, Kuiper M. Maere S, et al. Bioinformatics. 2005 Aug 15;21(16):3448-9. doi: 10.1093/bioinformatics/bti551. Epub 2005 Jun 21. Bioinformatics. 2005. PMID: 15972284
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.
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. Casneuf T, et al. Among authors: maere s. Genome Biol. 2006;7(2):R13. doi: 10.1186/gb-2006-7-2-r13. Epub 2006 Feb 20. Genome Biol. 2006. PMID: 16507168 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. Among authors: maere s. 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.
The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth.
Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GT, Neyt P, Anami S, Robles P, Micol JL, Inzé D, Van Lijsebettens M. Fleury D, et al. Among authors: maere s. Plant Cell. 2007 Feb;19(2):417-32. doi: 10.1105/tpc.106.041319. Epub 2007 Feb 28. Plant Cell. 2007. PMID: 17329565 Free PMC article.
Validating module network learning algorithms using simulated data.
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. Michoel T, et al. Among authors: maere s. BMC Bioinformatics. 2007 May 3;8 Suppl 2(Suppl 2):S5. doi: 10.1186/1471-2105-8-S2-S5. BMC Bioinformatics. 2007. PMID: 17493254 Free PMC article.
Integration of biological networks and gene expression data using Cytoscape.
Cline MS, 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 AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Cline MS, et al. Among authors: maere s. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. Nat Protoc. 2007. PMID: 17947979 Free PMC article.
Extracting expression modules from perturbational gene expression compendia.
Maere S, Van Dijck P, Kuiper M. Maere S, et al. BMC Syst Biol. 2008 Apr 10;2:33. doi: 10.1186/1752-0509-2-33. BMC Syst Biol. 2008. PMID: 18402676 Free PMC article.
PiNGO: a Cytoscape plugin to find candidate genes in biological networks.
Smoot M, Ono K, Ideker T, Maere S. Smoot M, et al. Among authors: maere s. Bioinformatics. 2011 Apr 1;27(7):1030-1. doi: 10.1093/bioinformatics/btr045. Epub 2011 Jan 28. Bioinformatics. 2011. PMID: 21278188 Free PMC article.
Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants.
Bhosale R, Jewell JB, Hollunder J, Koo AJ, Vuylsteke M, Michoel T, Hilson P, Goossens A, Howe GA, Browse J, Maere S. Bhosale R, et al. Among authors: maere s. Plant Cell. 2013 Aug;25(8):2865-77. doi: 10.1105/tpc.113.112268. Epub 2013 Aug 13. Plant Cell. 2013. PMID: 23943861 Free PMC article.
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