Yves Van de Peer - Publications

Bioinformatics & Systems Biology Ghent University, Ghent, Vlaanderen, Belgium 

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Year Citation  Score
2017 De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y. Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana. The Plant Cell. PMID 29070508 DOI: 10.1105/tpc.17.00531  0.32
2017 Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Research. PMID 29069403 DOI: 10.1093/nar/gkx1002  0.68
2016 Meysman P, Saeys Y, Sabaghian E, Bittremieux W, van de Peer Y, Goethals B, Laukens K. Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 27295680 DOI: 10.1109/TCBB.2016.2576440  0.32
2016 Lohaus R, Van de Peer Y. Of dups and dinos: evolution at the K/Pg boundary. Current Opinion in Plant Biology. 30: 62-69. PMID 26894611 DOI: 10.1016/j.pbi.2016.01.006  1
2016 Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, ... ... Van de Peer Y, et al. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature. PMID 26814964 DOI: 10.1038/nature16548  1
2016 Zhang GQ, Xu Q, Bian C, Tsai WC, Yeh CM, Liu KW, Yoshida K, Zhang LS, Chang SB, Chen F, Shi Y, Su YY, Zhang YQ, Chen LJ, Yin Y, ... ... Van de Peer Y, et al. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Scientific Reports. 6: 19029. PMID 26754549 DOI: 10.1038/srep19029  1
2015 Tzfadia O, Diels T, De Meyer S, Vandepoele K, Aharoni A, Van de Peer Y. CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool. Frontiers in Plant Science. 6: 1194. PMID 26779228 DOI: 10.3389/fpls.2015.01194  1
2015 Soltis PS, Marchant DB, Van de Peer Y, Soltis DE. Polyploidy and genome evolution in plants. Current Opinion in Genetics & Development. 35: 119-125. PMID 26656231 DOI: 10.1016/j.gde.2015.11.003  1
2015 Kaewphan S, Van Landeghem S, Ohta T, Van de Peer Y, Ginter F, Pyysalo S. Cell line name recognition in support of the identification of synthetic lethality in cancer from text. Bioinformatics (Oxford, England). PMID 26428294 DOI: 10.1093/bioinformatics/btv570  1
2015 Delhomme N, Sundström G, Zamani N, Lantz H, Lin YC, Hvidsten TR, Höppner MP, Jern P, Van de Peer Y, Lundeberg J, Grabherr MG, Street NR. Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). Plos One. 10: e0139080. PMID 26413905 DOI: 10.1371/journal.pone.0139080  1
2015 Potenza E, Racchi ML, Sterck L, Coller E, Asquini E, Tosatto SC, Velasco R, Van de Peer Y, Cestaro A. Exploration of alternative splicing events in ten different grapevine cultivars. Bmc Genomics. 16: 706. PMID 26380971 DOI: 10.1186/s12864-015-1922-5  1
2015 Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P. Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. Journal of Experimental Botany. 66: 5257-69. PMID 26195730 DOI: 10.1093/jxb/erv346  1
2015 Sundell D, Mannapperuma C, Netotea S, Delhomme N, Lin YC, Sjödin A, Van de Peer Y, Jansson S, Hvidsten TR, Street NR. The Plant Genome Integrative Explorer Resource: PlantGenIE.org. The New Phytologist. PMID 26192091 DOI: 10.1111/nph.13557  1
2015 Crauwels S, Van Assche A, de Jonge R, Borneman AR, Verreth C, Troels P, De Samblanx G, Marchal K, Van de Peer Y, Willems KA, Verstrepen KJ, Curtin CD, Lievens B. Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains. Applied Microbiology and Biotechnology. 99: 9123-34. PMID 26135985 DOI: 10.1007/s00253-015-6769-9  1
2015 Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, et al. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Scientific Reports. 5: 11571. PMID 26108467 DOI: 10.1038/srep11571  1
2015 Vanneste K, Sterck L, Myburg AA, Van de Peer Y, Mizrachi E. Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum. The Plant Cell. PMID 26002871 DOI: 10.1105/tpc.15.00157  1
2015 Zhang Z, Mao L, Chen H, Bu F, Li G, Sun J, Li S, Sun H, Jiao C, Blakely R, Pan J, Cai R, Luo R, Van de Peer Y, Jacobsen E, et al. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber. The Plant Cell. 27: 1595-604. PMID 26002866 DOI: 10.1105/tpc.114.135848  1
2015 De La Torre AR, Lin YC, Van de Peer Y, Ingvarsson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biology and Evolution. 7: 1002-15. PMID 25747252 DOI: 10.1093/gbe/evv044  1
2015 Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, ... ... Van de Peer Y, et al. The genome sequence of the orchid Phalaenopsis equestris. Nature Genetics. 47: 65-72. PMID 25420146 DOI: 10.1038/ng.3149  1
2015 Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, Vandepoele K. PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Research. 43: D974-81. PMID 25324309 DOI: 10.1093/nar/gku986  1
2015 Szakonyi D, Van Landeghem S, Baerenfaller K, Baeyens L, Blomme J, Casanova-Sáez R, De Bodt S, Esteve-Bruna D, Fiorani F, Gonzalez N, Grønlund J, Immink RGH, Jover-Gil S, Kuwabara A, Muñoz-Nortes T, ... ... Van de Peer Y, et al. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining Current Plant Biology. 2: 1-11. DOI: 10.1016/j.cpb.2014.12.002  1
2015 De Tiège A, Tanghe KB, Braeckman J, Van De Peer Y. Life's dual nature: A way out of the impasse of the gene-centred 'versus' complex systems controversy on life Evolutionary Biology: Biodiversification From Genotype to Phenotype. 35-52. DOI: 10.1007/978-3-319-19932-0_3  1
2014 Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. Bmc Genomics. 15: 1103. PMID 25494611 DOI: 10.1186/1471-2164-15-1103  1
2014 Lin YC, Boone M, Meuris L, Lemmens I, Van Roy N, Soete A, Reumers J, Moisse M, Plaisance S, Drmanac R, Chen J, Speleman F, Lambrechts D, Van de Peer Y, Tavernier J, et al. Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations. Nature Communications. 5: 4767. PMID 25182477 DOI: 10.1038/ncomms5767  1
2014 Ahmed S, Cock JM, Pessia E, Luthringer R, Cormier A, Robuchon M, Sterck L, Peters AF, Dittami SM, Corre E, Valero M, Aury JM, Roze D, Van de Peer Y, Bothwell J, et al. A haploid system of sex determination in the brown alga Ectocarpus sp. Current Biology : Cb. 24: 1945-57. PMID 25176635 DOI: 10.1016/j.cub.2014.07.042  1
2014 Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil Mdel R. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. Bmc Plant Biology. 14: 220. PMID 25143005 DOI: 10.1186/s12870-014-0220-8  1
2014 Mushthofa M, Torres G, Van de Peer Y, Marchal K, De Cock M. ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. Bioinformatics (Oxford, England). 30: 3086-92. PMID 25028722 DOI: 10.1093/bioinformatics/btu481  1
2014 Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, ... ... Van de Peer Y, et al. The genome of Eucalyptus grandis. Nature. 510: 356-62. PMID 24919147 DOI: 10.1038/nature13308  1
2014 Pajoro A, Biewers S, Dougali E, Leal Valentim F, Mendes MA, Porri A, Coupland G, Van de Peer Y, van Dijk AD, Colombo L, Davies B, Angenent GC. The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history. Journal of Experimental Botany. 65: 4731-45. PMID 24913630 DOI: 10.1093/jxb/eru233  1
2014 Vanneste K, Baele G, Maere S, Van de Peer Y. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Research. 24: 1334-47. PMID 24835588 DOI: 10.1101/gr.168997.113  1
2014 Morreel K, Saeys Y, Dima O, Lu F, Van de Peer Y, Vanholme R, Ralph J, Vanholme B, Boerjan W. Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks. The Plant Cell. 26: 929-45. PMID 24685999 DOI: 10.1105/tpc.113.122242  1
2014 Yao Y, Marchal K, Van de Peer Y. Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments. Plos One. 9: e90695. PMID 24599485 DOI: 10.1371/journal.pone.0090695  1
2014 Ciesielska K, Van Bogaert IN, Chevineau S, Li B, Groeneboer S, Soetaert W, Van de Peer Y, Devreese B. Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids. Journal of Proteomics. 98: 159-74. PMID 24418522 DOI: 10.1016/j.jprot.2013.12.026  1
2014 Zhurov V, Navarro M, Bruinsma KA, Arbona V, Santamaria ME, Cazaux M, Wybouw N, Osborne EJ, Ens C, Rioja C, Vermeirssen V, Rubio-Somoza I, Krishna P, Diaz I, Schmid M, ... ... Van de Peer Y, et al. Reciprocal responses in the interaction between Arabidopsis and the cell-content-feeding chelicerate herbivore spider mite. Plant Physiology. 164: 384-99. PMID 24285850 DOI: 10.1104/pp.113.231555  1
2014 Bolton MD, de Jonge R, Inderbitzin P, Liu Z, Birla K, Van de Peer Y, Subbarao KV, Thomma BP, Secor GA. The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution. Fungal Genetics and Biology : Fg & B. 62: 43-54. PMID 24216224 DOI: 10.1016/j.fgb.2013.10.011  1
2014 Chaves I, Lin YC, Pinto-Ricardo C, Van de Peer Y, Miguel C. miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns Tree Genetics and Genomes. 10: 721-737. DOI: 10.1007/s11295-014-0717-1  1
2014 De Tiège A, Tanghe K, Braeckman J, Van de Peer Y. From DNA- to NA-centrism and the conditions for gene-centrism revisited Biology and Philosophy. 29: 55-69. DOI: 10.1007/s10539-013-9393-z  1
2013 Van Bel M, Proost S, Van Neste C, Deforce D, Van de Peer Y, Vandepoele K. TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biology. 14: R134. PMID 24330842 DOI: 10.1186/gb-2013-14-12-r134  1
2013 Verhelst B, Van de Peer Y, Rouzé P. The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution. Genome Biology and Evolution. 5: 2393-401. PMID 24273312 DOI: 10.1093/gbe/evt189  1
2013 De Clercq I, Vermeirssen V, Van Aken O, Vandepoele K, Murcha MW, Law SR, Inzé A, Ng S, Ivanova A, Rombaut D, van de Cotte B, Jaspers P, Van de Peer Y, Kangasjärvi J, Whelan J, et al. The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. The Plant Cell. 25: 3472-90. PMID 24045019 DOI: 10.1105/tpc.113.117168  1
2013 Ciesielska K, Li B, Groeneboer S, Van Bogaert I, Lin YC, Soetaert W, Van de Peer Y, Devreese B. SILAC-based proteome analysis of Starmerella bombicola sophorolipid production. Journal of Proteome Research. 12: 4376-92. PMID 23964782 DOI: 10.1021/pr400392a  1
2013 Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, Van de Peer Y, Rensing SA, Reski R. Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. Bmc Genomics. 14: 498. PMID 23879659 DOI: 10.1186/1471-2164-14-498  1
2013 Vandepoele K, Van Bel M, Richard G, Van Landeghem S, Verhelst B, Moreau H, Van de Peer Y, Grimsley N, Piganeau G. pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. Environmental Microbiology. 15: 2147-53. PMID 23826978 DOI: 10.1111/1462-2920.12174  1
2013 Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, Gomes A, Rustad T, Dolganov G, Glotova I, Abeel T, Mahwinney C, Kennedy AD, Allard R, Brabant W, ... ... Van de Peer Y, et al. The Mycobacterium tuberculosis regulatory network and hypoxia. Nature. 499: 178-83. PMID 23823726 DOI: 10.1038/nature12337  1
2013 Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, Young J, Aguilar M, Claverie JM, Frickenhaus S, Gonzalez K, ... ... Van de Peer Y, et al. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature. 499: 209-13. PMID 23760476 DOI: 10.1038/nature12221  1
2013 Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, ... ... Van de Peer Y, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 497: 579-84. PMID 23698360 DOI: 10.1038/nature12211  1
2013 Van Landeghem S, Björne J, Wei CH, Hakala K, Pyysalo S, Ananiadou S, Kao HY, Lu Z, Salakoski T, Van de Peer Y, Ginter F. Large-scale event extraction from literature with multi-level gene normalization. Plos One. 8: e55814. PMID 23613707 DOI: 10.1371/journal.pone.0055814  1
2013 Van Landeghem S, De Bodt S, Drebert ZJ, Inzé D, Van de Peer Y. The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. The Plant Cell. 25: 794-807. PMID 23532071 DOI: 10.1105/tpc.112.108753  1
2013 Van Bogaert IN, Holvoet K, Roelants SL, Li B, Lin YC, Van de Peer Y, Soetaert W. The biosynthetic gene cluster for sophorolipids: a biotechnological interesting biosurfactant produced by Starmerella bombicola. Molecular Microbiology. 88: 501-9. PMID 23516968 DOI: 10.1111/mmi.12200  1
2013 Roelants SL, Saerens KM, Derycke T, Li B, Lin YC, Van de Peer Y, De Maeseneire SL, Van Bogaert IN, Soetaert W. Candida bombicola as a platform organism for the production of tailor-made biomolecules. Biotechnology and Bioengineering. 110: 2494-503. PMID 23475585 DOI: 10.1002/bit.24895  1
2013 Ruttink T, Sterck L, Rohde A, Bendixen C, Rouzé P, Asp T, Van de Peer Y, Roldan-Ruiz I. Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne. Plant Biotechnology Journal. 11: 605-17. PMID 23433242 DOI: 10.1111/pbi.12051  1
2013 De Smet R, Adams KL, Vandepoele K, Van Montagu MC, Maere S, Van de Peer Y. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proceedings of the National Academy of Sciences of the United States of America. 110: 2898-903. PMID 23382190 DOI: 10.1073/pnas.1300127110  1
2013 Andolfo G, Sanseverino W, Rombauts S, Van de Peer Y, Bradeen JM, Carputo D, Frusciante L, Ercolano MR. Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. The New Phytologist. 197: 223-37. PMID 23163550 DOI: 10.1111/j.1469-8137.2012.04380.x  1
2013 Vanneste K, Van de Peer Y, Maere S. Inference of genome duplications from age distributions revisited. Molecular Biology and Evolution. 30: 177-90. PMID 22936721 DOI: 10.1093/molbev/mss214  1
2013 Fawcett JA, Van de Peer Y, Maere S. Significance and biological consequences of polyploidization in land plant evolution Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes. 277-293. DOI: 10.1007/978-3-7091-1160-4_17  1
2012 Sterck L, Billiau K, Abeel T, Rouzé P, Van de Peer Y. ORCAE: online resource for community annotation of eukaryotes. Nature Methods. 9: 1041. PMID 23132114 DOI: 10.1038/nmeth.2242  1
2012 Klochendler A, Weinberg-Corem N, Moran M, Swisa A, Pochet N, Savova V, Vikeså J, Van de Peer Y, Brandeis M, Regev A, Nielsen FC, Dor Y, Eden A. A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation. Developmental Cell. 23: 681-90. PMID 23000141 DOI: 10.1016/j.devcel.2012.08.009  1
2012 Moreau H, Verhelst B, Couloux A, Derelle E, Rombauts S, Grimsley N, Van Bel M, Poulain J, Katinka M, Hohmann-Marriott MF, Piganeau G, Rouzé P, Da Silva C, Wincker P, Van de Peer Y, et al. Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage. Genome Biology. 13: R74. PMID 22925495 DOI: 10.1186/gb-2012-13-8-r74  1
2012 Murat F, Van de Peer Y, Salse J. Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biology and Evolution. 4: 917-28. PMID 22833223 DOI: 10.1093/gbe/evs066  1
2012 Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K. Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification. Molecular Biology and Evolution. 29: 3793-806. PMID 22821009 DOI: 10.1093/molbev/mss183  1
2012 Milner DA, Pochet N, Krupka M, Williams C, Seydel K, Taylor TE, Van de Peer Y, Regev A, Wirth D, Daily JP, Mesirov JP. Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters. Plos One. 7: e40739. PMID 22815802 DOI: 10.1371/journal.pone.0040739  1
2012 Van Landeghem S, Björne J, Abeel T, De Baets B, Salakoski T, Van de Peer Y. Semantically linking molecular entities in literature through entity relationships. Bmc Bioinformatics. 13: S6. PMID 22759460 DOI: 10.1186/1471-2105-13-S11-S6  1
2012 Van Landeghem S, Hakala K, Rönnqvist S, Salakoski T, Van de Peer Y, Ginter F. Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations. Advances in Bioinformatics. 2012: 582765. PMID 22719757 DOI: 10.1155/2012/582765  1
2012 Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, ... ... Van De Peer Y, et al. The tomato genome sequence provides insights into fleshy fruit evolution Nature. 485: 635-641. PMID 22660326 DOI: 10.1038/nature11119  1
2012 Brown JR, Hanna M, Tesar B, Werner L, Pochet N, Asara JM, Wang YE, Dal Cin P, Fernandes SM, Thompson C, Macconaill L, Wu CJ, Van de Peer Y, Correll M, Regev A, et al. Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 3791-802. PMID 22623730 DOI: 10.1158/1078-0432.CCR-11-2342  1
2012 Van de Peer Y, Pires JC. Getting up to speed. Current Opinion in Plant Biology. 15: 111-4. PMID 22483403 DOI: 10.1016/j.pbi.2012.03.012  1
2012 Whitford R, Fernandez A, Tejos R, Pérez AC, Kleine-Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin YC, Storme V, ... Van de Peer Y, et al. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 22: 678-85. PMID 22421050 DOI: 10.1016/j.devcel.2012.02.002  1
2012 Brown JR, Hanna M, Tesar B, Pochet N, Vartanov A, Fernandes SM, Werner L, Ash M, Roden CA, MacConaill L, Hainz U, Longtine J, Wang YE, Correll M, Van de Peer Y, et al. Germline copy number variation associated with Mendelian inheritance of CLL in two families. Leukemia. 26: 1710-3. PMID 22382893 DOI: 10.1038/leu.2012.33  1
2012 De Smet R, Van de Peer Y. Redundancy and rewiring of genetic networks following genome-wide duplication events. Current Opinion in Plant Biology. 15: 168-76. PMID 22305522 DOI: 10.1016/j.pbi.2012.01.003  1
2012 Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Evaluation and properties of the budding yeast phosphoproteome. Molecular & Cellular Proteomics : McP. 11: M111.009555. PMID 22286756 DOI: 10.1074/mcp.M111.009555  1
2012 Malacarne G, Perazzolli M, Cestaro A, Sterck L, Fontana P, Van de Peer Y, Viola R, Velasco R, Salamini F. Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes. Plos One. 7: e29762. PMID 22253773 DOI: 10.1371/journal.pone.0029762  1
2012 Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K. Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiology. 158: 590-600. PMID 22198273 DOI: 10.1104/pp.111.189514  1
2012 Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y. GenomeView: a next-generation genome browser. Nucleic Acids Research. 40: e12. PMID 22102585 DOI: 10.1093/nar/gkr995  1
2012 Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K. i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Research. 40: e11. PMID 22102584 DOI: 10.1093/nar/gkr955  1
2012 Hacquard S, Joly DL, Lin YC, Tisserant E, Feau N, Delaruelle C, Legué V, Kohler A, Tanguay P, Petre B, Frey P, Van de Peer Y, Rouzé P, Martin F, Hamelin RC, et al. A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust). Molecular Plant-Microbe Interactions : Mpmi. 25: 279-93. PMID 22046958 DOI: 10.1094/MPMI-09-11-0238  1
2012 Fawcett JA, Rouzé P, Van de Peer Y. Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Molecular Biology and Evolution. 29: 849-59. PMID 21998273 DOI: 10.1093/molbev/msr254  1
2011 Kano Y, Björne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen KB, Verspoor K, Roeder C, Hunter LE, Kilicoglu H, Bergler S, Van Landeghem S, Van Parys T, Van de Peer Y, et al. U-Compare bio-event meta-service: compatible BioNLP event extraction services. Bmc Bioinformatics. 12: 481. PMID 22177292 DOI: 10.1186/1471-2105-12-481  1
2011 Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P, Grbić V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F, Hernández-Crespo P, Diaz I, Martinez M, Navajas M, Sucena É, ... ... Van de Peer Y, et al. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature. 479: 487-92. PMID 22113690 DOI: 10.1038/nature10640  1
2011 Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 480: 520-4. PMID 22089132 DOI: 10.1038/nature10625  1
2011 Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, Kumar U, Saier M, Wang Y, Cai H, Gu J, ... ... Van de Peer Y, et al. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biology. 12: R100. PMID 22004680 DOI: 10.1186/gb-2011-12-10-r100  1
2011 Michoel T, Joshi A, Nachtergaele B, Van de Peer Y. Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks. Molecular Biosystems. 7: 2769-78. PMID 21860879 DOI: 10.1039/c1mb05241a  1
2011 Joshi A, Van de Peer Y, Michoel T. Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast. Nucleic Acids Research. 39: 9108-17. PMID 21840901 DOI: 10.1093/nar/gkr661  1
2011 Chancerel E, Lepoittevin C, Le Provost G, Lin YC, Jaramillo-Correa JP, Eckert AJ, Wegrzyn JL, Zelenika D, Boland A, Frigerio JM, Chaumeil P, Garnier-Géré P, Boury C, Grivet D, González-Martínez SC, ... ... Van de Peer Y, et al. Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. Bmc Genomics. 12: 368. PMID 21767361 DOI: 10.1186/1471-2164-12-368  1
2011 Van de Peer Y. A mystery unveiled. Genome Biology. 12: 113. PMID 21635712 DOI: 10.1186/gb-2011-12-5-113  1
2011 Baele G, Van de Peer Y, Vansteelandt S. Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes. Bmc Evolutionary Biology. 11: 145. PMID 21619569 DOI: 10.1186/1471-2148-11-145  1
2011 Movahedi S, Van de Peer Y, Vandepoele K. Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiology. 156: 1316-30. PMID 21571672 DOI: 10.1104/pp.111.177865  1
2011 Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Coutinho PM, Feau N, Field M, Frey P, ... ... Van de Peer Y, et al. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proceedings of the National Academy of Sciences of the United States of America. 108: 9166-71. PMID 21536894 DOI: 10.1073/pnas.1019315108  1
2011 Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, ... ... Van de Peer Y, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics. 43: 476-81. PMID 21478890 DOI: 10.1038/ng.807  1
2011 Audenaert P, Van Parys T, Brondel F, Pickavet M, Demeester P, Van de Peer Y, Michoel T. CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. Bioinformatics (Oxford, England). 27: 1587-8. PMID 21478195 DOI: 10.1093/bioinformatics/btr182  1
2011 Proost S, Pattyn P, Gerats T, Van de Peer Y. Journey through the past: 150 million years of plant genome evolution. The Plant Journal : For Cell and Molecular Biology. 66: 58-65. PMID 21443623 DOI: 10.1111/j.1365-313X.2011.04521.x  1
2011 Armañanzas R, Saeys Y, Inza I, García-Torres M, Bielza C, van de Peer Y, Larrañaga P. Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 760-74. PMID 21393653 DOI: 10.1109/TCBB.2010.18  1
2011 Van de Peer Y. Genomes: the truth is in there. Embo Reports. 12: 93. PMID 21283113 DOI: 10.1038/embor.2011.1  1
2011 Fostier J, Proost S, Dhoedt B, Saeys Y, Demeester P, Van de Peer Y, Vandepoele K. A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. Bioinformatics (Oxford, England). 27: 749-56. PMID 21216775 DOI: 10.1093/bioinformatics/btr008  1
2011 Van Landeghem S, De Baets B, Van De Peer Y, Saeys Y. High-precision bio-molecular event extraction from text using parallel binary classifiers Computational Intelligence. 27: 645-664. DOI: 10.1111/j.1467-8640.2011.00403.x  1
2011 Yao Y, Baele G, Van De Peer Y. A bio-inspired agent-based system for controlling robot behaviour Ieee Ssci 2011 - Symposium Series On Computational Intelligence - Ia 2011: 2011 Ieee Symposium On Intelligent Agents. 31-38. DOI: 10.1109/IA.2011.5953608  1
2011 Maere S, Van de Peer Y. Duplicate Retention After Small- and Large-Scale Duplications Evolution After Gene Duplication. 31-56. DOI: 10.1002/9780470619902.ch3  1
2010 Sánchez-Rodríguez A, Martens C, Engelen K, Van de Peer Y, Marchal K. The potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina. Bmc Evolutionary Biology. 10: 318. PMID 20964831 DOI: 10.1186/1471-2148-10-318  1
2010 Bonnet E, Michoel T, Van de Peer Y. Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics (Oxford, England). 26: i638-44. PMID 20823333 DOI: 10.1093/bioinformatics/btq395  1
2010 Van Landeghem S, Abeel T, Saeys Y, Van de Peer Y. Discriminative and informative features for biomolecular text mining with ensemble feature selection. Bioinformatics (Oxford, England). 26: i554-60. PMID 20823321 DOI: 10.1093/bioinformatics/btq381  1
2010 Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, ... ... Van de Peer Y, et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics. 42: 833-9. PMID 20802477 DOI: 10.1038/ng.654  1
2010 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, ... ... Van de Peer Y, et al. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Molecular Systems Biology. 6: 397. PMID 20706207 DOI: 10.1038/msb.2010.53  1
2010 Baele G, Van de Peer Y, Vansteelandt S. Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences. Bmc Evolutionary Biology. 10: 244. PMID 20698960 DOI: 10.1186/1471-2148-10-244  1
2010 Baele G, Van de Peer Y, Vansteelandt S. Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. Journal of Molecular Evolution. 71: 34-50. PMID 20623275 DOI: 10.1007/s00239-010-9362-y  1
2010 Martens C, Van de Peer Y. The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. Bmc Genomics. 11: 353. PMID 20525264 DOI: 10.1186/1471-2164-11-353  1
2010 Bonnet E, He Y, Billiau K, Van de Peer Y. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics (Oxford, England). 26: 1566-8. PMID 20430753 DOI: 10.1093/bioinformatics/btq233  1
2010 Bonnet E, Tatari M, Joshi A, Michoel T, Marchal K, Berx G, Van de Peer Y. Module network inference from a cancer gene expression data set identifies microRNA regulated modules. Plos One. 5: e10162. PMID 20418949 DOI: 10.1371/journal.pone.0010162  1
2010 Huysman MJ, Martens C, Vandepoele K, Gillard J, Rayko E, Heijde M, Bowler C, Inzé D, Van de Peer Y, De Veylder L, Vyverman W. Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling. Genome Biology. 11: R17. PMID 20146805 DOI: 10.1186/gb-2010-11-2-r17  0.68
2010 Amoutzias GD, He Y, Gordon J, Mossialos D, Oliver SG, Van de Peer Y. Posttranslational regulation impacts the fate of duplicated genes. Proceedings of the National Academy of Sciences of the United States of America. 107: 2967-71. PMID 20080574 DOI: 10.1073/pnas.0911603107  1
2010 Van de Peer Y, Maere S, Meyer A. 2R or not 2R is not the question anymore. Nature Reviews. Genetics. 11: 166. PMID 20051987 DOI: 10.1038/nrg2600-c2  1
2010 Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombauts S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L. AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiology. 152: 487-99. PMID 20032078 DOI: 10.1104/pp.109.150185  1
2010 Abeel T, Helleputte T, Van de Peer Y, Dupont P, Saeys Y. Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics (Oxford, England). 26: 392-8. PMID 19942583 DOI: 10.1093/bioinformatics/btp630  1
2010 Fawcett JA, van de Peer Y. Angiosperm polyploids and their road to evolutionary success Trends in Evolutionary Biology. 2: 16-21. DOI: 10.4081/eb.2010.e3  1
2010 Amoutzias G, Van de Peer Y. Single-Gene and Whole-Genome Duplications and the Evolution of Protein-Protein Interaction Networks Evolutionary Genomics and Systems Biology. 413-429. DOI: 10.1002/9780470570418.ch19  1
2009 Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K. PLAZA: a comparative genomics resource to study gene and genome evolution in plants. The Plant Cell. 21: 3718-31. PMID 20040540 DOI: 10.1105/tpc.109.071506  1
2009 Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K. The flowering world: a tale of duplications. Trends in Plant Science. 14: 680-8. PMID 19818673 DOI: 10.1016/j.tplants.2009.09.001  1
2009 Vermeirssen V, Joshi A, Michoel T, Bonnet E, Casneuf T, Van de Peer Y. Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. Molecular Biosystems. 5: 1817-30. PMID 19763340 DOI: 10.1039/B908108a  1
2009 Piganeau G, Vandepoele K, Gourbière S, Van de Peer Y, Moreau H. Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus. Journal of Molecular Evolution. 69: 249-59. PMID 19693423 DOI: 10.1007/s00239-009-9271-0  1
2009 Van de Peer Y, Maere S, Meyer A. The evolutionary significance of ancient genome duplications. Nature Reviews. Genetics. 10: 725-32. PMID 19652647 DOI: 10.1038/nrg2600  1
2009 De Bodt S, Proost S, Vandepoele K, Rouzé P, Van de Peer Y. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. Bmc Genomics. 10: 288. PMID 19563678 DOI: 10.1186/1471-2164-10-288  1
2009 Dittami SM, Scornet D, Petit JL, Ségurens B, Da Silva C, Corre E, Dondrup M, Glatting KH, König R, Sterck L, Rouzé P, Van de Peer Y, Cock JM, Boyen C, Tonon T. Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biology. 10: R66. PMID 19531237 DOI: 10.1186/gb-2009-10-6-r66  1
2009 Abeel T, Van de Peer Y, Saeys Y. Toward a gold standard for promoter prediction evaluation Bioinformatics. 25: i313-i320. PMID 19478005 DOI: 10.1093/bioinformatics/btp191  1
2009 De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouzé P, Van de Peer Y, Callewaert N. Genome sequence of the recombinant protein production host Pichia pastoris. Nature Biotechnology. 27: 561-6. PMID 19465926 DOI: 10.1038/nbt.1544  1
2009 Michoel T, De Smet R, Joshi A, Van de Peer Y, Marchal K. Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks Bmc Systems Biology. 3. PMID 19422680 DOI: 10.1186/1752-0509-3-49  1
2009 Baele G, Van De Peer Y, Vansteelandt S. Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences Bmc Evolutionary Biology. 9. PMID 19405957 DOI: 10.1186/1471-2148-9-87  1
2009 Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, ... ... Van de Peer Y, et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (New York, N.Y.). 324: 268-72. PMID 19359590 DOI: 10.1126/science.1167222  1
2009 Michoel T, De Smet R, Joshi A, Marchal K, Van De Peer Y. Reverse-engineering transcriptional modules from gene expression data Annals of the New York Academy of Sciences. 1158: 36-43. PMID 19348630 DOI: 10.1111/j.1749-6632.2008.03943.x  1
2009 Fawcett JA, Maere S, Van De Peer Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event Proceedings of the National Academy of Sciences of the United States of America. 106: 5737-5742. PMID 19325131 DOI: 10.1073/pnas.0900906106  1
2009 Joshi A, De Smet R, Marchal K, Van de Peer Y, Michoel T. Module networks revisited: Computational assessment and prioritization of model predictions Bioinformatics. 25: 490-496. PMID 19136553 DOI: 10.1093/bioinformatics/btn658  1
2009 Kernbach S, Hamann H, Stradner J, Thenius R, Schmickl T, Crailsheim K, Van Rossum AC, Sebag M, Bredeche N, Yao Y, Baele G, Van De Peer Y, Timmis J, Mohktar M, Tyrrell A, et al. On adaptive self-organization in artificial robot organisms Computation World: Future Computing, Service Computation, Adaptive, Content, Cognitive, Patterns, Computationworld 2009. 33-43. DOI: 10.1109/ComputationWorld.2009.9  1
2009 Baele G, Bredeche N, Haasdijk E, Maere S, Michiels N, Van De Peer Y, Schmickl T, Schwarzer C, Thenius R. Open-ended on-board evolutionary robotics for robot swarms 2009 Ieee Congress On Evolutionary Computation, Cec 2009. 1123-1130. DOI: 10.1109/CEC.2009.4983072  1
2009 Abeel T, Van De Peer Y, Saeys Y. Java-ML: A machine learning library Journal of Machine Learning Research. 10: 931-934.  1
2008 Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, ... ... Van de Peer Y, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 456: 239-44. PMID 18923393 DOI: 10.1038/nature07410  1
2008 Baele G, Van De Peer Y, Vansteelandt S. A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences Systematic Biology. 57: 675-692. PMID 18853356 DOI: 10.1080/10635150802422324  1
2008 Abeel T, Saeys Y, Rouzé P, Van de Peer Y. ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles Bioinformatics. 24: i24-i31. PMID 18586720 DOI: 10.1093/bioinformatics/btn172  1
2008 Amoutzias GD, Van de Peer Y, Mossialos D. Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases Future Microbiology. 3: 361-370. PMID 18505401 DOI: 10.2217/17460913.3.3.361  1
2008 Amoutzias G, Van de Peer Y. Together We Stand: Genes Cluster to Coordinate Regulation Developmental Cell. 14: 640-642. PMID 18477446 DOI: 10.1016/j.devcel.2008.04.006  1
2008 Van Bel M, Saeys Y, Van de Peer Y. FunSiP: A modular and extensible classifier for the prediction of functional sites in DNA Bioinformatics. 24: 1532-1533. PMID 18474505 DOI: 10.1093/bioinformatics/btn225  1
2008 Amoutzias GD, Robertson DL, Van de Peer Y, Oliver SG. Choose your partners: dimerization in eukaryotic transcription factors Trends in Biochemical Sciences. 33: 220-229. PMID 18406148 DOI: 10.1016/j.tibs.2008.02.002  1
2008 Martin F, Aerts A, Ahrén D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buée M, ... ... Van de Peer Y, et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 452: 88-92. PMID 18322534 DOI: 10.1038/nature06556  1
2008 Martens C, Vandepoele K, Van de Peer Y. Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proceedings of the National Academy of Sciences of the United States of America. 105: 3427-32. PMID 18299576 DOI: 10.1073/pnas.0712248105  1
2008 Vandenbroucke K, Robbens S, Vandepoele K, Inzé D, Van De Peer Y, Van Breusegem F. Hydrogen peroxide-induced gene expression across kingdoms: A comparative analysis Molecular Biology and Evolution. 25: 507-516. PMID 18187560 DOI: 10.1093/molbev/msm276  1
2008 Abeel T, Saeys Y, Bonnet E, Rouzé P, Van De Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA Genome Research. 18: 310-323. PMID 18096745 DOI: 10.1101/gr.6991408  1
2008 Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, ... ... Van de Peer Y, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (New York, N.Y.). 319: 64-9. PMID 18079367 DOI: 10.1126/science.1150646  1
2008 Robbens S, Rouzé P, Cock JM, Spring J, Worden AZ, Van de Peer Y. The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. Journal of Molecular Evolution. 66: 80-4. PMID 18058156 DOI: 10.1007/s00239-007-9059-z  1
2008 Joshi A, Van de peer Y, Michoel T. Analysis of a Gibbs sampler method for model-based clustering of gene expression data Bioinformatics. 24: 176-183. PMID 18033794 DOI: 10.1093/bioinformatics/btm562  1
2008 Tzika AC, Helaers R, Van de peer Y, Milinkovitch MC. MANTIS: A phylogenetic framework for multi-species genome comparisons Bioinformatics. 24: 151-157. PMID 18025004 DOI: 10.1093/bioinformatics/btm567  1
2008 Simillion C, Janssens K, Sterck L, Van de peer Y. i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles Bioinformatics. 24: 127-128. PMID 17947255 DOI: 10.1093/bioinformatics/btm449  1
2008 John U, Beszteri B, Derelle E, Van de Peer Y, Read B, Moreau H, Cembella A. Novel Insights into Evolution of Protistan Polyketide Synthases through Phylogenomic Analysis Protist. 159: 21-30. PMID 17931970 DOI: 10.1016/j.protis.2007.08.001  1
2008 Foissac S, Gouzy J, Rombauts S, Mathé C, Amselem J, Sterck L, Van De Peer Y, Rouzé P, Schiex T. Genome annotation in plants and fungi: EuGène as a model platform Current Bioinformatics. 3: 87-97. DOI: 10.2174/157489308784340702  1
2008 Fierro AC, Vandenbussche F, Engelen K, Van de Peer Y, Marchal K. Meta analysis of gene expression data within and across species Current Genomics. 9: 525-534. DOI: 10.2174/138920208786847935  1
2008 Saeys Y, Abeel T, Van De Peer Y. Robust feature selection using ensemble feature selection techniques Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5212: 313-325. DOI: 10.1007/978-3-540-87481-2_21  1
2008 Van Landeghem S, Saeys Y, Van De Peer Y, De Baets B. Extracting protein-protein interactions from text using rich feature vectors and feature selection 3rd International Symposium On Semantic Mining in Biomedicine, Smbm 2008 - Proceedings. 77-84.  1
2007 Van Hellemont R, Blomme T, Van De Peer Y, Marchal K. Divergence of regulatory sequences in duplicated fish genes Genome Dynamics. 3: 81-100. PMID 18753786 DOI: 10.1159/000107605  1
2007 Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, ... ... Van de Peer Y, et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. Plos One. 2: e1326. PMID 18094749 DOI: 10.1371/journal.pone.0001326  1
2007 Casneuf T, Van de Peer Y, Huber W. In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation Bmc Bioinformatics. 8. PMID 18039370 DOI: 10.1186/1471-2105-8-461  1
2007 Merks RMH, Van de Peer Y, Inzé D, Beemster GTS. Canalization without flux sensors: a traveling-wave hypothesis Trends in Plant Science. 12: 384-390. PMID 17765595 DOI: 10.1016/j.tplants.2007.08.004  1
2007 Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. Bmc Evolutionary Biology. 7: 130. PMID 17683536 DOI: 10.1186/1471-2148-7-130  1
2007 Saeys Y, Abeel T, Degroeve S, Van de Peer Y. Translation initiation site prediction on a genomic scale: Beauty in simplicity Bioinformatics. 23: i418-i423. PMID 17646326 DOI: 10.1093/bioinformatics/btm177  1
2007 Van de Peer Y. The future for plants and plants for the future Genome Biology. 8. PMID 17626611 DOI: 10.1186/gb-2007-8-7-308  1
2007 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. Validating module network learning algorithms using simulated data. Bmc Bioinformatics. 8: S5. PMID 17493254 DOI: 10.1186/1471-2105-8-S2-S5  1
2007 Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, ... ... Van de Peer Y, et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America. 104: 7705-10. PMID 17460045 DOI: 10.1073/pnas.0611046104  1
2007 Robbens S, Petersen J, Brinkmann H, Rouzé P, Van De Peer Y. Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus Journal of Molecular Evolution. 64: 601-604. PMID 17457634 DOI: 10.1007/s00239-006-0159-y  1
2007 Sterck L, Rombauts S, Vandepoele K, Rouzé P, Van de Peer Y. How many genes are there in plants (... and why are they there)? Current Opinion in Plant Biology. 10: 199-203. PMID 17289424 DOI: 10.1016/j.pbi.2007.01.004  1
2007 Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van De Peer Y. The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: Organelle genomes of the smallest eukaryote are examples of compaction Molecular Biology and Evolution. 24: 956-968. PMID 17251180 DOI: 10.1093/molbev/msm012  1
2007 Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, ... Van de Peer Y, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (New York, N.Y.). 315: 207-12. PMID 17218520 DOI: 10.1126/science.1132894  1
2007 Saeys Y, Rouzé P, Van de Peer Y. In search of the small ones: Improved prediction of short exons in vertebrates, plants, fungi and protists Bioinformatics. 23: 414-420. PMID 17204465 DOI: 10.1093/bioinformatics/btl639  1
2007 Saeys Y, Van De Peer Y. Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4366: 107-118.  1
2007 Bonet I, García MM, Saeys Y, Van De Peer Y, Grau R. Predicting human immunodeficiency virus (HIV) drug resistance using recurrent neural networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4527: 234-243.  1
2006 Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Scheix T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, ... ... Van de Peer Y, et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proceedings of the National Academy of Sciences of the United States of America. 103: 14959-64. PMID 17003129 DOI: 10.1073/pnas.0603228103  1
2006 Derelle E, Ferraz C, Rombauts S, Rouzé P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynié S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, ... ... Van de Peer Y, et al. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proceedings of the National Academy of Sciences of the United States of America. 103: 11647-52. PMID 16868079 DOI: 10.1073/pnas.0604795103  1
2006 Bonnet E, Van De Peer Y, Rouzé P. The small RNA world of plants New Phytologist. 171: 451-468. PMID 16866953 DOI: 10.1111/j.1469-8137.2006.01806.x  1
2006 Blomme T, Vandepoele K, De Bodt S, Simillion C, Maere S, Van de Peer Y. The gain and loss of genes during 600 million years of vertebrate evolution Genome Biology. 7. PMID 16723033 DOI: 10.1186/gb-2006-7-5-r43  1
2006 Baele G, Raes J, Van de Peer Y, Vansteelandt S. An improved statistical method for detecting heterotachy in nucleotide sequences. Molecular Biology and Evolution. 23: 1397-405. PMID 16672284 DOI: 10.1093/molbev/msl006  1
2006 De Bodt S, Theissen G, Van De Peer Y. Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting Molecular Biology and Evolution. 23: 1293-1303. PMID 16581940 DOI: 10.1093/molbev/msk016  1
2006 Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biology. 7: R13. PMID 16507168 DOI: 10.1186/gb-2006-7-2-r13  1
2006 Van De Peer Y. When duplicated genes don't stick to the rules Heredity. 96: 204-205. PMID 16288315 DOI: 10.1038/sj.hdy.6800771  1
2006 Vandepoele K, Casneuf T, Van de Peer Y. Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics Genome Biology. 7. DOI: 10.1186/gb-2006-7-11-r103  1
2006 Faes P, Minnaert B, Christiaens M, Bonnet E, Saeys Y, Stroobandt D, Van De Peer Y. Scalable hardware accelerator for comparing DNA and protein sequences Acm International Conference Proceeding Series. 152. DOI: 10.1145/1146847.1146880  1
2006 Michoel T, Van De Peer Y. Helicoidal transfer matrix model for inhomogeneous DNA melting Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 73. DOI: 10.1103/PhysRevE.73.011908  1
2006 Saeys Y, Degroeve S, Van De Peer Y. Feature ranking using an EDA-based wrapper approach Studies in Fuzziness and Soft Computing. 192: 243-257. DOI: 10.1007/11007937_10  1
2006 Bonet I, Saeys Y, Ábalo RG, García MM, Sanchez R, Van De Peer Y. Feature extraction using clustering of protein Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4225: 614-623.  1
2005 Van Hellemont R, Monsieurs P, Thijs G, De Moor B, Van de Peer Y, Marchal K. A novel approach to identifying regulatory motifs in distantly related genomes Genome Biology. 6. PMID 16420672 DOI: 10.1186/gb-2005-6-13-r113  1
2005 Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J. Opinion: Re-evaluating prokaryotic species. Nature Reviews. Microbiology. 3: 733-9. PMID 16138101 DOI: 10.1038/nrmicro1236  1
2005 Vandepoele K, Vlieghe K, Florquin K, Hennig L, Beemster GTS, Gruissem W, Van De Peer Y, Inzé D, De Veylder L. Genome-wide identification of potential plant E2F target genes Plant Physiology. 139: 316-328. PMID 16126853 DOI: 10.1104/pp.105.066290  1
2005 Meyer A, Van De Peer Y. From 2R to 3R: Evidence for a fish-specific genome duplication (FSGD) Bioessays. 27: 937-945. PMID 16108068 DOI: 10.1002/bies.20293  1
2005 Florquin K, Saeys Y, Degroeve S, Rouzé P, Van de Peer Y. Large-scale structural analysis of the core promoter in mammalian and plant genomes Nucleic Acids Research. 33: 4255-4264. PMID 16049029 DOI: 10.1093/nar/gki737  1
2005 Beysen D, Raes J, Leroy BP, Lucassen A, Yates JR, Clayton-Smith J, Ilyina H, Brooks SS, Christin-Maitre S, Fellous M, Fryns JP, Kim JR, Lapunzina P, Lemyre E, Meire F, ... ... Van de Peer Y, et al. Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome. American Journal of Human Genetics. 77: 205-18. PMID 15962237 DOI: 10.1086/432083  1
2005 Raes J, Van de Peer Y. Functional divergence of proteins through frameshift mutations. Trends in Genetics : Tig. 21: 428-31. PMID 15951050 DOI: 10.1016/j.tig.2005.05.013  1
2005 Coenye T, Gevers D, Van de Peer Y, Vandamme P, Swings J. Towards a prokaryotic genomic taxonomy. Fems Microbiology Reviews. 29: 147-67. PMID 15808739 DOI: 10.1016/j.femsre.2004.11.004  1
2005 Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. Modeling gene and genome duplications in eukaryotes. Proceedings of the National Academy of Sciences of the United States of America. 102: 5454-9. PMID 15800040 DOI: 10.1073/pnas.0501102102  1
2005 Vandepoele K, Van De Peer Y. Exploring the plant transcriptome through phylogenetic profiling Plant Physiology. 137: 31-42. PMID 15644465 DOI: 10.1104/pp.104.054700  1
2005 De Bodt S, Maere S, Van De Peer Y. Genome duplication and the origin of angiosperms Trends in Ecology and Evolution. 20: 591-597. DOI: 10.1016/j.tree.2005.07.008  1
2005 Van De Peer Y, Meyer A. Large-Scale Gene and Ancient Genome Duplications The Evolution of the Genome. 329-368. DOI: 10.1016/B978-012301463-4/50008-5  1
2004 Gevers D, Vandepoele K, Simillon C, Van de Peer Y. Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends in Microbiology. 12: 148-54. PMID 15116722 DOI: 10.1016/j.tim.2004.02.007  1
2003 Raes J, Van de Peer Y. Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico. Applied Bioinformatics. 2: 91-101. PMID 15130825  1
2003 Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W. Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiology. 133: 1051-71. PMID 14612585 DOI: 10.1104/pp.103.026484  1
2003 De Bodt S, Raes J, Van de Peer Y, Theissen G. And then there were many: MADS goes genomic. Trends in Plant Science. 8: 475-83. PMID 14557044 DOI: 10.1016/j.tplants.2003.09.006  1
2003 Raes J, Vandepoele K, Simillion C, Saeys Y, Van de Peer Y. Investigating ancient duplication events in the Arabidopsis genome. Journal of Structural and Functional Genomics. 3: 117-29. PMID 12836691 DOI: 10.1023/A:1022666020026  1
2003 De Bodt S, Raes J, Florquin K, Rombauts S, Rouzé P, Theissen G, Van de Peer Y. Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. Journal of Molecular Evolution. 56: 573-86. PMID 12698294 DOI: 10.1007/s00239-002-2426-x  1
2002 Vandepoele K, Saeys Y, Simillion C, Raes J, Van De Peer Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Research. 12: 1792-801. PMID 12421767 DOI: 10.1101/gr.400202  1
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