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Yves Van de Peer

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Co-Publications
Name
47
De Wachter, Rupert
23
Rouzé, Pierre
20
Vandepoele, Klaas
20
De Rijk, Peter
15
Meyer, Axel
15
Saeys, Yvan
13
Wuyts, Jan
10
Raes, Jeroen
9
Rombauts, Stephane
9
Simillion, Cedric
8
De Bodt, Stefanie
7
Maere, Steven
7
Robbens, Steven
7
De Baere, Raymond
7
Degroeve, Sven

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Publications

TOP 3
Van de Peer Yves; Maere Steven; Meyer Axel
The evolutionary significance of ancient genome duplications.
Piganeau Gwenael; Vandepoele Klaas; Gourbière Sébastien; Van de Peer Yves; Moreau Hervé
Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus.
Abeel Thomas; Van de Peer Yves; Saeys Yvan
Toward a gold standard for promoter prediction evaluation.

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All Publications

2009: Van de Peer Yves; Maere Steven; Meyer Axel
The evolutionary significance of ancient genome duplications.
Nature reviews. Genetics 2009;10(10):725-32.
2009: Piganeau Gwenael; Vandepoele Klaas; Gourbière Sébastien; Van de Peer Yves; Moreau Hervé
Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus.
Journal of molecular evolution 2009;69(3):249-59.
2009: Abeel Thomas; Van de Peer Yves; Saeys Yvan
Toward a gold standard for promoter prediction evaluation.
Bioinformatics (Oxford, England) 2009;25(12):i313-20.
2009: De Schutter Kristof; Lin Yao-Cheng; Tiels Petra; Van Hecke Annelies; Glinka Sascha; Weber-Lehmann Jacqueline; Rouzé Pierre; Van de Peer Yves; Callewaert Nico
Genome sequence of the recombinant protein production host Pichia pastoris.
Nature biotechnology 2009;27(6):561-6.
2009: Vandepoele Klaas; Quimbaya Mauricio; Casneuf Tine; De Veylder Lieven; Van de Peer Yves
Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks.
Plant physiology 2009;150(2):535-46.
2009: Fawcett Jeffrey A; Maere Steven; Van de Peer Yves
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 2009;106(14):5737-42.
2009: Michoel Tom; De Smet Riet; Joshi Anagha; Marchal Kathleen; Van de Peer Yves
Reverse-engineering transcriptional modules from gene expression data.
Annals of the New York Academy of Sciences 2009;1158():36-43.
2009: Joshi Anagha; De Smet Riet; Marchal Kathleen; Van de Peer Yves; Michoel Tom
Module networks revisited: computational assessment and prioritization of model predictions.
Bioinformatics (Oxford, England) 2009;25(4):490-6.
2009: De Bodt Stefanie; Proost Sebastian; Vandepoele Klaas; Rouzé Pierre; Van de Peer Yves
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression.
BMC genomics 2009;10():288.
2009: Dittami Simon M; Scornet Delphine; Petit Jean-Louis; Ségurens Béatrice; Da Silva Corinne; Corre Erwan; Dondrup Michael; Glatting Karl-Heinz; König Rainer; Sterck Lieven; Rouzé Pierre; Van de Peer Yves; Cock J Mark; Boyen Catherine; Tonon Thierry
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress.
Genome biology 2009;10(6):R66.
2009: Michoel Tom; De Smet Riet; Joshi Anagha; Van de Peer Yves; Marchal Kathleen
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks.
BMC systems biology 2009;3():49.
2009: Baele Guy; Peer Yves Van de; Vansteelandt Stijn
Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences.
BMC evolutionary biology 2009;9():87.
2008: Fierro Ana C; Vandenbussche Filip; Engelen Kristof; Van de Peer Yves; Marchal Kathleen
Meta Analysis of Gene Expression Data within and Across Species.
Current genomics 2008;9(8):525-34.
2008: Baele Guy; Van de Peer Yves; Vansteelandt Stijn
A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences.
Systematic biology 2008;57(5):675-92.
2008: Abeel Thomas; Saeys Yvan; Rouzé Pierre; Van de Peer Yves
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles.
Bioinformatics (Oxford, England) 2008;24(13):i24-31.
2008: Van Bel Michiel; Saeys Yvan; Van de Peer Yves
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.
Bioinformatics (Oxford, England) 2008;24(13):1532-3.
2008: Amoutzias Grigoris D; Van de Peer Yves; Mossialos Dimitris
Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases.
Future microbiology 2008;3():361-70.
2008: Amoutzias Grigoris; Van de Peer Yves
Together we stand: genes cluster to coordinate regulation.
Developmental cell 2008;14(5):640-2.
2008: Amoutzias Grigoris D; Robertson David L; Van de Peer Yves; Oliver Stephen G
Choose your partners: dimerization in eukaryotic transcription factors.
Trends in biochemical sciences 2008;33(5):220-9.
2008: Martens Cindy; Vandepoele Klaas; Van de Peer Yves
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 2008;105(9):3427-32.
2008: Vandenbroucke Korneel; Robbens Steven; Vandepoele Klaas; Inzé Dirk; Van de Peer Yves; Van Breusegem Frank
Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis.
Molecular biology and evolution 2008;25(3):507-16.
2008: Abeel Thomas; Saeys Yvan; Bonnet Eric; Rouzé Pierre; Van de Peer Yves
Generic eukaryotic core promoter prediction using structural features of DNA.
Genome research 2008;18(2):310-23.
2008: Robbens Steven; Rouzé Pierre; Cock J Mark; Spring Jürg; Worden Alexandra Z; Van de Peer Yves
The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae.
Journal of molecular evolution 2008;66(1):80-4.
2008: Joshi Anagha; Van de Peer Yves; Michoel Tom
Analysis of a Gibbs sampler method for model-based clustering of gene expression data.
Bioinformatics (Oxford, England) 2008;24(2):176-83.
2008: Tzika Athanasia C; Helaers Raphaël; Van de Peer Yves; Milinkovitch Michel C
MANTIS: a phylogenetic framework for multi-species genome comparisons.
Bioinformatics (Oxford, England) 2008;24(2):151-7.
2008: Simillion Cedric; Janssens Koen; Sterck Lieven; Van de Peer Yves
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.
Bioinformatics (Oxford, England) 2008;24(1):127-8.
2008: John Uwe; Beszteri Bánk; Derelle Evelyne; Van de Peer Yves; Read Betsy; Moreau Hervé; Cembella Allan
Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis.
Protist 2008;159(1):21-30.
2007: Merks Roeland M H; Van de Peer Yves; Inzé Dirk; Beemster Gerrit T S
Canalization without flux sensors: a traveling-wave hypothesis.
Trends in plant science 2007;12(9):384-90.
2007: Saeys Yvan; Abeel Thomas; Degroeve Sven; Van de Peer Yves
Translation initiation site prediction on a genomic scale: beauty in simplicity.
Bioinformatics (Oxford, England) 2007;23(13):i418-23.
2007: Robbens Steven; Petersen Jörn; Brinkmann Henner; Rouzé Pierre; Van de Peer Yves
Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus.
Journal of molecular evolution 2007;64(5):601-4.
2007: Sterck Lieven; Rombauts Stephane; Vandepoele Klaas; Rouzé Pierre; Van de Peer Yves
How many genes are there in plants (... and why are they there)?
Current opinion in plant biology 2007;10(2):199-203.
2007: Robbens Steven; Derelle Evelyne; Ferraz Conchita; Wuyts Jan; Moreau Hervé; Van de Peer Yves
The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction.
Molecular biology and evolution 2007;24(4):956-68.
2007: Saeys Yvan; Rouzé Pierre; Van de Peer Yves
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists.
Bioinformatics (Oxford, England) 2007;23(4):414-20.
2007: Casneuf Tineke; Van de Peer Yves; Huber Wolfgang
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.
BMC bioinformatics 2007;8():461.
2007: Rensing Stefan A; Ick Julia; Fawcett Jeffrey A; Lang Daniel; Zimmer Andreas; Van de Peer Yves; Reski Ralf
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens.
BMC evolutionary biology 2007;7():130.
2007: Van de Peer Yves
The future for plants and plants for the future.
Genome biology 2007;8(7):308.
2007: Michoel Tom; Maere Steven; Bonnet Eric; Joshi Anagha; Saeys Yvan; Van den Bulcke Tim; Van Leemput Koenraad; van Remortel Piet; Kuiper Martin; Marchal Kathleen; Van de Peer Yves
Validating module network learning algorithms using simulated data.
BMC bioinformatics 2007;8 Suppl 2():S5.
2006: Cannon Steven B; Sterck Lieven; Rombauts Stephane; Sato Shusei; Cheung Foo; Gouzy Jérôme; Wang Xiaohong; Mudge Joann; Vasdewani Jayprakash; Schiex Thomas; Spannagl Manuel; Monaghan Erin; Nicholson Christine; Humphray Sean J; Schoof Heiko; Mayer Klaus F X; Rogers Jane; Quétier Francis; Oldroyd Giles E; Debellé Frédéric; Cook Douglas R; Retzel Ernest F; Roe Bruce A; Town Christopher D; Tabata Satoshi; Van de Peer Yves; Young Nevin D
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 2006;103(40):14959-64.
2006: Derelle Evelyne; Ferraz Conchita; Rombauts Stephane; Rouzé Pierre; Worden Alexandra Z; Robbens Steven; Partensky Frédéric; Degroeve Sven; Echeynié Sophie; Cooke Richard; Saeys Yvan; Wuyts Jan; Jabbari Kamel; Bowler Chris; Panaud Olivier; Piégu Benoît; Ball Steven G; Ral Jean-Philippe; Bouget François-Yves; Piganeau Gwenael; De Baets Bernard; Picard André; Delseny Michel; Demaille Jacques; Van de Peer Yves; Moreau Hervé
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 2006;103(31):11647-52.
2006: Baele Guy; Raes Jeroen; Van de Peer Yves; Vansteelandt Stijn
An improved statistical method for detecting heterotachy in nucleotide sequences.
Molecular biology and evolution 2006;23(7):1397-405.
2006: De Bodt Stefanie; Theissen Guenter; Van de Peer Yves
Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.
Molecular biology and evolution 2006;23(6):1293-303.
2006: Van de Peer Y
Evolutionary genetics: when duplicated genes don't stick to the rules.
Heredity 2006;96(3):204-5.
2006: Michoel Tom; Van de Peer Yves
Helicoidal transfer matrix model for inhomogeneous DNA melting.
Physical review. E, Statistical, nonlinear, and soft matter physics 2006;73(1 Pt 1):011908.
2006: Vandepoele Klaas; Casneuf Tineke; Van de Peer Yves
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics.
Genome biology 2006;7(11):R103.
2006: Bonnet Eric; Van de Peer Yves; Rouzé Pierre
The small RNA world of plants.
The New phytologist 2006;171(3):451-68.
2006: Blomme Tine; Vandepoele Klaas; De Bodt Stefanie; Simillion Cedric; Maere Steven; Van de Peer Yves
The gain and loss of genes during 600 million years of vertebrate evolution.
Genome biology 2006;7(5):R43.
2006: Casneuf Tineke; De Bodt Stefanie; Raes Jeroen; Maere Steven; Van de Peer Yves
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana.
Genome biology 2006;7(2):R13.
2005: De Bodt Stefanie; Maere Steven; Van de Peer Yves
Genome duplication and the origin of angiosperms.
Trends in ecology & evolution (Personal edition) 2005;20(11):591-7.
2005: Gevers Dirk; Cohan Frederick M; Lawrence Jeffrey G; Spratt Brian G; Coenye Tom; Feil Edward J; Stackebrandt Erko; Van de Peer Yves; Vandamme Peter; Thompson Fabiano L; Swings Jean
Opinion: Re-evaluating prokaryotic species.
Nature reviews. Microbiology 2005;3(9):733-9.
2005: Vandepoele Klaas; Vlieghe Kobe; Florquin Kobe; Hennig Lars; Beemster Gerrit T S; Gruissem Wilhelm; Van de Peer Yves; Inzé Dirk; De Veylder Lieven
Genome-wide identification of potential plant E2F target genes.
Plant physiology 2005;139(1):316-28.
2005: Meyer Axel; Van de Peer Yves
From 2R to 3R: evidence for a fish-specific genome duplication (FSGD).
BioEssays : news and reviews in molecular, cellular and developmental biology 2005;27(9):937-45.
2005: Raes Jeroen; Van de Peer Yves
Functional divergence of proteins through frameshift mutations.
Trends in genetics : TIG 2005;21(8):428-31.
2005: Sterck Lieven; Rombauts Stephane; Jansson Stefan; Sterky Fredrik; Rouzé Pierre; Van de Peer Yves
EST data suggest that poplar is an ancient polyploid.
The New phytologist 2005;167(1):165-70.
2005: Coenye Tom; Gevers Dirk; Van de Peer Yves; Vandamme Peter; Swings Jean
Towards a prokaryotic genomic taxonomy.
FEMS microbiology reviews 2005;29(2):147-67.
2005: Maere Steven; De Bodt Stefanie; Raes Jeroen; Casneuf Tineke; Van Montagu Marc; Kuiper Martin; Van de Peer Yves
Modeling gene and genome duplications in eukaryotes.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(15):5454-9.
2005: Degroeve Sven; Saeys Yvan; De Baets Bernard; Rouzé Pierre; Van de Peer Yves
SpliceMachine: predicting splice sites from high-dimensional local context representations.
Bioinformatics (Oxford, England) 2005;21(8):1332-8.
2005: Paterson Andrew H; Bowers John E; Van de Peer Yves; Vandepoele Klaas
Ancient duplication of cereal genomes.
The New phytologist 2005;165(3):658-61.
2005: Robbens Steven; Khadaroo Basheer; Camasses Alain; Derelle Evelyne; Ferraz Conchita; Inzé Dirk; Van de Peer Yves; Moreau Hervé
Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri.
Molecular biology and evolution 2005;22(3):589-97.
2005: Vandepoele Klaas; Van de Peer Yves
Exploring the plant transcriptome through phylogenetic profiling.
Plant physiology 2005;137(1):31-42.
2005: Van Hellemont Ruth; Monsieurs Pieter; Thijs Gert; de Moor Bart; Van de Peer Yves; Marchal Kathleen
A novel approach to identifying regulatory motifs in distantly related genomes.
Genome biology 2005;6(13):R113.
2005: Florquin Kobe; Saeys Yvan; Degroeve Sven; Rouzé Pierre; Van de Peer Yves
Large-scale structural analysis of the core promoter in mammalian and plant genomes.
Nucleic acids research 2005;33(13):4255-64.
2005: Van de Peer Yves
'Horizontal' plant biology on the rise.
Genome biology 2005;6(1):302.
2004: Simillion Cedric; Vandepoele Klaas; Van de Peer Yves
Recent developments in computational approaches for uncovering genomic homology.
BioEssays : news and reviews in molecular, cellular and developmental biology 2004;26(11):1225-35.
2004: Bonnet Eric; Wuyts Jan; Rouzé Pierre; Van de Peer Yves
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
Bioinformatics (Oxford, England) 2004;20(17):2911-7.
2004: Van de Peer Yves
Computational approaches to unveiling ancient genome duplications.
Nature reviews. Genetics 2004;5(10):752-63.
2004: Bonnet Eric; Wuyts Jan; Rouzé Pierre; Van de Peer Yves
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(31):11511-6.
2004: Alvares Lúcia E; Wuyts Jan; Van de Peer Yves; Silva Eduardo P; Coutinho Luiz L; Brison Olivier; Ruiz Itamar R G
The 18S rRNA from Odontophrynus americanus 2n and 4n (Amphibia, Anura) reveals unusual extra sequences in the variable region V2.
Genome / National Research Council Canada = Génome / Conseil national de recherches Canada 2004;47(3):421-8.
2004: Simillion Cedric; Vandepoele Klaas; Saeys Yvan; Van de Peer Yves
Building genomic profiles for uncovering segmental homology in the twilight zone.
Genome research 2004;14(6):1095-106.
2004: Saeys Yvan; Degroeve Sven; Aeyels Dirk; Rouzé Pierre; Van de Peer Yves
Feature selection for splice site prediction: a new method using EDA-based feature ranking.
BMC bioinformatics 2004;5():64.
2004: Gevers Dirk; Vandepoele Klaas; Simillon Cedric; Van de Peer Yves
Gene duplication and biased functional retention of paralogs in bacterial genomes.
Trends in microbiology 2004;12(4):148-54.
2004: Khadaroo B; Robbens S; Ferraz C; Derelle E; Eychenié S; Cooke R; Peaucellier G; Delseny M; Demaille J; Van de Peer Y; Picard A; Moreau H
The first green lineage cdc25 dual-specificity phosphatase.
Cell cycle (Georgetown, Tex.) 2004;3(4):513-8.
2004: Vandepoele Klaas; De Vos Wouter; Taylor John S; Meyer Axel; Van de Peer Yves
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(6):1638-43.
2004: Wuyts Jan; Perrière Guy; Van De Peer Yves
The European ribosomal RNA database.
Nucleic acids research 2004;32(Database issue):D101-3.
2004: Van de Peer Yves
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids.
Genome biology 2004;5(12):250.
2003: Raes Jeroen; Rohde Antje; Christensen Jørgen Holst; Van de Peer Yves; Boerjan Wout
Genome-wide characterization of the lignification toolbox in Arabidopsis.
Plant physiology 2003;133(3):1051-71.
2003: De Bodt Stefanie; Raes Jeroen; Van de Peer Yves; Theissen Günter
And then there were many: MADS goes genomic.
Trends in plant science 2003;8(10):475-83.
2003: Saeys Yvan; Degroeve Sven; Aeyels Dirk; Van De Peer Yves; Rouzé Pierre
Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii179-88.
2003: Vlieghe Kobe; Vuylsteke Marnik; Florquin Kobe; Rombauts Stephane; Maes Sara; Ormenese Sandra; Van Hummelen Paul; Van de Peer Yves; Inze Dirk; De Veylder Lieven
Microarray analysis of E2Fa-DPa-overexpressing plants uncovers a cross-talking genetic network between DNA replication and nitrogen assimilation.
Journal of cell science 2003;116(Pt 20):4249-59.
2003: Vandepoele Klaas; Simillion Cedric; Van de Peer Yves
Evidence that rice and other cereals are ancient aneuploids.
The Plant cell 2003;15(9):2192-202.
2003: Vandenbussche Michiel; Theissen Günter; Van de Peer Yves; Gerats Tom
Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations.
Nucleic acids research 2003;31(15):4401-9.
2003: Rombauts Stephane; Florquin Kobe; Lescot Magali; Marchal Kathleen; Rouzé Pierre; van de Peer Yves
Computational approaches to identify promoters and cis-regulatory elements in plant genomes.
Plant physiology 2003;132(3):1162-76.
2003: De Bodt Stefanie; Raes Jeroen; Florquin Kobe; Rombauts Stephane; Rouzé Pierre; Theissen Günter; Van de Peer Yves
Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants.
Journal of molecular evolution 2003;56(5):573-86.
2003: Rombauts Stephane; Van De Peer Yves; Rouzé Pierre
AFLPinSilico, simulating AFLP fingerprints.
Bioinformatics (Oxford, England) 2003;19(6):776-7.
2003: Taylor John S; Braasch Ingo; Frickey Tancred; Meyer Axel; Van de Peer Yves
Genome duplication, a trait shared by 22000 species of ray-finned fish.
Genome research 2003;13(3):382-90.
2003: Raes Jeroen; Van de Peer Yves
Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico.
Applied bioinformatics 2003;2(2):91-101.
2003: Raes Jeroen; Vandepoele Klaas; Simillion Cedric; Saeys Yvan; Van de Peer Yves
Investigating ancient duplication events in the Arabidopsis genome.
Journal of structural and functional genomics 2003;3(1-4):117-29.
2003: Van de Peer Yves; Taylor John S; Meyer Axel
Are all fishes ancient polyploids?
Journal of structural and functional genomics 2003;3(1-4):65-73.
2003: Meyer Axel; Van de Peer Yves
'Natural selection merely modified while redundancy created'--Susumu Ohno's idea of the evolutionary importance of gene and genome duplications.
Journal of structural and functional genomics 2003;3(1-4):vii-ix.
2002: Rensing Stefan A; Rombauts Stephane; Van de Peer Yves; Reski Ralf
Moss transcriptome and beyond.
Trends in plant science 2002;7(12):535-8.
2002: Vandepoele Klaas; Simillion Cedric; Van de Peer Yves
Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice.
Trends in genetics : TIG 2002;18(12):606-8.
2002: Vandepoele Klaas; Saeys Yvan; Simillion Cedric; Raes Jeroen; Van De Peer Yves
The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice.
Genome research 2002;12(11):1792-801.
2002: Simillion Cedric; Vandepoele Klaas; Van Montagu Marc C E; Zabeau Marc; Van de Peer Yves
The hidden duplication past of Arabidopsis thaliana.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(21):13627-32.
2002: Van de Peer Yves; Frickey Tancred; Taylor John; Meyer Axel
Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes.
Gene 2002;295(2):205-11.
2002: Ben Ali Abdelghani; De Baere Raymond; De Wachter Rupert; Van de Peer Yves
Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA.
Protist 2002;153(2):123-32.
2002: Oborník Miroslav; Van de Peer Yves; Hypsa Václav; Frickey Tancred; Slapeta Jan R; Meyer Axel; Lukes Julius
Phylogenetic analyses suggest lateral gene transfer from the mitochondrion to the apicoplast.
Gene 2002;285(1-2):109-18.
2002: Lescot Magali; Déhais Patrice; Thijs Gert; Marchal Kathleen; Moreau Yves; Van de Peer Yves; Rouzé Pierre; Rombauts Stephane
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
Nucleic acids research 2002;30(1):325-7.
2002: Wuyts Jan; Van de Peer Yves; Winkelmans Tina; De Wachter Rupert
The European database on small subunit ribosomal RNA.
Nucleic acids research 2002;30(1):183-5.
2002: Van de Peer Yves; Taylor John S; Joseph Jayabalan; Meyer Axel
Wanda: a database of duplicated fish genes.
Nucleic acids research 2002;30(1):109-12.
2002: Degroeve Sven; De Baets Bernard; Van de Peer Yves; Rouzé Pierre
Feature subset selection for splice site prediction.
Bioinformatics (Oxford, England) 2002;18 Suppl 2():S75-83.
2001: Wuyts J; Van de Peer Y; De Wachter R
Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA.
Nucleic acids research 2001;29(24):5017-28.
2001: Van de Peer Y; Taylor J S; Braasch I; Meyer A
The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes.
Journal of molecular evolution 2001;53(4-5):436-46.
2001: Taylor J S; Van de Peer Y; Braasch I; Meyer A
Comparative genomics provides evidence for an ancient genome duplication event in fish.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2001;356(1414):1661-79.
2001: Taylor J S; Van de Peer Y; Meyer A
Genome duplication, divergent resolution and speciation.
Trends in genetics : TIG 2001;17(6):299-301.
2001: Ben Ali A; De Baere R; Van der Auwera G; De Wachter R; Van de Peer Y
Phylogenetic relationships among algae based on complete large-subunit rRNA sequences.
International journal of systematic and evolutionary microbiology 2001;51(Pt 3):737-49.
2001: Wuyts J; De Rijk P; Van de Peer Y; Winkelmans T; De Wachter R
The European Large Subunit Ribosomal RNA Database.
Nucleic acids research 2001;29(1):175-7.
2000: Van de Peer Y; Baldauf S L; Doolittle W F; Meyer A
An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances.
Journal of molecular evolution 2000;51(6):565-76.
2000: Wuyts J; De Rijk P; Van de Peer Y; Pison G; Rousseeuw P; De Wachter R
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.
Nucleic acids research 2000;28(23):4698-708.
2000: Van de Peer Y; Ben Ali A; Meyer A
Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi.
Gene 2000;246(1-2):1-8.
2000: De Rijk P; Wuyts J; Van de Peer Y; Winkelmans T; De Wachter R
The European large subunit ribosomal RNA database.
Nucleic acids research 2000;28(1):177-8.
2000: Van de Peer Y; De Rijk P; Wuyts J; Winkelmans T; De Wachter R
The European small subunit ribosomal RNA database.
Nucleic acids research 2000;28(1):175-6.
1999: Ben Ali A; Wuyts J; De Wachter R; Meyer A; Van de Peer Y
Construction of a variability map for eukaryotic large subunit ribosomal RNA.
Nucleic acids research 1999;27(14):2825-31.
1999: Van de Peer Y; Robbrecht E; de Hoog S; Caers A; De Rijk P; De Wachter R
Database on the structure of small subunit ribosomal RNA.
Nucleic acids research 1999;27(1):179-83.
1999: De Rijk P; Robbrecht E; de Hoog S; Caers A; Van de Peer Y; De Wachter R
Database on the structure of large subunit ribosomal RNA.
Nucleic acids research 1999;27(1):174-8.
1998: Vandamme P; Segers P; Ryll M; Hommez J; Vancanneyt M; Coopman R; De Baere R; Van de Peer Y; Kersters K; De Wachter R; Hinz K H
Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory disease in pigeons: taxonomic structure and phylogenetic allocation.
International journal of systematic bacteriology 1998;48 Pt 2():431-40.
1998: De Rijk P; Caers A; Van de Peer Y; De Wachter R
Database on the structure of large ribosomal subunit RNA.
Nucleic acids research 1998;26(1):183-6.
1998: Van de Peer Y; Caers A; De Rijk P; De Wachter R
Database on the structure of small ribosomal subunit RNA.
Nucleic acids research 1998;26(1):179-82.
1997: Van de Peer Y; De Wachter R
Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA.
Journal of molecular evolution 1997;45(6):619-30.
1997: De Rijk P; Van de Peer Y; De Wachter R
Database on the structure of large ribosomal subunit RNA.
Nucleic acids research 1997;25(1):117-22.
1997: Van de Peer Y; Jansen J; De Rijk P; De Wachter R
Database on the structure of small ribosomal subunit RNA.
Nucleic acids research 1997;25(1):111-6.
1996: Van de Peer Y; Chapelle S; De Wachter R
A quantitative map of nucleotide substitution rates in bacterial rRNA.
Nucleic acids research 1996;24(17):3381-91.
1996: Van de Peer Y; Rensing S A; Maier U G; De Wachter R
Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(15):7732-6.
1996: Van de Peer Y; Van der Auwera G; De Wachter R
The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA.
Journal of molecular evolution 1996;42(2):201-10.
1996: De Rijk P; Van de Peer Y; De Wachter R
Database on the structure of large ribosomal subunit RNA.
Nucleic acids research 1996;24(1):92-7.
1996: Van de Peer Y; Nicolaï S; De Rijk P; De Wachter R
Database on the structure of small ribosomal subunit RNA.
Nucleic acids research 1996;24(1):86-91.
1995: Nelissen B; Van de Peer Y; Wilmotte A; De Wachter R
An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences.
Molecular biology and evolution 1995;12(6):1166-73.
1995: De Rijk P; Van de Peer Y; Van den Broeck I; De Wachter R
Evolution according to large ribosomal subunit RNA.
Journal of molecular evolution 1995;41(3):366-75.
1995: Van der Auwera G; De Baere R; Van de Peer Y; De Rijk P; Van den Broeck I; De Wachter R
The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides.
Molecular biology and evolution 1995;12(4):671-8.
1995: Winnepenninckx B; Van de Peer Y; Backeljau T; De Wachter R
CARD: a drawing tool for RNA secondary structure models.
BioTechniques 1995;18(6):1060-3.
1994: Van de Peer Y; De Wachter R
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment.
Computer applications in the biosciences : CABIOS 1994;10(5):569-70.
1994: De Rijk P; Van de Peer Y; Chapelle S; De Wachter R
Database on the structure of large ribosomal subunit RNA.
Nucleic acids research 1994;22(17):3495-501.
1994: Van de Peer Y; Van den Broeck I; De Rijk P; De Wachter R
Database on the structure of small ribosomal subunit RNA.
Nucleic acids research 1994;22(17):3488-94.
1993: Van de Peer Y; Neefs J M; De Rijk P; De Wachter R
Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock.
Journal of molecular evolution 1993;37(2):221-32.
1993: Neefs J M; Van de Peer Y; De Rijk P; Chapelle S; De Wachter R
Compilation of small ribosomal subunit RNA structures.
Nucleic acids research 1993;21(13):3025-49.
1993: Van de Peer Y; De Wachter R
TREECON: a software package for the construction and drawing of evolutionary trees.
Computer applications in the biosciences : CABIOS 1993;9(2):177-82.
1992: Winnepennickx B; Backeljau T; van de Peer Y; De Wachter R
Structure of the small ribosomal subunit RNA of the pulmonate snail, Limicolaria kambeul, and phylogenetic analysis of the Metazoa.
FEBS letters 1992;309(2):123-6.
1992: De Rijk P; Neefs J M; Van de Peer Y; De Wachter R
Compilation of small ribosomal subunit RNA sequences.
Nucleic acids research 1992;20 Suppl():2075-89.
1992: De Wachter R; Neefs J M; Goris A; Van de Peer Y
The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron.
Nucleic acids research 1992;20(6):1251-7.
1991: Hendriks L; Goris A; Van de Peer Y; Neefs J M; Vancanneyt M; Kersters K; Hennebert G L; De Wachter R
Phylogenetic analysis of five medically important Candida species as deduced on the basis of small ribosomal subunit RNA sequences.
Journal of general microbiology 1991;137(5):1223-30.
1991: Neefs J M; Van de Peer Y; De Rijk P; Goris A; De Wachter R
Compilation of small ribosomal subunit RNA sequences.
Nucleic acids research 1991;19 Suppl():1987-2015.
1991: Hendriks L; De Baere R; Van de Peer Y; Neefs J; Goris A; De Wachter R
The evolutionary position of the rhodophyte Porphyra umbilicalis and the basidiomycete Leucosporidium scottii among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA.
Journal of molecular evolution 1991;32(2):167-77.
1990: Van den Eynde H; Van de Peer Y; Vandenabeele H; Van Bogaert M; De Wachter R
5S rRNA sequences of myxobacteria and radioresistant bacteria and implications for eubacterial evolution.
International journal of systematic bacteriology 1990;40(4):399-404.
1990: Hendriks L; Van de Peer Y; Van Herck M; Neefs J M; De Wachter R
The 18S ribosomal RNA sequence of the sea anemone Anemonia sulcata and its evolutionary position among other eukaryotes.
FEBS letters 1990;269(2):445-9.
1990: Van de Peer Y; Neefs J M; De Wachter R
Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins.
Journal of molecular evolution 1990;30(5):463-76.
1990: Neefs J M; Van de Peer Y; Hendriks L; De Wachter R
Compilation of small ribosomal subunit RNA sequences.
Nucleic acids research 1990;18 Suppl():2237-317.
1990: Van den Eynde H; Van de Peer Y; Perry J; De Wachter R
5S rRNA sequences of representatives of the genera Chlorobium, Prosthecochloris, Thermomicrobium, Cytophaga, Flavobacterium, Flexibacter and Saprospira and a discussion of the evolution of eubacteria in general.
Journal of general microbiology 1990;136(1):11-8.
1989: Van den Eynde H; De Baere R; Shah H N; Gharbia S E; Fox G E; Michalik J; Van de Peer Y; De Wachter R
5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general.
International journal of systematic bacteriology 1989;39(1):78-84.
1988: Hendriks L; Van Broeckhoven C; Vandenberghe A; Van de Peer Y; De Wachter R
Primary and secondary structure of the 18S ribosomal RNA of the bird spider Eurypelma californica and evolutionary relationships among eukaryotic phyla.
European journal of biochemistry / FEBS 1988;177(1):15-20.
1988: Van den Eynde H; De Baere R; De Roeck E; Van de Peer Y; Vandenberghe A; Willekens P; De Wachter R
The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast. Implications for the evolution of plastids and cyanobacteria.
Journal of molecular evolution 1988;27(2):126-32.
1988: Dams E; Hendriks L; Van de Peer Y; Neefs J M; Smits G; Vandenbempt I; De Wachter R
Compilation of small ribosomal subunit RNA sequences.
Nucleic acids research 1988;16 Suppl():r87-173.

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