Research Explorer

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Researcher

Yves Van de Peer

584 Results

2023

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

Aiping SongJiangshuo SuHaibin WangZhongren ZhangXingtan ZhangYves Van de PeerFei ChenWeimin FangZhiyong GuanFei Zhang et al.

U Journal Article in Nature Communications

Inference of ancient polyploidy from genomic data

Hengchi ChenArthur Zwaenepoel

Bookchapter in Polyploidy : methods and protocols

Inference of ancient polyploidy using transcriptome data

Jia LiYves Van de PeerZhen Li

Bookchapter in Polyploidy : methods and protocols

Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems

Felipe Kauai PereiraFrederik MortierSilvija MilosavljevićYves Van de PeerDries Bonte

A1 Journal Article in PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Polyploidy : methods and protocols

Revisiting ancient polyploidy in leptosporangiate ferns

Hengchi ChenYuhan FangArthur ZwaenepoelSanwen HuangYves Van de PeerZhen Li

A1 Journal Article in NEW PHYTOLOGIST

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Sonja KerstenJiyang ChangChristian D. HuberYoav VoichekChrista LanzTimo HagmaierPatricia LangUlrich LutzInsa HirschbergJens Lerchl et al.

U Journal Article in Proceedings of the National Academy of Sciences

Studying whole-genome duplication using experimental evolution of Chlamydomonas

Quinten BafortLucas ProstEylem Aydogdu LohausAntoine Van de VloetGriet CasteleynYves Van de PeerOlivier De Clerck

Bookchapter in Polyploidy : methods and protocols

Studying whole-genome duplication using experimental evolution of Spirodela polyrhiza

Tian WuAnnelore NatranLucas ProstEylem Aydogdu LohausYves Van de PeerQuinten Bafort

Bookchapter in Polyploidy : methods and protocols

The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids

Jia‐Yu XueZhen LiShuai‐Ya HuShu-Min KaoTao ZhaoJie‐Yu WangYue WangMin ChenYichun QiuHai‐Yun Fan et al.

A1 Journal Article in PLANT JOURNAL

The genome of the king protea, Protea cynaroides

Jiyang ChangTuan A. DuongCassandra SchoemanXiao MaDanielle RoodtNigel BarkerZhen LiYves Van de PeerEshchar Mizrachi

A1 Journal Article in PLANT JOURNAL

The immediate effects of polyploidization of <i>Spirodela polyrhiza</i> change in a strain-specific way along environmental gradients

Quinten BafortTian WuAnnelore NatranOlivier De ClerckYves Van de Peer

U Journal Article in Evolution Letters

syntenet : an R/Bioconductor package for the inference and analysis of synteny networks

Fabricio De Almeida SilvaTao ZhaoKristian K UllrichM Eric SchranzYves Van de Peer

A1 Journal Article in BIOINFORMATICS

2022

A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago

Theresa CataniaYi LiThilo WinzerDavid HarveyFergus MeadeAnna CaridiAndrew LeechTony R. LarsonZemin NingJiyang Chang et al.

A1 Journal Article in NATURE COMMUNICATIONS

Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program

Li Lian WongSiti Aisyah RazaliZulaikha Mat DerisMuhd Danish-DanielMin Pau TanSiti Azizah Mohd NorHongyu MaWang MinLiang Yantao Liang YantaoMd Asaduzzaman et al.

A1 Journal Article in AQUACULTURE

Bayesian statistical methods in evolutionary genomics

Arthur ZwaenepoelYves Van de Peer

Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication

Jiyang ChangJuan Pablo Marczuk‐RojasCarrie WatermanArmando Garcia‐LlanosShiyu ChenXiao MaAmanda Hulse‐KempAllen Van DeynzeYves Van de PeerLorenzo Carretero‐Paulet

A1 Journal Article in PLANT GENOME

Correction : divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

Zhilin YuanIrina S. DruzhininaJohn G. GibbonsZhenhui ZhongYves Van de PeerRussell J. RodriguezZhongjian LiuXinyu WangHuanshen WeiQi Wu et al.

Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

Ticao ZhangQin QiaoXiao DuXiao ZhangYali HouXin WeiChao SunRengang ZhangQuanzheng YunM. James C. Crabbe et al.

A1 Journal Article in JOURNAL OF INTEGRATIVE PLANT BIOLOGY

Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches

Hui XuZhen LiPeng‐Fei JiangLi ZhaoChang QuYves Van de PeerYan‐Jing LiuQing‐Yin Zeng

A1 Journal Article in PLANT JOURNAL

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Yue ZhangXingyu YangYves Van de PeerJinming ChenKathleen MarchalTao Shi

A1 Journal Article in PLANT JOURNAL

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Renhai PengYanchao XuShilin TianTurgay UnverZhen LiuZhongli ZhouXiaoyan CaiKunbo WangYangyang WeiYuling Liu et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy

Ming-He LiKe-Wei LiuZhen LiHsiang-Chia LuQin-Liang YeDiyang ZhangJie-Yu WangYu-Feng LiZhi-Ming ZhongXuedie Liu et al.

A1 Journal Article in NATURE PLANTS

Genomes shed light on the evolution of Begonia, a mega‐diverse genus

Lingfei LiXiaoli ChenDongming FangShanshan DongXing GuoNa LiLucia Campos‐DominguezWenguang WangYang LiuXiaoan Lang et al.

A1 Journal Article in NEW PHYTOLOGIST

Genomic and metabolomic analyses of the marine fungus Emericellopsis cladophorae : insights into saltwater adaptability mechanisms and its biosynthetic potential

Micael F. M. GonçalvesSandra HilárioYves Van de PeerAna C. EstevesArtur Alves

A1 Journal Article in JOURNAL OF FUNGI

MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode

Inês Sofia Barrios ModestoVera InácioYves Van de PeerCélia M. Miguel

A1 Journal Article in SCIENTIFIC REPORTS

Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

Jia‐Yu XueShanshan DongMing‐Qiang WangTian‐Qiang SongGuang‐Can ZhouZhen LiYves Van de PeerZhu‐Qing ShaoWei WangMin Chen et al.

A1 Journal Article in JOURNAL OF SYSTEMATICS AND EVOLUTION

Nearby transposable elements impact plant stress gene regulatory networks : a meta-analysis in A. thaliana and S. lycopersicum

Jan DenewethYves Van de PeerVanessa Vermeirssen

A1 Journal Article in BMC GENOMICS

Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

Zhen-Hui WangXin-Feng WangTianyuan LuMing-Rui LiPeng JiangJing ZhaoSi-Tong LiuXue-Qi FuJonathan F. WendelYves Van de Peer et al.

A1 Journal Article in NATURE COMMUNICATIONS

Revisiting ancient polyploidy in leptosporangiate ferns

Hengchi ChenYuhan FangArthur ZwaenepoelSanwen HuangYves Van de PeerZhen Li

U Journal Article in New Phytologist

SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode

Inês Sofia Barrios ModestoVera InácioPolina NovikovaIsabel CarrasquinhoYves Van de PeerCélia M. Miguel

A1 Journal Article in FORESTS

The Cycas genome and the early evolution of seed plants

Yang LiuSibo WangLinzhou LiTing YangShanshan DongTong WeiShengdan WuYongbo LiuYiqing GongXiuyan Feng et al.

A1 Journal Article in NATURE PLANTS

The Larix kaempferi genome reveals new insights into wood properties

Chao SunYun‐hui XieZhen LiYan‐jing LiuXiao‐mei SunJing‐jing LiWei‐peng QuanQing‐yin ZengYves Van de PeerShou‐gong Zhang

A1 Journal Article in JOURNAL OF INTEGRATIVE PLANT BIOLOGY

The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales

Zhichao XuZhen LiFengming RenRanran GaoZhe WangJinlan ZhangTao ZhaoXiao MaXiangdong PuTianyi Xin et al.

A1 Journal Article in PLANT JOURNAL

The genome of Hibiscus hamabo reveals its adaptation to saline and waterlogged habitat

Zhiquan WangJia-Yu XueShuai-Ya HuFengjiao ZhangRanran YuDijun ChenYves Van de PeerJiafu JiangAiping SongLongjie Ni et al.

A1 Journal Article in HORTICULTURE RESEARCH

The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences

Yuhan FangXing QinQinggang LiaoRan DuXizhi LuoQian ZhouZhen LiHengchi ChenWanting JinYaning Yuan et al.

A1 Journal Article in NATURE PLANTS

The neighborhood of the Spike gene is a hotspot for modular intertypic homologous and nonhomologous recombination in Coronavirus genomes

Marios NikolaidisPanayotis MarkoulatosYves Van de PeerStephen G OliverGrigorios D Amoutzias

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

2021

A chromosome‐level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop

Xiao MaFabián E. VaistijYi LiWillem S. Jansen van RensburgSarah HarveyMichael W. BairuSonja L. VenterSydney MavengahamaZemin NingIan A. Graham et al.

A1 Journal Article in PLANT JOURNAL

A non-duplicated magnoliid genome

Zhen LiYves Van de Peer

Editorial material

Chromosome scale assembly of the genome sequences of malus x domestica (apple) and Pyrus communis (European pear)

Gareth LinsmithYves Van de PeerMichela Troggio

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

Kai-Hua JiaHui LiuRen-Gang ZhangJie XuShan-Shan ZhouSi-Qian JiaoXue-Mei YanXue-Chan TianTian-Le ShiHang Luo et al.

A1 Journal Article in HORTICULTURE RESEARCH

Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

Zhilin YuanIrina S. DruzhininaJohn G. GibbonsZhenhui ZhongYves Van de PeerRussell J. RodriguezZhongjian LiuXinyu WangHuanshen WeiQi Wu et al.

A1 Journal Article in ISME JOURNAL

Evolution of NLR resistance genes in magnoliids : dramatic expansions of CNLs and multiple losses of TNLs

Jia-Yi WuJia-Yu XueYves Van de Peer

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Qin QiaoPatrick P. EdgerLi XueLa QiongJie LuYichen ZhangQiang CaoAlan E. YoccaAdrian E. PlattsSteven J. Knapp et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome and metabolome MS-based mining of a marine strain of Aspergillus affinis

Micael F. M. GonçalvesSandra HilárioMarta TacãoYves Van de PeerArtur AlvesAna C. Esteves

A1 Journal Article in JOURNAL OF FUNGI

Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)

Xuewen WangShiyu ChenXiao MaAnna E J YsselSrinivasa R ChaluvadiMatthew S JohnsonPrakash GangashettyFalalou HamidouMoussa D SanogoArthur Zwaenepoel et al.

A1 Journal Article in GIGASCIENCE

Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation

Yong‐Peng MaHafiz Muhammad WarissRong‐Li LiaoRen‐Gang ZhangQuan‐Zheng YunRichard G. OlmsteadJohn H. ChauRichard I. MilneYves Van de PeerWei‐Bang Sun

A1 Journal Article in NEW PHYTOLOGIST

Genomic resources to guide improvement of the shea tree

Iago HaleXiao MaArthur T. O. MeloFrancis Kwame PadiPrasad S. HendreSarah B. KinganShawn T. SullivanShiyu ChenJean-Marc BoffaAlice Muchugi et al.

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger

Shi-Ping ChengKai-Hua JiaHui LiuRen-Gang ZhangZhi-Chao LiShan-Shan ZhouTian-Le ShiAi-Chu MaCong-Wen YuChan Gao et al.

A1 Journal Article in HORTICULTURE RESEARCH

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

Xiao MaJeanine L. OlsenThorsten B.H. ReuschGabriele ProcacciniDave KudrnaMelissa WilliamsJane GrimwoodShanmugam RajasekarJerry JenkinsJeremy Schmutz et al.

A2 Journal Article in F1000RESEARCH

Insights into the mechanisms implicated in Pinus pinaster resistance to pinewood nematode

Inês Sofia Barrios ModestoLieven SterckVicent ArbonaAurelio Gómez-CadenasIsabel CarrasquinhoYves Van de PeerCélia M. Miguel

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Polyploidy : an evolutionary and ecological force in stressful times

Yves Van de PeerTia-Lynn AshmanPamela S. SoltisDouglas E. Soltis

A1 Journal Article in PLANT CELL

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Sarah FarhatPhuong LEEhsan KayalBenjamin NoelEstelle BigeardErwan CorreFlorian MaumusIsabelle FlorentAdriana AlbertiJean-Marc Aury et al.

A1 Journal Article in BMC BIOLOGY

Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production

Chi SongFangfang FuLulu YangYan NiuZhaoyang TianXiangxiang HeXiaoming YangJie ChenWei SunTao Wan et al.

A1 Journal Article in COMMUNICATIONS BIOLOGY

The Cymbidium genome reveals the evolution of unique morphological traits

Ye AiZhen LiWei-Hong SunJuan ChenDiyang ZhangLiang MaQing-Hua ZhangMing-Kun ChenQing-Dong ZhengJiang-Feng Liu et al.

A1 Journal Article in HORTICULTURE RESEARCH

The Euscaphis japonica genome and the evolution of malvids

Wei‐Hong SunZhen LiShuang XiangLin NiDiyang ZhangDe‐Qiang ChenMeng‐Yuan QiuQi‐Gong ZhangLin XiaoLe Din et al.

A1 Journal Article in PLANT JOURNAL

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

Tao WanZhiming LiuIlia J. LeitchHaiping XinGillian Maggs-KöllingYanbing GongZhen LiEugene MaraisYiying LiaoCan Dai et al.

A1 Journal Article in NATURE COMMUNICATIONS

The emergence and evolution of intron‐poor and intronless genes in intron‐rich plant gene families

Hui LiuHai‐Meng LyuKaikai ZhuYves Van de PeerZong‐Ming (Max) Cheng

A1 Journal Article in PLANT JOURNAL

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

Stephanie De VosStephane RombautsLouis CoussementWannes DermauwMarnik VuylstekePatrick SorgeloosJames S. CleggZiro NambuFilip Van NieuwerburghParisa Norouzitallab et al.

A1 Journal Article in BMC GENOMICS

Transcriptomic analysis of the poultry red mite, Dermanyssus gallinae, across all stages of the lifecycle

Kathryn BartleyWan ChenRichard I. Lloyd MillsFrancesca NunnDaniel R. G. PriceStephane RombautsYves Van de PeerLise RoyAlasdair J. NisbetStewart T. G. Burgess

A1 Journal Article in BMC GENOMICS

Whole-genome microsynteny-based phylogeny of angiosperms

Tao ZhaoArthur ZwaenepoelJia-Yu XueShu-Min KaoZhen LiM. Eric SchranzYves Van de Peer

A1 Journal Article in NATURE COMMUNICATIONS

Wolfberry genomes and the evolution of Lycium (Solanaceae)

You-Long CaoYan-long LiYun-Fang FanZhen LiKouki YoshidaJie-Yu WangXiao-Kai MaNing WangNobutaka MitsudaToshihisa Kotake et al.

A1 Journal Article in COMMUNICATIONS BIOLOGY

2020

'Winter is coming' : how did polyploid plants survive?

Zhen LiYves Van de Peer

Editorial material

Chromosome-level genome assembly of a parent species of widely cultivated azaleas

Fu-Sheng YangShuai NieHui LiuTian-Le ShiXue-Chan TianShan-Shan ZhouYu-Tao BaoKai-Hua JiaJing-Fang GuoWei Zhao et al.

A1 Journal Article in NATURE COMMUNICATIONS

De novo assembly of transcriptomes from a B73 maize line introgressed with a QTL for resistance to gray leaf spot disease reveals a candidate allele of a lectin receptor-like kinase

Tanya WelgemoedRian PierneefLieven SterckYves Van de PeerVelushka SwartKevin Daniel ScheepersDave K. Berger

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants

Tao ShiRazgar Seyed RahmaniPaul F. GuggerMuhua WangHui LiYue ZhangZhizhong LiQingfeng WangYves Van de PeerKathleen Marchal et al.

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Draft genomes of two Artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis)

Sunil Kumar SahuMin LiuAnna YsselRobert KaribaSamuel MuthembaSanjie JiangBo SongPrasad S. HendreAlice MuchugiRamni Jamnadass et al.

A1 Journal Article in GENES

First draft genome assembly of the desert locust, Schistocerca gregaria

Heleen VerlindenLieven SterckJia LiZhen LiAnna YsselYannick GansemansRik VerdonckMichiel HoltofHojun SongSpencer T. Behmer et al.

A2 Journal Article in F1000RESEARCH

Genome assembly and annotation : from reads to biology

Shu-Min KaoYves Van de Peer

Genome streamlining in a minute herbivore that manipulates its host plant

Robert GreenhalghWannes DermauwJoris J. GlasStephane RombautsNicky WybouwJainy ThomasJuan M. AlbaEllen J. PrithamSaioa LegarreaRené Feyereisen et al.

A1 Journal Article in ELIFE

Genomes of early-diverging streptophyte algae shed light on plant terrestrialization

Sibo WangLinzhou LiHaoyuan LiSunil Kumar SahuHongli WangYan XuWenfei XianBo SongHongping LiangShifeng Cheng et al.

A1 Journal Article in NATURE PLANTS

Model-based detection of whole-genome duplications in a phylogeny

Arthur ZwaenepoelYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution

Dick RoelofsArthur ZwaenepoelTom SistermansJoey NapAndries A. KampfraathYves Van de PeerJacintha EllersKen Kraaijeveld

A1 Journal Article in BMC BIOLOGY

Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

Riaan F. RifkinSurendra VikramJean-Baptiste RamondAlba Rey-IglesiaTina B. BrandGuillaume PorrazAurore ValGrant HallStephan WoodborneMatthieu Le Bailly et al.

A1 Journal Article in MICROBIOME

Nymphaea colorata (Blue-petal water lily)

Haibao TangLiangsheng ZhangFei ChenXingtan ZhangFeng ChenHong MaYves Van de Peer

Editorial material

Phages actively challenge niche communities in Antarctic soils

Oliver K. I. BezuidtPedro Humberto LebreRian PierneefCarlos León-SobrinoEvelien M. AdriaenssensDon A. CowanYves Van de PeerThulani P. Makhalanyane

A1 Journal Article in MSYSTEMS

Polyploidy : a biological force from cells to ecosystems

Donald T. FoxDouglas E. SoltisPamela S. SoltisTia-Lynn AshmanYves Van de Peer

A1 Journal Article in TRENDS IN CELL BIOLOGY

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Polina NovikovaIan G. BrennanWilliam BookerMichael MahonyPaul DoughtyAlan R. LemmonEmily Moriarty LemmonJ. Dale RobertsLevi YantYves Van de Peer et al.

A1 Journal Article in PLOS GENETICS

Sequencing and analyzing the transcriptomes of a thousand species across the tree of life for green plants

Gane Ka-Shu WongDouglas E. SoltisJim Leebens-MackNorman J. WickettMichael S. BarkerYves Van de PeerSean W. GrahamMichael Melkonian

A1 Journal Article in ANNUAL REVIEW OF PLANT BIOLOGY

Special issue : Plant synthetic biology

Dhirendra KumarYves Van de Peer

Editorial material

The Litsea genome and the evolution of the laurel family

Yi-Cun ChenZhen LiYun-Xiao ZhaoMing GaoJie-Yu WangKe-Wei LiuXue WangLi-Wen WuYu-Lian JiaoZi-Long Xu et al.

A1 Journal Article in NATURE COMMUNICATIONS

The evolutionary conundrum of whole‐genome duplication

Lorenzo Carretero‐PauletYves Van de Peer

A1 Journal Article in AMERICAN JOURNAL OF BOTANY

The evolutionary origin and domestication history of goldfish (Carassius auratus)

Duo ChenQing ZhangWeiqi TangZhen HuangGang WangYongjun WangJiaxian ShiHuimin XuLianyu LinZhen Li et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

Linzhou LiSibo WangHongli WangSunil Kumar SahuBirger MarinHaoyuan LiYan XuHongping LiangZhen LiShifeng Cheng et al.

A1 Journal Article in NATURE ECOLOGY & EVOLUTION

The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration

Xiangdong PuZhen LiYa TianRanran GaoLijun HaoYating HuChunnian HeWei SunMeimei XuReuben J. Peters et al.

A1 Journal Article in NEW PHYTOLOGIST

The hornwort genome and early land plant evolution

Jian ZhangXin-Xing FuRui-Qi LiXiang ZhaoYang LiuMing-He LiArthur ZwaenepoelHong MaBernard GoffinetYan-Long Guan et al.

A1 Journal Article in NATURE PLANTS

The seagrass Methylome is associated with variation in photosynthetic performance among clonal shoots

Alexander JueterbockChristoffer BoströmJames A. CoyerJeanine L. OlsenMartina KoppAnusha K. S. DhanasiriIrina SmolinaSophie Arnaud-HaondYves Van de PeerGalice Hoarau

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

The water lily genome and the early evolution of flowering plants

Liangsheng ZhangFei ChenXingtan ZhangZhen LiYiyong ZhaoRolf LohausXiaojun ChangWei DongSimon YW HoXing Liu et al.

A1 Journal Article in NATURE

Understanding and exploiting the hostpathogen interactions in brown algae with their marine oomycete pathogens using omics data

Srilakshmy Lakshminarayanapuram HarikrishnanYves Van de Peer

Virus-host coexistence in phytoplankton through the genomic lens

Sheree YauMarc KrasovecL. Felipe BenitesStephane RombautsMathieu GroussinEmmelien VancaesterJean-Marc AuryEvelyne DerelleYves DesdevisesMarie-Line Escande et al.

A1 Journal Article in SCIENCE ADVANCES

2019

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

Stewart TG BurgessEdward J MarrKathryn BartleyFrancesca G NunnRachel E DownRobert J WeaverJessica C PrickettJackie DunnStephane RombautsThomas Van Leeuwen et al.

A1 Journal Article in BMC GENOMICS

A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes

Carina FelixRodrigo Silva MenesesMicael F. M. GoncalvesLaurentijn TillemanAna S. DuarteJesus V. Jorrin-NovoYves Van de PeerDieter DeforceFilip Van NieuwerburghAna C. Esteves et al.

A1 Journal Article in SCIENTIFIC REPORTS

Applications of next-generation sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies : a short review

Min Pau TanLi Lian WongSiti Aisyah RazaliNor Afiqah-AlengSiti Azizah Mohd NorYeong Yik SungYves Van de PeerPatrick SorgeloosMuhd Danish-Daniel

A1 Journal Article in EVOLUTIONARY BIOINFORMATICS

Draft genome assembly of the false spider mite Brevipalpus yothersi

Denise NaviaValdenice M. NovelliStephane RombautsJuliana Freitas-AstuaRenata Santos de MendoncaMaria Andreia NunesMarcos A. MachadoYao-Cheng LinPhuong LEZaichao Zhang et al.

A2 Journal Article in MICROBIOLOGY RESOURCE ANNOUNCEMENTS

Dual RNA sequencing of Vitis vinifera during Lasiodiplodia theobromae infection unveils host-pathogen interactions

Micael FM GonçalvesRui B NunesLaurentijn TillemanYves Van de PeerDieter DeforceFilip Van NieuwerburghAna C EstevesArtur Alves

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Error correction of Illumina sequencing data

Mahdi HeydariJan FostierYves Van de Peer

Evaluation of plant produced novel vaccines and camelid derived immunoglobulins against post-weaning diarrhea in piglets

Jorge Palací BatallerAnna DepickerYves Van de Peer

Finding evidence for whole genome duplications : a reappraisal

Arthur ZwaenepoelZhen LiRolf LohausYves Van de Peer

A1 Journal Article in MOLECULAR PLANT

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Ticao ZhangQin QiaoPolina NovikovaQia WangJipei YueYanlong GuanShengping MingTianmeng LiuJi DeYixuan Liu et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence of Malania oleifera, a tree with great value for nervonic acid production

Chao-Qun XuHui LiuShan-Shan ZhouDong-Xu ZhangWei ZhaoSihai WangFu ChenYan-Qiang SunShuai NieKai-Hua Jia et al.

A1 Journal Article in GIGASCIENCE

Illumina error correction near highly repetitive DNA regions improves de novo genome assembly

Mahdi HeydariGiles MiclotteYves Van de PeerJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

Inference of ancient whole-genome duplications and the evolution of gene duplication and loss rates

Arthur ZwaenepoelYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Loss of wood formation genes in monocot genomes

Danielle RoodtZhen LiYves Van de PeerEshchar Mizrachi

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Mining the enriched subgraphs for specific vertices in a biological graph

Pieter MeysmanYvan SaeysEhsan SabaghianWout BittremieuxYves Van de PeerBart GoethalsKris Laukens

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Multiple independent recruitment of sodefrin precursor-like factors in anuran sexually dimorphic glands

Franky BossuytLisa M SchulteMargo MaexSunita JanssenswillenPolina NovikovaSD BijuYves Van de PeerSeverine MatthijsKim RoelantsAn Martel et al.

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

ORCAE-AOCC : a centralized portal for the annotation of African orphan crop genomes

Anna EJ YsselShu-Min KaoYves Van de PeerLieven Sterck

A1 Journal Article in GENES

Optimising orbit counting of arbitrary order by equation selection

Ine MelckenbeeckPieter AudenaertThomas Van ParysYves Van de PeerDidier ColleMario Pickavet

A1 Journal Article in BMC BIOINFORMATICS

Pseudo-chromosome-length genome assembly of a double haploid 'Bartlett' pear (Pyrus communis L.)

Gareth LinsmithStephane RombautsSara MontanariCecilia H DengJean-Marc CeltonPhilippe GuérifChang LiuRolf LohausJason D ZurnAlessandro Cestaro et al.

A1 Journal Article in GIGASCIENCE

Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos

Andreia S. RodriguesInês ChavesBruno Vasques CostaYao-Cheng LinSusana LopesAna MilhinhosYves Van de PeerCélia M. Miguel

A1 Journal Article in SCIENTIFIC REPORTS

The draft genomes of five agriculturally important African orphan crops

Yue ChangHuan LiuMin LiuXuezhu LiaoSunil Kumar SahuYuan FuBo SongShifeng ChengRobert KaribaSamuel Muthemba et al.

A1 Journal Article in GIGASCIENCE

The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication

Jonas DefoortYves Van de PeerLorenzo Carretero-Paulet

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

The impact of genome duplications on the dynamics of gene family evolution in plants

Setareh TasdighianSteven MaereYves Van de Peer

Unravelling gene functions in Arabidopsis thaliana by means of network biology and machine learning

Ehsan SabaghianYves Van de PeerYvan Saeys

Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy

Yao YaoLorenzo Carretero-PauletYves Van de Peer

A1 Journal Article in PLOS ONE

wgd-simple command line tools for the analysis of ancient whole genome duplications

Arthur ZwaenepoelYves Van de Peer

A1 Journal Article in BIOINFORMATICS

2018

A genome for gnetophytes and early evolution of seed plants

Tao WanZhi-Ming LiuLing-Fei LiAndrew R LeitchIlia J LeitchRolf LohausZhong-Jian LiuHai-Ping XinYan-Bing GongYang Liu et al.

A1 Journal Article in NATURE PLANTS

A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils

Marc W Van GoethemRian PierneefOliver KI BezuidtYves Van de PeerDon A CowanThulani P Makhalanyane

A1 Journal Article in MICROBIOME

Agulhas Current properties shape microbial community diversity and potential functionality

Sandra PhomaSurendra VikramJanet K JanssonIsabelle J AnsorgeDon A CowanYves Van de PeerThulani P Makhalanyane

A1 Journal Article in SCIENTIFIC REPORTS

BrownieAligner : accurate alignment of Illumina sequencing data to de Bruijn graphs

Mahdi HeydariGiles MiclotteYves Van de PeerJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

Draft genome assembly of the poultry red mite, Dermanyssus gallinae

Stewart TG BurgessKathryn BartleyFrancesca NunnHarry W WrightMargaret HughesMatthew GemmellSam HaldenbySteve PatersonStephane RombautsFiona M Tomley et al.

A2 Journal Article in MICROBIOLOGY RESOURCE ANNOUNCEMENTS

Draft genome assembly of the sheep scab mite, Psoroptes ovis

Stewart TG BurgessKathryn BartleyEdward J MarrHarry W WrightRobert J WeaverJessica C PrickettMargaret HughesSam HaldenbyPhuong LEStephane Rombauts et al.

A2 Journal Article in MICROBIOLOGY RESOURCE ANNOUNCEMENTS

Editorial overview: Genome studies and molecular genetics : treasure troves of evolution

Yves Van de PeerJ Chris Pires

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Fay-Wei LiPaul BrouwerLorenzo Carretero-PauletShifeng ChengJan de VriesPierre-Marc DelauxAriana EilyNils KoppersLi-Yaung KuoZheng Li et al.

A1 Journal Article in NATURE PLANTS

First draft genome assembly of the Argane tree (Argania spinosa)

Slimane KhayiNour Elhouda AzzaFatima GabounStacy PirroOussama BadadM Gonzalo ClarosDavid A LightfootTurgay UnverBouchra ChaouniRedouane Merrouch et al.

A2 Journal Article in F1000RESEARCH

Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant

Jonas DefoortYves Van de PeerVanessa Vermeirssen

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Yao-Cheng LinJing WangNicolas DelhommeBastian SchiffthalerGorel SundstromAndrea ZuccoloBjorn NystedtTorgeir R HvidstenAmanda de la TorreRosa M Cossu et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum

Ronnie de JongeMalaika K EbertCallie R Huitt-RoehlParamita PalJeffrey C SuttleRebecca E SpannerJonathan D NeubauerWayne M, II Jurick,Karina A StottGary A Secor et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into the evolution of multicellularity from the sea lettuce genome

Olivier De ClerckShu-Min KaoKenny BogaertJonas BlommeFatima FoflonkerMichiel KwantesEmmelien VancaesterLisa VanderstraetenEylem Aydogdu LohausJens Boesger et al.

A1 Journal Article in CURRENT BIOLOGY

MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants

Arthur ZwaenepoelTim DielsDavid AmarThomas Van ParysRon ShamirYves Van de PeerOren Tzfadia

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Network modeling unravels mechanisms of crosstalk between ethylene and salicylate signaling in potato

Ziva RamsakAnna CollTjasa StareOren TzfadiaSpela BaeblerYves Van de PeerKristina Gruden

A1 Journal Article in PLANT PHYSIOLOGY

PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

Michiel Van BelTim DielsEmmelien VancaesterLukasz KreftAlexander BotzkiYves Van de PeerFrederik CoppensKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Polyploid Arabidopsis species originated around recent glaciation maxima

Polina NovikovaNora HohmannYves Van de Peer

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Retention and integration of gene duplicates in eukaryotes

Jonas DefoortYves Van de Peer

Size does matter

Yves Van de Peer

Editorial material

The 'TranSeq' 3'-end sequencing method for high-throughput transcriptomics and gene space refinement in plant genomes

Oren TzfadiaSamuel BocobzaJonas DefoortEfrat Almekias-SieglSayantan PandaMatan LevyVeronique StormeStephane RombautsDiego Adhemar JaitinHadas Keren-Shaul et al.

A1 Journal Article in PLANT JOURNAL

The Chara genome : secondary complexity and implications for plant terrestrialization

Tomoaki NishiyamaHidetoshi SakayamaJan de VriesHenrik BuschmannDenis Saint-MarcouxKristian K UllrichFabian B HaasLisa VanderstraetenDirk BeckerDaniel Lang et al.

A1 Journal Article in CELL

The sociobiology of genes : the gene's eye view as a unifying behavioural-ecological framework for biological evolution

Alexis De TiègeYves Van de PeerJohan BraeckmanKoen Tanghe

A1 Journal Article in HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES

The study of plant genome evolution by means of phylogenomics

Zhen LiYves Van de Peer

2017

A Cytoscape app for motif enumeration with ISMAGS

Thomas Van ParysIne MelckenbeeckMaarten HoubrakenPieter AudenaertDidier ColleMario PickavetPiet DemeesterYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Conservation of nonsense-mediated mRNA decay complex components throughout eukaryotic evolution

Barry CausierZhen LiRiet De SmetJames PB LloydYves Van de PeerBrendan Davies

A1 Journal Article in SCIENTIFIC REPORTS

Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants

Amanda R De La TorreZhen LiYves Van de PeerPär K Ingvarsson

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana

Riet De SmetEhsan SabaghianZhen LiYvan SaeysYves Van de Peer

A1 Journal Article in PLANT CELL

Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips

Brenda D WingfieldDave K BergerEmma T SteenkampHye-Jin LimTuan A DuongBurton H BluhmZ Wilhelm De BeerLieschen De VosG FourieKershney Naidoo et al.

A1 Journal Article in IMA FUNGUS

Draft genome sequences of two unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, isolated from environmental samples

Russell JS OrrStephane RombautsYves Van de PeerKamran Shalchian-Tabrizi

A2 Journal Article in GENOME ANNOUNCEMENTS

Draft genome sequences of two unclassified bacteria, Hydrogenophaga sp. strains IBVHS1 and IBVHS2, isolated from environmental samples

Russel J. S. OrrStephane RombautsYves Van de PeerKamran Shalchian-Tabrizi

A2 Journal Article in GENOME ANNOUNCEMENTS

Draft genome sequences of two unclassified bacteria, Sphingomonas sp. strains IBVSS1 and IBVSS2, isolated from environmental samples

Russell J. S. OrrStephane RombautsYves Van de PeerKamran Shalchian-Tabrizi

A2 Journal Article in GENOME ANNOUNCEMENTS

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

Panayotis VlastaridisPelagia KyriakidouAnargyros ChaliotisYves Van de PeerStephen G OliverGrigoris D Amoutzias

A1 Journal Article in GIGASCIENCE

Evaluation of the impact of Illumina error correction tools on de novo genome assembly

Mahdi HeydariGiles MiclottePiet DemeesterYves Van de PeerJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

Evidence for an ancient whole genome duplication in the cycad lineage

Danielle RoodtRolf LohausLieven SterckRiaan L SwanepoelYves Van de PeerEshchar Mizrachi

A1 Journal Article in PLOS ONE

Genome of wild olive and the evolution of oil biosynthesis

Turgay UnverZhangyan WuLieven SterckMine TurktasRolf LohausZhen LiMing YangLijuan HeTianquan DengFrancisco Javier Escalante et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Life's gene-centred nature : five essays on the causal role of genes in 21st century biology

Alexis De TiègeJohan BraeckmanYves Van de Peer

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Eshchar MizrachiLieven VerbekeNanette ChristieAna Carolina Elisa Fierro GutierrezShawn D MansfieldMark F DavisErica GjersingGerald A TuskanMarc Van MontaguYves Van de Peer et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OMSim : a simulator for optical map data

Giles MiclotteStéphane PlaisanceStephane RombautsYves Van de PeerPieter AudenaertJan Fostier

A1 Journal Article in BIOINFORMATICS

Principles of systems biology, no. 14 : [...] Network analysis of woody biomass

Eshchar MizrachiLieven VerbekeYves Van de PeerKathleen MarchalAlexander A Myburg

Editorial material

Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

Alexandre CormierKomlan AviaLieven SterckThomas DerrienValentin WucherGwendoline AndresMisharl MonsoorOlivier GodfroyAgnieszka LipinskaMarie-Mathilde Perrineau et al.

A1 Journal Article in NEW PHYTOLOGIST

Reciprocally retained genes in the angiosperm lineage show the hallmarks of dosage balance sensitivity

Setareh TasdighianMichiel Van BelZhen LiYves Van de PeerLorenzo Carretero-PauletSteven Maere

A1 Journal Article in PLANT CELL

Revisiting ancestral polyploidy in plants

Colin RuprechtRolf LohausKevin VannesteMarek MutwilZoran NikoloskiYves Van de PeerStaffan Persson

A1 Journal Article in SCIENCE ADVANCES

Simulating biological complexity through artificial evolution

Yao YaoYves Van de Peer

Single-copy genes as molecular markers for phylogenomic studies in seed plants

Zhen LiAmanda R De La TorreLieven SterckFrancisco M CánovasConcepción AvilaIrene MerinoJose Antonio CabezasMaría Teresa CerveraPar K IngvarssonYves Van de Peer

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem

Nanette ChristieAlexander A MyburgFourie JoubertShane L MurrayMaryke CarstensYao-Cheng LinJacqueline MeyerBridget G CramptonShawn A ChristensenJean F Ntuli et al.

A1 Journal Article in PLANT JOURNAL

The Apostasia genome and the evolution of orchids

Guo-Qiang ZhangKe-Wei LiuZhen LiRolf LohausYu-Yun HsiaoShan-Ce NiuJie-Yu WangYao-Cheng LinQing XuLi-Jun Chen et al.

A1 Journal Article in NATURE

The evolutionary significance of polyploidy

Yves Van de PeerEshchar MizrachiKathleen Marchal

A1 Journal Article in NATURE REVIEWS GENETICS

The gene expression landscape of pine seedling tissues

Rafael A CañasZhen LiM Belén PascualVanessa Castro-RodríguezConcepción ÁvilaLieven SterckYves Van de PeerFrancisco M Cánovas

A1 Journal Article in PLANT JOURNAL

2016

Adaptive self-organizing organisms using a bio-inspired gene regulatory network controller: for the aggregation of evolutionary robots under a changing environment

Yao YaoKathleen MarchalYves Van de Peer

Bookchapter in Handbook of research on design, control and modeling of swarm robotics

Annotation of marine eukaryotic genomes

Bram VerhelstYves Van de Peer

Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Suwisa KaewphanSofie Van LandeghemTomoko OhtaYves Van de PeerFilip GinterSampo Pyysalo

A1 Journal Article in BIOINFORMATICS

CoExpNetViz: comparative co-expression networks construction and visualization tool

Oren TzfadiaTim DielsSam De MeyerKlaas VandepoeleAsaph AharoniYves Van de Peer

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts

Phuong LEThulani P MakhalanyaneLeandro D GuerreroSurendra VikramYves Van de PeerDon A Cowan

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Complete mitochondrial genome of the Verticillium-wilt causing plant pathogen Verticillium nonalfalfae

Vid JelenRonnie de JongeYves Van de PeerBranka JavornikJernej Jakše

A1 Journal Article in PLOS ONE

Complex evolutionary dynamics of massively expanded chemosensory receptor families in an extreme generalist chelicerate herbivore

Thi Ngoc Phuong CaoRobert GreenhalghWannes DermauwStephane RombautsSabina Bajda-WybouwVladimir ZhurovMiodrag GrbićYves Van de PeerThomas Van LeeuwenPierre Rouzé et al.

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Sofie Van LandeghemThomas Van ParysMarieke DuboisDirk InzéYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

Editorial overview: Genome studies and molecular genetics : of plant genes, genomes, and genomics

Yves Van de PeerJ Chris Pires

Editorial material

Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment

Yao YaoVeronique StormeKathleen MarchalYves Van de Peer

A1 Journal Article in PEERJ

Gene duplicability of core genes is highly consistent across all angiosperms

Zhen LiJonas DefoortSetareh TasdighianSteven MaereYves Van de PeerRiet De Smet

A1 Journal Article in PLANT CELL

Jabba: hybrid error correction for long sequencing reads

Giles MiclotteMahdi HeydariPiet DemeesterStephane RombautsYves Van de PeerPieter AudenaertJan Fostier

A1 Journal Article in ALGORITHMS FOR MOLECULAR BIOLOGY

Lack of GLYCOLATE OXIDASE1, but not GLYCOLATE OXIDASE2, attenuates the photorespiratory phenotype of CATALASE2-deficient Arabidopsis

Pavel KerchevCezary WaszczakAleksandra LewandowskaPatrick WillemsAlexey ShapiguzovZhen LiSaleh AlseekhPer MühlenbockFrank HoeberichtsJingjing Huang et al.

A1 Journal Article in PLANT PHYSIOLOGY

Of dups and dinos : evolution at the K/Pg boundary

Rolf LohausYves Van de Peer

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

RNA-sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction

Melvin D BoltonMalaika K EbertLuigi FainoVivivana Rivera-VarasRonnie de JongeYves Van de PeerBart PHJ ThommaGary A Secor

A1 Journal Article in FUNGAL GENETICS AND BIOLOGY

The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution

Guo-Qiang ZhangQing XuChao BianWen-Chieh TsaiChuan-Ming YehKe-Wei LiuKouki YoshidaLiang-Sheng ZhangSong-Bin ChangFei Chen et al.

A1 Journal Article in SCIENTIFIC REPORTS

The challenges of interpreting phosphoproteomics data : a critical view through the bioinformatics lens

Panayotis VlastaridisStephen G OliverYves Van de PeerGrigoris D Amoutzias

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Jeanine L OlsenPierre RouzéBram VerhelstYao-Cheng LinTill BayerJonas CollenEmanuela DattoloEmanuele De PaoliSimon DittamiFlorian Maumus et al.

A1 Journal Article in NATURE

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Michele PerazzolliNoemí HerreroLieven SterckLuisa LenziAlberto PellegriniGerardo PuopoloYves Van de PeerIlaria Pertot

A1 Journal Article in BMC GENOMICS

hfAIM: a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms

Qingjun XieOren TzfadiaMatan LevyEfrat WeithornHadas Peled-ZehaviThomas Van ParysYves Van de PeerGad Galili

A1 Journal Article in AUTOPHAGY

2015

Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)

Sonali Sachin RanadeYao-Cheng LinYves Van de PeerMaria Rosario García-Gil

A1 Journal Article in BMC GENETICS

Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains

S CrauwelsA Van AsscheRonnie de JongeAR BornemanC VerrethP TroelsG De SamblanxKathleen MarchalYves Van de PeerKA Willems et al.

A1 Journal Article in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

Guillaume MorelLieven SterckDominique SwennenMarina Marcet-HoubenDjamila OnesimeAnthony LevasseurNoémie JacquesSandrine MalletArnaux CoulouxKarine Labadie et al.

A1 Journal Article in SCIENTIFIC REPORTS

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Sarieh GhorbaniYao-Cheng LinBoris ParizotAna Fernandez SalinaMaria NjoYves Van de PeerTom BeeckmanPierre Hilson

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

Exploration of alternative splicing events in ten different grapevine cultivars

Emilio PotenzaMilvia Luisa RacchiLieven SterckEmanuela CollerElisa AsquiniSilvio CE TosattoRiccardo VelascoYves Van de PeerAlessandro Cestaro

A1 Journal Article in BMC GENOMICS

Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families

Amanda R De La TorreYao-Cheng LinYves Van de PeerPär K Ingvarsson

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber

Zhonghua ZhangLinyong MaoHuiming ChenFengjiao BuGuangcun LiJinjing SunShuai LiHonghe SunChen JiaoRachel Blakely et al.

A1 Journal Article in PLANT CELL

Horsetails are ancient polyploids : evidence from Equisetum giganteum

Kevin VannesteLieven SterckAlexander Andrew MyburgYves Van de PeerEshchar Mizrachi

A1 Journal Article in PLANT CELL

Identifying prokaryotic consortia that live in close interactions with algae

Assia SaltykovaSergio Pulido-TamayoMarie PazoutovaStefan A RensingTomoaki NishiyamaYves Van de PeerKathleen MarchalStephane Rombauts

Life's dual nature: a way out of the impasse of the gene-centred 'versus' complex systems controversy on life

Alexis De TiègeKoen TangheJohan BraeckmanYves Van de Peer

Bookchapter in Evolutionary biology : biodiversification from genotype to phenotype

PLAZA 3.0 : an access point for plant comparative genomics

Sebastian ProostMichiel Van BelDries VaneechoutteYves Van de PeerDirk InzéBernd Mueller-RoeberKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Polyploidy and genome evolution in plants

Pamela S SoltisD Blaine MarchantYves Van de PeerDouglas E Soltis

A1 Journal Article in CURRENT OPINION IN GENETICS & DEVELOPMENT

Quantifying expression divergence of duplicated genes with microarrays

Koen Van den BergeRiet De SmetYves Van de PeerLieven Clement

Serendipitous meta-transcriptomics : the fungal community of Norway spruce (Picea abies)

Nicolas DelhommeGorel SundstromNeda ZamaniHenrik LantzYao-Cheng LinTorgeir R HvidstenMarc P HoppnerPatric JernYves Van de PeerJoakim Lundeberg et al.

A1 Journal Article in PLOS ONE

The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

Dora SzakonyiSofie Van LandeghemKatja BaerenfallerLieven BaeyensJonas BlommeRubén Casanova-SáezStefanie De BodtDavid Esteve-BrunaFabio FioraniNathalie Gonzalez Sanchez et al.

A2 Journal Article in CURRENT PLANT BIOLOGY

The genome sequence of the orchid Phalaenopsis equestris

Jing CaiXin LiuKevin VannesteSebastian ProostWen-Chieh TsaiKe-Wei LiuLi-Jun ChenYing HeQing XuChao Bian et al.

A1 Journal Article in NATURE GENETICS

The plant genome integrative explorer resource : PlantGenIE.org

David SundellChanaka MannapperumaSergiu NetoteaNicolas DelhommeYao-Cheng LinAndreas SjödinYves Van de PeerStefan JanssonTorgeir R HvidstenNathaniel R Street

A1 Journal Article in NEW PHYTOLOGIST

Using a novel bio-inspired robotic model to study artificial evolution

Yao YaoYves Van de Peer

2014

A haploid system of sex determination in the brown alga Ectocarpus sp.

Sophia AhmedJ Mark CockEugenie PessiaRemy LuthringerAlexandre CormierMarine RobuchonLieven SterckAkira F PetersSimon M DittamiErwan Corre et al.

A1 Journal Article in CURRENT BIOLOGY

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

Mushthofa MushthofaGustavo Adolfo Torres TorresYves Van de PeerKathleen MarchalMartine De Cock

A1 Journal Article in BIOINFORMATICS

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Romain Blanc-MathieuBram VerhelstEvelyne DerelleStephane RombautsFrançois-Yves BougetIsabelle CarreAnnie ChateauAdam Eyre-WalkerNigel GrimsleyHervé Moreau et al.

A1 Journal Article in BMC GENOMICS

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary

Kevin VannesteGuy BaeleSteven MaereYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress

Vanessa VermeirssenInge De ClercqThomas Van ParysFrank Van BreusegemYves Van de Peer

A1 Journal Article in PLANT CELL

Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera

Sonali Sachin RanadeYao-Cheng LinAndrea ZuccoloYves Van de PeerMaria del Rosario Garcia-Gil

A1 Journal Article in BMC PLANT BIOLOGY

Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids

Katarzyna CiesielskaInge Van BogaertSamia ChevineauBing LiSara GroeneboerWim SoetaertYves Van de PeerBart Devreese

A1 Journal Article in JOURNAL OF PROTEOMICS

From DNA- to NA-centrism and the conditions for gene-centrism revisited

Alexis De TiègeKoen TangheJohan BraeckmanYves Van de Peer

A1 Journal Article in BIOLOGY & PHILOSOPHY

Genome annotation and evolution of chemosensory receptors in spider mites

Thi Ngoc Phuong CaoYves Van de Peer

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Yao-Cheng LinMorgane BooneLeander MeurisIrma LemmensNadine Van RoyArne SoeteJoke ReumersMatthieu MoisseStéphane PlaisanceRadoje Drmanac et al.

A1 Journal Article in NATURE COMMUNICATIONS

Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments

Yao YaoKathleen MarchalYves Van de Peer

A1 Journal Article in PLOS ONE

Reciprocal responses in the interaction between Arabidopsis and the cell-content feeding chelicerate herbivore spider mite

Vladimir ZhurovMarie NavarroKristie A BruinsmaVicent ArbonaM Estrella SantamariaMarc CazauxNicky WybouwEdward J OsborneCherise EnsCristina Rioja et al.

A1 Journal Article in PLANT PHYSIOLOGY

Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks

Kris MorreelYvan SaeysOana DimaFachuang LuYves Van de PeerRuben VanholmeJohn RalphBartel VanholmeWout Boerjan

A1 Journal Article in PLANT CELL

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

Kevin VannesteSteven MaereYves Van de Peer

A1 Journal Article in PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history

Alice PajoroSandra BiewersEvangelia DougaliFelipe Leal ValentimMarta Adelina MendesAimone PorriGeorge CouplandYves Van de PeerAalt DJ van DijkLucia Colombo et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

Heather Bracken-GrissomAllen G CollinsTimothy CollinsKeith CrandallDaniel DistelCasey DunnGonzalo GiribetSteven HaddockNancy KnowltonMark Martindale et al.

A1 Journal Article in JOURNAL OF HEREDITY

The evolutionary significance of gene and genome duplications

Kevin VannesteYves Van de PeerSteven Maere

The genome of Eucalyptus grandis

Alexander A MyburgDario GrattapagliaGerald A TuskanUffe HellstenRichard D HayesJane GrimwoodJerry JenkinsErika LindquistHope TiceDiane Bauer et al.

A1 Journal Article in NATURE

The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution

Melvin D BoltonRonnie de JongePatrik InderbitzinZhaohui LiuKeshav BirlaYves Van de PeerKrishna V SubbaraoBart PHJ ThommaGary A Secor

A1 Journal Article in FUNGAL GENETICS AND BIOLOGY

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

Inês ChavesYao-Cheng LinC Pinto-RicardoYves Van de PeerCélia Miguel

A1 Journal Article in TREE GENETICS & GENOMES

2013

Candida bombicola as a platform organism for the production of tailor-made biomolecules

Sophie RoelantsKaren SaerensThibaut DeryckeBing LiYao-Cheng LinYves Van de PeerSofie De MaeseneireInge Van BogaertWim Soetaert

A1 Journal Article in BIOTECHNOLOGY AND BIOENGINEERING

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Riet De SmetKeith L AdamsKlaas VandepoeleMarc Van MontaguSteven MaereYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomewide analysis of gene expression in Vitis vinifera ssp.

Emilio PotenzaMilvia Luisa RacchiYves Van de Peer

Inference of genome duplications from age distributions revisited

Kevin VannesteYves Van de PeerSteven Maere

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Large-scale event extraction from literature with multi-level gene normalization

Sofie Van LandeghemJari BjorneChih-Hsuan WeiKai HakalaSampo PyysaloSophia AnaniadouHung-Yu KaoZhiyong LuTapio SalakoskiYves Van de Peer et al.

A1 Journal Article in PLOS ONE

Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne

Tom RuttinkLieven SterckAntje RohdeChristian BendixenPierre RouzéTorben AspYves Van de PeerIsabel Roldán-Ruiz

A1 Journal Article in PLANT BIOTECHNOLOGY JOURNAL

Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics

G AndolfoW SanseverinoStephane RombautsYves Van de PeerJM BradeenD CarputoL FruscianteMR Ercolano

A1 Journal Article in NEW PHYTOLOGIST

Pan genome of the phytoplankton Emiliania underpins its global distribution

Betsy A ReadJessica KegelMary J KluteAlan KuoStephane C LefebvreFlorian MaumusChristoph MayerJohn MillerAdam MonierAsaf Salamov et al.

A1 Journal Article in NATURE

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

Andreas D ZimmerDaniel LangKarol BuchtaStephane RombautsTomoaki NishiyamaMitsuyasu HasebeYves Van de PeerStefan A RensingRalf Reski

A1 Journal Article in BMC GENOMICS

SILAC-based proteome analysis of Starmerella bombicola sophorolipid production

Katarzyna CiesielskaBing LiSara GroeneboerInge Van BogaertYao-Cheng LinWim SoetaertYves Van de PeerBart Devreese

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Significance and biological consequences of polyploidization in land plant evolution

Jeffrey FawcettYves Van de PeerSteven Maere

Bookchapter in Physical structure, behaviour and evolution of plant genomes

TRAPID : an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Michiel Van BelSebastian ProostChristophe Van NesteDieter DeforceYves Van de PeerKlaas Vandepoele

A1 Journal Article in GENOME BIOLOGY

The Mycobacterium tuberculosis regulatory network and hypoxia

James E GalaganKyle MinchMatthew PetersonAnna LyubetskayaElham AziziLinsday SweetAntonio GomesTige RustadGregory DolganovIrina Glotova et al.

A1 Journal Article in NATURE

The Norway spruce genome sequence and conifer genome evolution

Björn NystedtNathaniel R StreetAnna WetterbomAndrea ZuccoloYao-Cheng LinDouglas G ScofieldFrancesco VezziNicolas DelhommeStefania GiacomelloAndrey Alexeyenko et al.

A1 Journal Article in NATURE

The biosynthetic gene cluster for sophorolipids : a biotechnological interesting biosurfactant produced by Starmerella bombicola

Inge Van BogaertKevin HolvoetSophie RoelantsBing LiYao-Cheng LinYves Van de PeerWim Soetaert

A1 Journal Article in MOLECULAR MICROBIOLOGY

The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution

Bram VerhelstYves Van de PeerPierre Rouzé

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis

Inge De ClercqVanessa VermeirssenElke VaeckKlaas VandepoeleMonika W MurchaSimon R LawAnnelies InzéSophia NgAneta IvanovaDebbie Rombaut et al.

A1 Journal Article in PLANT CELL

The potential of text mining in data integration and network biology for plant research : a case study on Arabidopsis

Sofie Van LandeghemStefanie De BodtZuzanna DrebertDirk InzéYves Van de Peer

A1 Journal Article in PLANT CELL

pico-PLAZA, a genome database of microbial photosynthetic eukaryotes

Klaas VandepoeleMichiel Van BelGuilhem RichardSofie Van LandeghemBram VerhelstHervé MoreauYves Van de PeerNigel GrimsleyGwenael Piganeau

A1 Journal Article in ENVIRONMENTAL MICROBIOLOGY

2012

A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust)

Stéphane HacquardDavid L JolyYao-Cheng LinEmilie TisserantNicolas FeauChristine DelaruelleValérie LeguéAnnegret KohlerPhilippe TanguayBenjamin Petre et al.

A1 Journal Article in MOLECULAR PLANT-MICROBE INTERACTIONS

A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation

Agnes KlochendlerNoa Weinberg-CoremMaya MoranAvital SwisaNathalie PochetVirginia SavovaJonas VikesåYves Van de PeerMichael BrandeisAviv Regev et al.

A1 Journal Article in DEVELOPMENTAL CELL

An ASP-based simulation method for finding all synchronous and asynchronous attractors in genetic regulatory networks

Gustavo Adolfo Torres TorresKathleen MarchalYves Van de PeerMartine De Cock

Comparative analysis of plant genomes through data integration

Michiel Van BelYves Van de PeerKlaas Vandepoele

Comparative transcriptomics in plants

Sara MovahediYves Van de PeerKlaas Vandepoele

Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes

Florent MuratYves Van de PeerJérôme Salse

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes

Giulia MalacarneMichele PerazzolliAlessandro CestaroLieven SterckPaolo FontanaYves Van de PeerRoberto ViolaRiccardo VelascoFrancesco Salamini

A1 Journal Article in PLOS ONE

Dissecting plant genomes with the PLAZA comparative genomics platform

Michiel Van BelSebastian ProostElisabeth WischnitzkiSara MovahediChristopher ScheerlinckYves Van de PeerKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Ensemble optimisation of cis-regulatory element discovery : in planta benchmark and discovery in Eucalyptus

I Van JaarsveldE MizrachiF JoubertYves Van de PeerAA Myburg

Evaluation and properties of the budding yeast phosphoproteome

Grigoris D AmoutziasYing HeKathryn S LilleyYves Van de PeerSthephen G Oliver

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Exploring biomolecular literature with EVEX : connecting genes through events, homology, and indirect associations

Sofie Van LandeghemKai HakalaSamuel RönnqvistTapio SalakoskiYves Van de PeerFilip Ginter

A1 Journal Article in ADVANCES IN BIOINFORMATICS

GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses

Ryan WhitfordAna Fernandez SalinaRicardo Tejos UlloaAmparo Cuéllar PérezJürgen Kleine-VehnSteffen VannesteAndrzej DrozdzeckiJohannes LeitnerLindy AbasMaarten Aerts et al.

A1 Journal Article in DEVELOPMENTAL CELL

Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification

Dries VekemansSebastian ProostKevin VannesteHeleen CoenenTom ViaenePhilip RuelensSteven MaereYves Van de PeerKoen Geuten

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Hervé MoreauBram VerhelstArnaud CoulouxEvelyne DerelleStephane RombautsNigel GrimsleyMichiel Van BelJulie PoulainMichaël KatinkaMartin F Hohmann-Marriott et al.

A1 Journal Article in GENOME BIOLOGY

GenomeView : a next-generation genome browser

Thomas AbeelThomas Van ParysYvan SaeysJames GalaganYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Germline copy number variation associated with Mendelian inheritance of CLL in two families

JR BrownM HannaB TesarNathalie PochetA VartanovSM FernandesL WernerM AshCA RodenL MacConaill et al.

A1 Journal Article in LEUKEMIA

Getting up to speed

Yves Van de PeerJ ChrisPires

Editorial material

Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome

Jeffrey FawcettPierre RouzéYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Integration of genomic data to study genome evolution in plants

Sebastian ProostYves Van de PeerKlaas Vandepoele

Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia

Jennifer R BrownMegan HannaBethany TesarLilian WernerNathalie PochetJohn M AsaraYaoyu E WangPaola dal CinStacey M FernandesChristina Thompson et al.

A1 Journal Article in CLINICAL CANCER RESEARCH

ORCAE: online resource for community annotation of eukaryotes

Lieven SterckKenny BilliauThomas AbeelPierre RouzéYves Van de Peer

A1 Journal Article in NATURE METHODS

Playing hide and seek on the genomic playground: unveiling biological function from literature

Sofie Van LandeghemYves Van de PeerBernard De BaetsYvan Saeys

Predicting long term behavior of genetic regulatory networks with answer set programming

Gustavo Adolfo Torres TorresKathleen MarchalYves Van de PeerMartine De Cock

PubMed-scale event extraction for post-translational modifications, epigenetics and protein structural relations

Jari BjörneSofie Van LandeghemSampo PyysaloTomoko OhtaFilip GinterYves Van de PeerSophia AnaniadouTapio Salakoski

Redundancy and rewiring of genetic networks following genome-wide duplication events

Riet De SmetYves Van de Peer

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

Semantically linking molecular entities in literature through entity relationships

Sofie Van LandeghemJari BjörneThomas AbeelBernard De BaetsTapio SalakoskiYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

The Ectocarpus genome and brown algal genomics : the Ectocarpus Genome Consortium

J Mark CockLieven SterckSophia AhmedAndrew E AllenGrigoris AmoutziasVeronique AnthouardFrançois ArtiguenaveAlok ArunJean-Marc AuryJonathan H Badger et al.

A1 Journal Article in Advances in Botanical Research

The tomato genome sequence provides insights into fleshy fruit evolution

Shusei SatoSatoshi TabataHideki HirakawaErika AsamizuKenta ShirasawaSachiko IsobeTakakazu KanekoYasukazu NakamuraDaisuke ShibataKoh Aoki et al.

A1 Journal Article in NATURE

Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters

Danny A, Jr MilnerNathalie PochetMalkie KrupkaChris WilliamsKarl SeydelTerrieE TaylorYves Van de PeerAviv RegevDyann WirthJohanna P Daily et al.

A1 Journal Article in PLOS ONE

i-ADHoRe 3.0 : fast and sensitive detection of genomic homology in extremely large data sets

Sebastian ProostJan FostierDieter De WitteBart DhoedtPiet DemeesterYves Van de PeerKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2011

A bio-inspired agent-based system for controlling robot behaviour

Yao YaoGuy BaeleYves Van de Peer

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

Jan FostierSebastian ProostBart DhoedtYvan SaeysPiet DemeesterYves Van de PeerKlaas Vandepoele

A1 Journal Article in BIOINFORMATICS

A mystery unveiled

Yves Van de Peer

Editorial material

Annotation and comparative analysis of fungal genomes: a hitchhiker's guide to genomics

Yao-Cheng LinYves Van de Peer

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

Robert S CoyneLinda HannickDhanasekaran ShanmugamJessica B HostetlerDaniel BramiVinita S JoardarJustin JohnsonDiana RaduneIrtisha SinghJonathan H Badger et al.

A1 Journal Article in GENOME BIOLOGY

Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice

Sara MovahediYves Van de PeerKlaas Vandepoele

A1 Journal Article in PLANT PHYSIOLOGY

Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes

Guy BaeleYves Van de PeerStijn Vansteelandt

A1 Journal Article in BMC EVOLUTIONARY BIOLOGY

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

Pieter AudenaertThomas Van ParysFlorian BrondelMario PickavetPiet DemeesterYves Van de PeerTom Michoel

A1 Journal Article in BIOINFORMATICS

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

Emilie ChancerelCamille LepoittevinGregoire Le ProvostYao-Cheng LinJuan Pablo Jaramillo-CorreaAndrew J EckertJill L WegrzynDiana ZelenikaAnne BolandJean-Marc Frigerio et al.

A1 Journal Article in BMC GENOMICS

EVEX: a PubMed-scale resource for homology-based generalization of text mining predictions

Sofie Van LandeghemFilip GinterYves Van de PeerTapio Salakoski

Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks

Tom MichoelAnagha JoshiBruno NachtergaeleYves Van de Peer

A1 Journal Article in MOLECULAR BIOSYSTEMS

Genomes: the truth is in there

Yves Van de Peer

Editorial material

High-precision bio-molecular event extraction from text using parallel binary classifiers

Sofie Van LandeghemBernard De BaetsYves Van de PeerYvan Saeys

A1 Journal Article in COMPUTATIONAL INTELLIGENCE

Journey through the past: 150 million years of plant genome evolution

Sebastian ProostPedro PattynAntonius GeratsYves Van de Peer

A1 Journal Article in PLANT JOURNAL

Nature, nurture and the structure of macroalgal genomes

J Mark CockJonas CollénLieven SterckPierre RouzéDelphine ScornetVeronique AnthouardFrançois ArtiguenaveJean-Marie AuryKenny BilliauEric Bonnet et al.

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

Sébastien DuplessisChristina A CuomoYao-Cheng LinAndrea AertsEmilie TisserantClaire Veneault-FourreyDavid L JolyStéphane HacquardJoëlle AmselemBrandi L Cantarel et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms

Rubén ArmananzasYvan SaeysIñaki InzaMiguel Garcia-TorresConcha BielzaYves Van de PeerPedro Larranaga

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Post-translational regulation and the evolution of eukaryotic genomes

Ying HeYves Van de Peer

Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast

Anagha JoshiYves Van de PeerTom Michoel

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Tina T HuPedro PattynErica G BakkerJun CaoJan-Fang ChengRichard M ClarkNoah FahlgrenJeffrey FawcettJane GrimwoodHeidrun Gundlach et al.

A1 Journal Article in NATURE GENETICS

The Medicago genome provides insight into the evolution of rhizobial symbioses

Nevin D YoungFrédéric DebelléGiles ED OldroydRene GeurtsSteven B CannonMichael K UdvardiVagner A BeneditoKlaus FX MayerJérôme GouzyHeiko Schoof et al.

A1 Journal Article in NATURE

The genome of Tetranychus urticae reveals herbivorous pest adaptations

Miodrag GrbićThomas Van LeeuwenRichard M ClarkStephane RombautsPierre RouzéVojislava GrbićEdward J OsborneWannes DermauwThi Ngoc Phuong CaoFélix Ortego et al.

A1 Journal Article in NATURE

U-Compare bio-event meta-service : compatible BioNLP event extraction services

Yoshinobu KanoJari BjorneFilip GinterTapio SalakoskiEkaterina BuykoUdo HahnKevin CohenKarin VerspoorChristophe RoederLawrence Hunter et al.

A1 Journal Article in BMC BIOINFORMATICS

2010

2R or not 2R is not the question anymore

Yves Van de PeerSteven MaereAxel Meyer

A1 Journal Article in NATURE REVIEWS GENETICS

AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling

Hubert RehrauerCatherine AquinoWilhelm GruissemStefan R HenzPierre HilsonSascha LaubingerNaïra NaouarAndrea PatrignaniStephane RombautsHuan Shu et al.

A1 Journal Article in PLANT PHYSIOLOGY

Angiosperm polyploids and their road to evolutionary success

Jeffrey FawcettYves Van de Peer

A2 Journal Article in TRENDS IN EVOLUTIONARY BIOLOGY

Characterizing regulatory path motifs in integrated networks using perturbational data

Anagha JoshiThomas Van ParysYves Van de PeerTom Michoel

A1 Journal Article in GENOME BIOLOGY

Deciphering the evolution of plant genomes using a bioinformatics approach

Jeffrey FawcettYves Van de Peer

Discriminative and informative features for biomolecular text mining with ensemble feature selection

Sofie Van LandeghemThomas AbeelYvan SaeysYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Duplicate retention after small- and large-scale duplications

Steven MaereYves Van de Peer

Bookchapter in Evolution after gene duplication

Event based text mining for integrated network construction

Yvan SaeysSofie Van LandeghemYves Van de Peer

Gene and genome evolution in chromalveolate protists

Cindy MartensYves Van de Peer

Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling

Marie HuysmanCindy MartensKlaas VandepoeleJeroen GillardEdda RaykoMarc HeijdeChris BowlerDirk InzéYves Van de PeerLieven De Veylder et al.

A1 Journal Article in GENOME BIOLOGY

Highlights of the BioTM 2010 workshop on advances in bio text mining

Thomas AbeelSofie Van LandeghemRoser MoranteVincent Van AschYves Van de PeerWalter DaelemansYvan Saeys

Editorial material

In-silico prediction methods for genome annotation : promoter prediction, biomarker discovery and next-generation sequencing analysis

Thomas AbeelYves Van de PeerYvan Saeys

Integration of static relations to enhance event extraction from text

Sofie Van LandeghemSampo PyysaloTomoko OhtaYves Van de Peer

Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences

Guy BaeleYves Van de PeerStijn Vansteelandt

A1 Journal Article in BMC EVOLUTIONARY BIOLOGY

Module network inference from a cancer gene expression data set identifies microRNA regulated modules

Eric BonnetMarianthi TatariAnagha JoshiTom MichoelKathleen MarchalGeert BerxYves Van de Peer

A1 Journal Article in PLOS ONE

Posttranslational regulation impacts the fate of duplicated genes

Grigoris AmoutziasYing HeJonathan GordonDimitris MossialosStephen G OliverYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data

Eric BonnetTom MichoelYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods

Thomas AbeelThibault HelleputteYves Van de PeerPierre DupontYvan Saeys

A1 Journal Article in BIOINFORMATICS

Single-gene and whole-genome duplications and the evolution of protein-protein interaction networks

Grigoris AmoutziasYves Van de Peer

Bookchapter in Evolutionary genomics and systems biology

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

Eric BonnetYing HeKenny BilliauYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Jelle Van LeeneJens HollunderDominique EeckhoutGeert PersiauEveline Van De SlijkeHilde StalsGert Van IsterdaelAurine VerkestSandy NeirynckYelle Buffel et al.

A1 Journal Article in MOLECULAR SYSTEMS BIOLOGY

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

J Mark CockLieven SterckPierre RouzéDelphine ScornetAndrew E AllenGrigoris AmoutziasVéronique AnthouardFrançois ArtiguenaveJean-Marc AuryJonathan H Badger et al.

A1 Journal Article in NATURE

The genome of the domesticated apple (Malus x domestica Borkh.)

Riccardo VelascoAndrey ZharkikhJason AffourtitAmit DhingraAlessandro CestaroAnanth KalyanaramanPaolo FontanaSatish K BhatnagarMichela TroggioDmitry Pruss et al.

A1 Journal Article in NATURE GENETICS

The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection

Cindy MartensYves Van de Peer

A1 Journal Article in BMC GENOMICS

The potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

Animael Sanchez-RodriguezCindy MartensKristof EngelenYves Van de PeerKathleen Marchal

A1 Journal Article in BMC EVOLUTIONARY BIOLOGY

The role and implications of gene duplication events on vertebrate genome evolution

Tine BlommeYves Van de Peer

Towards system level modeling of functional modules and regulatory pathways using genome-scale data

Tom MichoelAnagha JoshiEric BonnetVanessa VermeirssenYves Van de Peer

Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences

Guy BaeleYves Van de PeerStijn Vansteelandt

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

2009

A snapshot of the emerging tomato genome sequence

Lukas MuellerRené Klein LankhorstSteven D TanksleyJames J GiovannoniRuth WhiteJulia VrebalovZhangjun FeiJoyce van EckRobert BuelsAdri A Mills et al.

A1 Journal Article in PLANT GENOME

Analyzing text in search of bio-molecular events: a high-precision machine learning framework

Sofie Van LandeghemYvan SaeysBernard De BaetsYves Van de Peer

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Tom MichoelRiet De SmetAnagha JoshiYves Van de PeerKathleen Marchal

A1 Journal Article in BMC Systems Biology

Computational analysis of regulatory networks using genome-scale data

Anagha JoshiYves Van de Peer

Computational approaches to unveiling ancient genome duplications

Yves Van de Peer

Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences

Guy BaeleYves Van de PeerStijn Vansteelandt

A1 Journal Article in BMC Evolutionary Biology

Evolution of multicellularity in the heterokont lineage : analysis of the Ectocarpus siliculosus genome sequence

J Mark CockDelphine ScornetAkira F PetersLieven SterckPierre RouzéYves Van de PeerJean WeissenbachPatrick Wincker

Genome sequence of the recombinant protein production host Pichia pastoris

Kristof De SchutterYao-Cheng LinPetra TielsAnnelies Van HeckeS GlinkaJ Weber-LehmannPierre RouzéYves Van de PeerNico Callewaert

A1 Journal Article in NATURE BIOTECHNOLOGY

Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

Simon DittamiDelphine ScornetJean-Louis PetitBéatrice SégurensCorinne Da SilvaErwan CorreMichael DondrupKarl-Heinz GlattingRainer KönigLieven Sterck et al.

A1 Journal Article in Genome Biology

Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas

Alexandra Z WordenJea-Hyeok LeeThomas MockPierre RouzéMelinda P SimmonsAndrea L AertsAndrew E AllenMarie L CuvelierEvelyne DerelleMeredith V Everett et al.

A1 Journal Article in SCIENCE

Java-ML: a machine learning library

Thomas AbeelYves Van de PeerYvan Saeys

A1 Journal Article in JOURNAL OF MACHINE LEARNING RESEARCH

Module networks revisited: computational assessment and prioritization of model predictions

Anagha JoshiRiet De SmetKathleen MarchalYves Van de PeerTom Michoel

A1 Journal Article in BIOINFORMATICS

On adaptive self-organization in artificial robot organisms

Serge KernbachHeiko HamannJürgen StradnerRonald TheniusThomas SchmicklKarl CrailsheimAnne C van RossumMichele SebagNicolas BredecheYao Yao et al.

Open-ended on-board evolutionary robotics for robot swarms

Guy BaeleNicolas BredecheEvert HaasdijkSteven MaereNico MichielsYves Van de PeerThomas SchmicklChristopher SchwarzerRonald Thenius

PLAZA : a comparative genomics resource to study gene and genome evolution in plants

Sebastian ProostMichiel Van BelLieven SterckKenny BilliauThomas Van ParysYves Van de PeerKlaas Vandepoele

A1 Journal Article in PLANT CELL

Phylogenetic inference based on distance methods : theory

Yves Van de Peer

Bookchapter in The phylogenetic handbook : a practical approach to phylogenetic analysis and hypothesis testing

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

Jeffrey FawcettSteven MaereYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

Stefanie De BodtSebastian ProostKlaas VandepoelePierre RouzéYves Van de Peer

A1 Journal Article in BMC Genomics

Reverse-engineering transcriptional modules from gene expression data

Tom MichoelRiet De SmetAnagha JoshiKathleen MarchalYves Van de Peer

A1 Journal Article in Annals of the New York Academy of Sciences

The evolutionary significance of ancient genome duplications

Yves Van de PeerSteven MaereAxel Meyer

A1 Journal Article in Nature Reviews Genetics

The flowering world: a tale of duplications

Yves Van de PeerJeffrey FawcettSebastian ProostLieven SterckKlaas Vandepoele

A1 Journal Article in TRENDS IN PLANT SCIENCE

Toward a gold standard for promoter prediction evaluation

Thomas AbeelYves Van de PeerYvan Saeys

A1 Journal Article in BIOINFORMATICS

Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development

Vanessa VermeirssenAnagha JoshiTom MichoelEric BonnetTine CasneufYves Van de Peer

A1 Journal Article in MOLECULAR BIOSYSTEMS

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

Klaas VandepoeleMauricio Quimbaya GomezTine CasneufLieven De VeylderYves Van de Peer

A1 Journal Article in Plant Physiology

Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus

Gwenael PiganeauKlaas VandepoeleSébastien GourbièreYves Van de PeerHervé Moreau

A1 Journal Article in Journal of Molecular Evolution

2008

A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences

Guy BaeleYves Van de PeerStijn Vansteelandt

A1 Journal Article in SYSTEMATIC BIOLOGY

A review of estimation of distribution algorithms in bioinformatics

Rubén ArmañanzasIñaki InzaRoberto SantanaYvan SaeysJose Luis FloresJose Antonio LozanoYves Van de PeerRosa BlancoVictor RoblesConcha Bielza et al.

A1 Journal Article in BIODATA MINING

Analysis of a Gibbs sampler method for model-based clustering of gene expression data

Anagha JoshiYves Van de PeerTom Michoel

A1 Journal Article in BIOINFORMATICS

Benchmarking machine learning techniques for the extraction of protein-protein interactions from text

Sofie Van LandeghemYvan SaeysYves Van de PeerBernard De Baets

Biological knowledge management and gene network analysis: a heuristic road to System Biology

Steven VercruysseYves Van de PeerMartin Kuiper

Choose your partners: dimerization in eukaryotic transcription factors

Grigoris AmoutziasDavid L RobertsonYves Van de PeerStephen G Oliver

A1 Journal Article in TRENDS IN BIOCHEMICAL SCIENCES

Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases

Grigoris AmoutziasYves Van de PeerDimitris Mossialos

A1 Journal Article in FUTURE MICROBIOLOGY

Extracting protein-protein interactions from text using rich feature vectors and feature selection

Sofie Van LandeghemYvan SaeysYves Van de PeerBernard De Baets

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA

Michiel Van BelYvan SaeysYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Generic eukaryotic core promoter prediction using structural features of DNA

Thomas AbeelYvan SaeysEric BonnetPierre RouzéYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Genome annotation in plants and fungi: EuGène as a model platform

Sylvain FoissacJérôme GouzyStephane RombautsCatherine MatheJoëlle AmselemLieven SterckYves Van de PeerPierre RouzéThomas Schiex

A1 Journal Article in CURRENT BIOINFORMATICS

Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis

Korneel VandenbrouckeSteven RobbensKlaas VandepoeleDirk InzéYves Van de PeerFrank Van Breusegem

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

MANTIS : a phylogenetic framework for multi-species genome comparisons

Athanasia C TzikaRaphaël HelaersYves Van de PeerMichel C Milinkovitch

A1 Journal Article in BIOINFORMATICS

Meta analysis of gene expression data within and across species

Ana Carolina FierroFilip VandenbusscheKristof EngelenYves Van de PeerKathleen Marchal

A1 Journal Article in CURRENT GENOMICS

Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis

Uwe JohnBánk BeszteriEvelyne DerelleYves Van de PeerBetsy ReadHervé MoreauAllan Cembella

A1 Journal Article in PROTIST

ProSOM: core promoter identification in the human genome

Thomas AbeelYvan SaeysYves Van de Peer

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

Thomas AbeelYvan SaeysPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Robust feature selection using ensemble feature selection techniques

Yvan SaeysThomas AbeelYves Van de Peer

The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae

Steven RobbensPierre RouzéJ Mark CockJürg SpringAlexandra Z WordenYves Van de Peer

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Chris BowlerAndrew E AllenJonathan H BadgerJane GrimwoodKamel JabbariAlan KuoUma MaheswariCindy MartensFlorian MaumusRobert P Otillar et al.

A1 Journal Article in NATURE

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

Stefan A RensingDaniel LangAndreas D ZimmerAstrid TerryAsaf SalamovHarris ShapiroTomoaki NishiyamaPierre-François PerroudErika A LindquistYasuko Kamisugi et al.

A1 Journal Article in SCIENCE

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

F MartinA AertsD AhrénA BrunEGJ DanchinF DuchaussoyJ GibonA KohlerE LindquistV Pereda et al.

A1 Journal Article in NATURE

Together we stand: genes cluster to coordinate regulation

Grigoris AmoutziasYves Van de Peer

Editorial material

Towards robust feature selection techniques

Yvan SaeysThomas AbeelYves Van de Peer

Unravelling the complexity of eukaryotic genomes through gene annotation and evolutionary analysis

Lieven SterckYves Van de Peer

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Cindy MartensKlaas VandepoeleYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles

Cedric SimillionKoen JanssensLieven SterckYves Van de Peer

A1 Journal Article in BIOINFORMATICS

2007

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

Riccardo VelascoAndrey ZharkikhMichela TroggioDustin A CartwrightAlessandro CestaroDmitry PrussMassimo PindoLisa M FitzGeraldSilvia VezzulliJulia Reid et al.

A1 Journal Article in PLOS ONE

An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens

Stefan A RensingJulia IckJeffrey FawcettDaniel LangAndreas ZimmerYves Van de PeerRalf Reski

A1 Journal Article in BMC EVOLUTIONARY BIOLOGY

Barely visible but highly unique : the Ostreococcus genome unveils its secrets

Steven RobbensYves Van de Peer

Canalization without flux sensors: a traveling-wave hypothesis

Roeland MerksYves Van de PeerDirk InzéGerrit Beemster

A1 Journal Article in TRENDS IN PLANT SCIENCE

Divergence of regulatory sequences in duplicated fish genes

R Van HellemontTine BlommeYves Van de PeerKathleen Marchal

Bookchapter in Gene and protein evolution

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

Jane M CarltonRobert P HirtJoana C SilvaArthur L DelcherMichael SchatzQi ZhaoJennifer R WortmanShelby L BidwellU Cecilia M AlsmarkSébastien Besteiro et al.

A1 Journal Article in SCIENCE

Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection

Yvan SaeysYves Van de Peer

How many genes are there in plants (... and why are they there)?

Lieven SterckStephane RombautsKlaas VandepoelePierre RouzéYves Van de Peer

A1 Journal Article in CURRENT OPINION IN PLANT BIOLOGY

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

Yvan SaeysPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation

Tineke CasneufYves Van de PeerWolfgang Huber

A1 Journal Article in BMC BIOINFORMATICS

Predicting human immunodeficiency virus (HIV) drug resistance using recurrent neural networks

Isis BonetMaria M GarcíaYvan SaeysYves Van de PeerRicardo Grau

The annotation and analysis of the genome of Arabidopsis lyrata

Jeffrey FawcettStephane RombautsPedro PattynLieven SterckYves Van de Peer

The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction

Steven RobbensEvelyne DerelleConchita FerrazJan WuytsHervé MoreauYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

The future for plants and plants for the future

Yves Van de Peer

Editorial material

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Brian PalenikJane GrimwoodAndrea AertsPierre RouzéAsaf SalamovNicholas PutnamChris DupontRichard JorgensenEvelyne DerelleStephane Rombauts et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The use of microarray technology to analyse the evolution and functional divergence of duplicated genes

Tineke CasneufYves Van de Peer

Translation initiation site prediction on a genomic scale : beauty in simplicity

Yvan SaeysThomas AbeelSven DegroeveYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus

Steven RobbensJörn PetersenHenner BrinkmannPierre RouzéYves Van de Peer

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Validating module network learning algorithms using simulated data

Tom MichoelSteven MaereEric BonnetAnagha JoshiYvan SaeysTim Van den BulckeKoenraad Van LeemputPiet Van RemortelMartin KuiperKathleen Marchal et al.

A1 Journal Article in BMC BIOINFORMATICS

2006

A Scalable Hardware Accelerator for Comparing Protein Sequences

Philippe FaesBram MinnaertM CHRISTIAENSEric BonnetYvan SaeysDirk StroobandtYves Van de Peer

An improved statistical method for detecting heterotachy in nucleotide sequences

Guy BaeleJeroen RaesYves Van de PeerStijn Vansteelandt

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Annual Machine Learning Conference of Belgium and The Netherlands

Combining signal processing and machine learning techniques for coding potential prediction

Yvan SaeysYves Van de Peer

Detecting the undetectabele : using genomic homology to uncover ancient genome duplications in plants

Cedric SimillionYves Van de Peer

Effect of gene and genome duplication on the development and evolution of angiosperms

Stefanie De BodtYves Van de Peer

Enhancing coding potential prediction for short sequences using complementary sequence features and feature selection

Yvan SaeysYves Van de Peer

Feature extraction using clustering of protein

Iris BonetYvan SaeysRicardo Grau ÁbaloMaria M GarcíaRobersy SanchezYves Van de Peer

A1 Journal Article in Lecture Notes in Computer Science

Feature ranking using an EDA-based wrapper approach

Yvan SaeysSven DegroeveYves Van de Peer

Bookchapter in Towards a new evolutionary computation : advances in estimation of distribution algorithms

Gene duplicates in vibrio genomes

Dirk GeversYves Van de Peer

Bookchapter in The biology of vibrios

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

Evelyne DerelleConchita FerrazStephane RombautsPierre RouzéAlexandra Z WordenSteven RobbensFrédéric PartenskySven DegroeveSophie EcheyniéRichard Cooke et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Helicoidal transfer matrix model for inhomogeneous DNA melting

Tom MichoelYves Van de Peer

A1 Journal Article in PHYSICAL REVIEW E

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

Klaas VandepoeleTineke CasneufYves Van de Peer

A1 Journal Article in GENOME BIOLOGY

Improved core promoter prediction using ensembles of Support Vector Machines

Thomas AbeelYvan SaeysYves Van de Peer

Inferring transcriptional networks by mining 'omics' data

Tim Van den BulckeKaren LemmensYves Van de PeerKathleen Marchal

A1 Journal Article in CURRENT BIOINFORMATICS

Large-scale in silico analysis of the RNA polymerase II promoter

Kobe FlorquinYves Van de Peer

Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

Steven B CannonLieven SterckStephane RombautsShusei SatoFoo CheungJérôme GouzyXiaohong WangJoann MudgeJayprakash VasdewaniThomas Schiex et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana

Tineke CasneufStefanie De BodtJeroen RaesSteven MaereYves Van de Peer

A1 Journal Article in GENOME BIOLOGY

Predicting human immunodeficiency virus (HIV) drug resistance using recurrent neural networks

Isis BonetMaria M GarcíaSain SalazarRobersy SanchezYvan SaeysYves Van de PeerRicardo Grau

Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting

Stefanie De BodtGuenter TheissenYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

The gain and loss of genes during 600 million years of vertebrate evolution

Tine BlommeKlaas VandepoeleStefanie De BodtCedric SimillionSteven MaereYves Van de Peer

A1 Journal Article in GENOME BIOLOGY

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

GA TuskanS DiFazioS JanssonJ BohlmannI GrigorievU HellstenN PutnamS RalphStephane RombautsA Salamov et al.

A1 Journal Article in SCIENCE

The small RNA world of plants

Eric BonnetYves Van de PeerPierre Rouzé

A1 Journal Article in NEW PHYTOLOGIST

When duplicated genes don't stick to the rules

Yves Van de Peer

Editorial material

2005

A novel approach to identifying regulatory motifs in distantly related genomes

Ruth Van HellemontPieter MonsieursGert ThijsBart De MoorYves Van de PeerKathleen Marchal

A1 Journal Article in GENOME BIOLOGY

Ancient duplication of cereal genomes

Andrew H PatersonJoch E BowersYves Van de PeerKlaas Vandepoele

Editorial material

Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in Blepharophimosis syndrome

Diane BeysenJeroen RaesBart LeroyA LucassenJRW YatesJ Clayton-SmithH IlyinaSS BrooksS Christin-MaitreMarc Fellous et al.

A1 Journal Article in AMERICAN JOURNAL OF HUMAN GENETICS

EST data suggest that poplar is an ancient polyploid

Lieven SterckStephane RombautsStefan JanssonFredrik SterkyPierre RouzéYves Van de Peer

A1 Journal Article in NEW PHYTOLOGIST

Exploring the plant transcriptome through phylogenetic profiling

Klaas VandepoeleYves Van de Peer

A1 Journal Article in PLANT PHYSIOLOGY

From 2R to 3R: evidence for a fish-specific genome duplication (FSGD)

Axel MeyerYves Van de Peer

A1 Journal Article in BIOESSAYS

Functional divergence of proteins through frameshift mutations

Jeroen RaesYves Van de Peer

A1 Journal Article in TRENDS IN GENETICS

Genome analysis of the world's smallest free-living eukaryote Ostreococcus tauri unveils unique genome heterogeneity

Steven RobbensStephane RombautsPierre RouzéJan WuytsYvan SaeysHervé MoreauYves Van de Peer

Genome duplication and the origin of angiosperms

Stefanie De BodtSteven MaereYves Van de Peer

Editorial material

Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri

Steven RobbensBasheer KhadarooAlain CamassesEvelyne DerelleConchita FerrazDirk InzéYves Van de PeerHervé Moreau

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide identification of potential plant E2F target genes

Klaas VandepoeleKobe VliegheKobe FlorquinLars HennigGerrit BeemsterWilhelm GruissemYves Van de PeerDirk InzéLieven De Veylder

A1 Journal Article in PLANT PHYSIOLOGY

Large-scale gene and ancient genome duplications

Yves Van de PeerAxel Meyer

Bookchapter in The evolution of the genome

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Kobe FlorquinYvan SaeysSven DegroevePierre RouzéYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Kobe FlorquinYvan SaeysSven DegroeveYves Van de Peer

Mode and tempo of gene and genome evolution in plants

Klaas VandepoeleYves Van de Peer

Modeling gene and genome duplications in eukaryotes

Steven MaereStefanie De BodtJeroen RaesTineke CasneufMarc Van MontaguMartin KuiperYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Re-evaluating prokaryotic species

Dirk GeversFrederick M CohanJeffrey G LawrenceBrian G SprattTom CoenyeEdward J FeilErko StackebrandtYves Van de PeerPeter VandammeFabiano L Thompson et al.

A1 Journal Article in NATURE REVIEWS MICROBIOLOGY

SpliceMachine: predicting splice sites from high-dimensional local context representations

Sven DegroeveYvan SaeysBernard De BaetsPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Towards a prokaryotic genomic taxonomy

Tom CoenyeDirk GeversYves Van de PeerPeter VandammeJean Swings

A1 Journal Article in FEMS MICROBIOLOGY REVIEWS

2004

'Horizontal' plant biology on the rise

Yves Van de Peer

Editorial material

Belo Horizonte virus: a vaccinia-like virus lacking the A-type inclusion body gene isolated from infected mice

Giliane S TrindadeFlávio G da FonsecaJoão T MarquesSueli DinizJuliana A LeiteStefanie De BodtYves Van de PeerCláudio A BonjardimPaulo CP FerreiraErna G Kroon

A1 Journal Article in JOURNAL OF GENERAL VIROLOGY

Building genomic profiles for uncovering segmental homology in the twilight zone

Cedric SimillionKlaas VandepoeleYvan SaeysYves Van de Peer

Building genomic profiles for uncovering segmental homology in the twilight zone

Cedric SimillionKlaas VandepoeleYvan SaeysYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Computational approaches to unveiling ancient genome duplications

Yves Van de Peer

A1 Journal Article in NATURE REVIEWS GENETICS

Design and evaluation of a linear classification strategy for gene structural element recognition

Sven DegroeveBernard, de BaetsYves Van de Peer

Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes

Eric BonnetJan WuytsPierre RouzéYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Digging into acceptor splice site prediction : an iterative feature selection approach

Yvan SaeysSven DegroeveYves Van de Peer

A1 Journal Article in LECTURE NOTES IN ARTIFICIAL INTELLIGENCE

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences

Eric BonnetJan WuytsPierre RouzéYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Feature selection for classification of nucleic acid sequences

Yvan SaeysYves Van de PeerDirk Aeyels

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Yvan SaeysSven DegroeveDirk AeyelsPierre RouzéYves Van de Peer

A1 Journal Article in BMC BIOINFORMATICS

Gene duplication and biased functional retention of paralogs in bacterial genomes

Dirk GeversKlaas VandepoeleCedric SimillionYves Van de Peer

A1 Journal Article in TRENDS IN MICROBIOLOGY

Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates

Klaas VandepoeleWouter De VosJohn S TaylorAxel MeyerYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent developments in computational approaches for uncovering genomic homology

Cedric SimillionKlaas VandepoeleYves Van de Peer

A1 Journal Article in BIOESSAYS

Selecting relevant features for gene structure prediction

Yvan SaeysSven DegroeveDirk AeyelsPierre RouzéYves Van de Peer

Splice site prediction in eukaryote genome sequences : the algorithmic issues

Sven DegroeveYvan SaeysBernard De BaetsYves Van de PeerPierre Rouzé

Bookchapter in The new avenues in bioinformatics

Tetraodon genome confirms Takifugu findings : most fish are ancient polyploids

Yves Van de Peer

A1 Journal Article in GENOME BIOLOGY

The 18S rRNA from Odontophrynus americanus 2n and 4n (Amphibia, Anura) reveals unusual extra sequences in the variable region V2

Lúcia E AlvaresJan WuytsYves Van de PeerEduardo P SilvaLuiz L CoutinhoOlivier BrisonItamar RG Ruiz

A1 Journal Article in GENOME

The European ribosomal RNA database

Jan WuytsGuy PerrièreYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The first green lineage cdc25 dual-specificity phosphatase

B KhadarooSteven RobbensC FerrazE DerelleS EycheniéR CookeG PeaucellierM DelsenyJ DemailleYves Van de Peer et al.

A1 Journal Article in CELL CYCLE

The quest for genomic homology

Klaas VandepoeleCedric SimillionYves Van de Peer

A2 Journal Article in CURRENT GENOMICS

The role of non-linear DNA structures in transcription

Kobe FlorquinSven DegroeveYvan SaeysYves Van de Peer

2003

'Natural selection merely modified while redundancy created': Susumu Ohno's idear of the evolutionary importance of gene and genome duplications

Axel MeyerYves Van de Peer

A2 Journal Article in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS

AFLPinSilico, simulating AFLP fingerprints

Stephane RombautsYves Van de PeerPierre Rouzé

A1 Journal Article in BIOINFORMATICS

Analysis of nucleotide sequences using TREECON

Yves Van de Peer

Bookchapter in The phylogenetic handbook : a practical approach to DNA and protein phylogeny

Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using Bayesian inference: implications for the origin of HIV-1

D ParaskevisP LemeyM SalemiM SuchardYves Van de PeerA-M Vandamme

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

And then there were many: MADS goes genomic

Stefanie De BodtJeroen RaesYves Van de PeerGünter Theißen

A1 Journal Article in TRENDS IN PLANT SCIENCE

Are all fishes ancient polyploids?

Yves Van de PeerJohn S TaylorAxel Meyer

Bookchapter in Genome evolution : gene and genome duplications and the origin of novel gene functions

Are all fishes ancient polyploids?

Yves Van de PeerJohn S TaylorAxel Meyer

A2 Journal Article in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS

Computational approaches to identify promoters and cis-regulatory elements in plant genomes

Stephane RombautsKobe FlorquinMagali LescotKathleen MarchalPierre RouzéYves Van de Peer

A1 Journal Article in PLANT PHYSIOLOGY

Evidence that rice and other cereals are ancient aneuploids

Klaas VandepoeleCedric SimillionYves Van de Peer

A1 Journal Article in PLANT CELL

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

A1 Journal Article in BIOINFORMATICS

Feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico

Jeroen RaesYves Van de Peer

A2 Journal Article in APPLIED BIOINFORMATICS

Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Functions

Genome duplication, a trait shared by 22,000 species of ray-finned fish

John S TaylorIngo BraaschTancred FrickeyAxel MeyerYves Van de Peer

A1 Journal Article in GENOME RESEARCH

Genome-wide characterization of the lignification toolbox in Arabidopsis

Jeroen RaesAntje RohdeJorgen ChristensenYves Van de PeerWout Boerjan

A1 Journal Article in PLANT PHYSIOLOGY

Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants

Stefanie De BodtJeroen RaesKobe FlorquinStephane RombautsPierre RouzéGünter TheißenYves Van de Peer

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Investigating ancient duplication events in the Arabidopsis genome

Jeroen RaesKlaas VandepoeleCedric SimillionYvan SaeysYves Van de Peer

Bookchapter in Genome evolution : gene and genome duplications and the origin of novel gene functions

Investigating ancient duplication events in the Arabidopsis genome

Jeroen RaesKlaas VandepoeleCedric SimillionYvan SaeysYves Van de Peer

A2 Journal Article in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS

Microarray analysis of E2Fa-DPa-overexpressing plants uncovers a cross-talking genetic network between DNA replication and nitrogen assimilation

Kobe VliegheMarnik VuylstekeKobe FlorquinStephane RombautsSara MaesSandra OrmenesePaul Van HummelenYves Van de PeerDirk InzéLieven De Veylder

A1 Journal Article in JOURNAL OF CELL SCIENCE

Phylogeny inference based on distance methods : theory

Yves Van de Peer

Bookchapter in The phylogenetic handbook : a practical approach to DNA and protein phylogeny

Power in numbers : in silico analysis of multigene families in Arabidopsis thaliana

Jeroen RaesYves Van de Peer

Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations

Michiel VandenbusscheGünter TheißenYves Van de PeerAntonius Gerats

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2002

Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes

Yves Van de PeerTancred FrickeyJohn S TaylorAxel Meyer

A1 Journal Article in GENE

Detecting microcolinearity between Arabidopsis and Rice

Klaas VandepoeleYvan SaeysCedric SimillionJ RAESYves Van de Peer

Detecting the undetectable : uncovering duplicated segments in Arabidopsis by comparison with rice.

Klaas VandepoeleCedric SimillionYves Van de Peer

A1 Journal Article in TRENDS IN GENETICS

Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA

Abdelghani Ben AliRaymond De BaereRupert De WachterYves Van de Peer

A1 Journal Article in PROTIST

Feature subset selection for splice site prediction

Sven DegroeveBernard De BaetsYves Van de PeerPierre Rouzé

A1 Journal Article in BIOINFORMATICS

Feature subset selection for splice site prediction by estimation of distribution algorithms

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

Moss transcriptome and beyond

Stefan A RensingStephane RombautsYves Van de PeerRalf Reski

Editorial material

Phylogenetic analyses suggest lateral gene transfer from the mitochondrion to the apicoplast

Miroslav OborníkYves Van de PeerVáclav HypšaTancredi FrickeyJan R ŠlapetaAxel MeyerJulius Lukeš

A1 Journal Article in GENE

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Magali LescotPatrice DehaisGert ThijsKathleen MarchalYves MoreauYves Van de PeerPierre RouzéStephane Rombauts

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Retrieving DNA sequence information from mass spectra of nucleic acids: application to the detection and identification of SNPs

Yvan SaeysDirk AeyelsPatrick StanssensYves Van de PeerMarc Zabeau

Selecting Relevant Features for Splice Site Prediction by Estimation of Distribution Algorithms.

Yvan SaeysSven DegroeveDirk AeyelsYves Van de PeerPierre Rouzé

The European database on small subunit ribosomal RNA

Jan WuytsYves Van de PeerTina WinkelmansRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The PlantCARE database and tools for in silico search of plant cis-acting regulatory elements

Stephane RombautsMagali LescotGert ThijsKathleen MarchalYves MoreauPatrice DehaisYves Van de PeerPierre Rouzé

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

Klaas VandepoeleYvan SaeysCedric SimillionJeroen RaesYves Van de Peer

A1 Journal Article in GENOME RESEARCH

The hidden duplication past of Arabidopsis thaliana

Cedric SimillionKlaas VandepoeleMarc Van MontaguMarc ZabeauYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wanda : a database of duplicated fish genes

Yves Van de PeerJohn S TaylorJayabalan JosephAxel Meyer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

zt : a sofware tool for simple and partial Mantel tests

Eric BonnetYves Van de Peer

A2 Journal Article in JOURNAL OF STATISTICAL SOFTWARE

2001

Comparative genomics provides evidence for an ancient genome duplication event in fish

John S TaylorYves Van de PeerIngo BraaschAxel Meyer

A1 Journal Article in PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA

Jan WuytsYves Van de PeerRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Genome duplication, divergent resolution and speciation

John S TaylorYves Van de PeerAxel Meyer

Phylogenetic relationships among algae based on complete large-subunit rRNA sequences

Abdelghani Ben AliRaymond De BaereGert Van der AuweraRupert De WachterYves Van de Peer

A1 Journal Article in INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Phylogeny branches out

Yves Van de Peer

Revisiting recent challenges to the ancient fish-specific genome duplication hypothesis

John S TaylorYves Van de PeerAxel Meyer

A1 Journal Article in CURRENT BIOLOGY

The European Large Subunit Ribosomal RNA database

Jan WuytsPeter De RijkYves Van de PeerTina WinkelmansRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes

Yves Van de PeerJohn S TaylorIngo BraaschAxel Meyer

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

2000

An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances

Yves Van de PeerSandra L BaldaufW Ford DoolittleAxel Meyer

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA

Jan WuytsPeter De RijkYves Van de PeerGreet PisonPeter RousseeuwRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

How molecules evolve in eubacteria

Peter J LockhartDaniel HusonUwe MaierMartin J FraunholzYves Van de PeerAdrian C BarbrookChristopher J HoweMike A Steel

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Microsporidia : accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi

Yves Van de PeerAbdelghani Ben AliAxel Meyer

A1 Journal Article in GENE

The European Large Subunit Ribosomal RNA database

Peter De RijkJan WuytsYves Van de PeerTina WinkelmansRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The European Small Subunit Ribosomal RNA database

Yves Van de PeerPeter De RijkJan WuytsTina WinkelmansRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

1999

Construction of a variability map for eukaryotic large subunit ribosomal RNA

Abdelghani Ben AliJan WuytsRupert De WachterAxel MeyerYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Database on the structure of large subunit ribosomal RNA

Peter De RijkElmar RobbrechtSybren de HoogAn CaersYves Van de PeerRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Database on the structure of small subunit ribosomal RNA

Yves Van de PeerElmar RobbrechtSybren de HoogAn CaersPeter De RijkRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

ForCon : a software tool for the conversion of sequence alignments

Jeroen RaesYves Van de Peer

A4 Journal Article in EMBNET NEWS

Molecular evolution and the incorporation of site-to-site rate variation in distance tree construction methods

Yves Van de Peer

A1 Journal Article in BELGIAN JOURNAL OF ZOOLOGY

Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae

Robert A AndersenYves Van de PeerDaniel PotterJulianne P SextonMasanobu KawachiTodd LaJeunesse

A1 Journal Article in PROTIST

The taxonomic position of Chlamydomyxa labyrinthuloides

Klaus WenderothJürgen MarquardtMartin FraunholzYves Van de PeerJürgen WastlUwe-G Maier

A1 Journal Article in EUROPEAN JOURNAL OF PHYCOLOGY

1998

Database on the structure of large ribosomal subunit RNA

Peter De RijkAn CaersYves Van de PeerRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Database on the structure of small ribosomal subunit RNA

Yves Van de PeerAn CaersPeter De RijkRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake

Gabriël ZwartRaymond HuismansMiranda P van AgterveldYves Van de PeerPeter De RijkHugo EenhoornGerard MuyzerErik J van HannenHerman J GonsHendrikus J Laanbroek

A1 Journal Article in FEMS MICROBIOLOGY ECOLOGY

Metazoan relationships on the basis of 18S rRNA sequences : a few years later...

Birgitta MH WinnepenninckxYves Van de PeerThierry Backeljau

A1 Journal Article in AMERICAN ZOOLOGIST

Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory disease in pigeons: taxonomic structure and phylogenetic allocation

Peter VandammePaul SegersM RyllJ HommezMarc VancanneytRenata CoopmanR De BaereYves Van de PeerKarel KerstersRupert De Wachter et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY

1997

Construction of evolutionary distance trees with TREECON for Windows : accounting for variation in nucleotide substitution rate among sites

Yves Van de PeerRupert De Wachter

A1 Journal Article in COMPUTER APPLICATIONS IN THE BIOSCIENCES

Database on the structure of large ribosomal subunit RNA

Peter De RijkYves Van de PeerRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Database on the structure of small ribosomal subunit RNA

Yves Van de PeerJan JansenPeter De RijkRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA

Yves Van de PeerRupert De Wachter

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Molecular phylogeny of the stress-70 protein family with reference to algal relationships

Stefan A RensingPeter ObrdlikNicole Rober-KleberSabine B MüllerCaudia JB HofmannYves Van de PeerUwe-G Maier

A1 Journal Article in EUROPEAN JOURNAL OF PHYCOLOGY

Phylogenetic analysis of a fish tapeworm, Proteocephalus exiguus, based on the small subunit rRNA gene

Ivica Král'ováYves Van de PeerMilan JirkůMarc Van RanstTomáš ScholzJullius Lukeš

A1 Journal Article in MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Secundary structure of the large ribosomal subunit RNA of the moss Funaria hygrometrica

Ingrid CapesiusYves Van de Peer

A1 Journal Article in JOURNAL OF PLANT PHYSIOLOGY

1996

18S Ribosomal RNA genes of insects : primary structure of the genes and molecular phylogeny of the Holometabola

Nicolas ChalwatzisJörg HaufYves Van de PeerRagnar KinzelbachFriedrich K Zimmermann

A1 Journal Article in ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA

A quantitative map of nucleotide substitution rates in bacterial rRNA

Yves Van de PeerSabine ChapelleRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Compilation of pseudomonad sequences present in a database on the structure of ribosomal RNA

Yves Van de PeerMarc VancanneytRupert De Wachter

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Database on the structure of large ribosomal subunit RNA

Peter De RijkYves Van de PeerRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Database on the structure of small ribosomal subunit RNA

Yves Van de PeerStefan NicolaïPeter De RijkRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships

Luc MoensJacques VanfleterenYves Van de PeerKris PeetersOscar KappJohn CzeluzniakMorris GoodmanMark BlaxterSerge Vinogradov

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis of the env gene of HIV-1 isolates taking into account individual nucleotide substitution rates

Yves Van de PeerWouter JanssensLleo HeyndrickxKatrien FransenGuido van der GroenRupert De Wachter

A1 Journal Article in AIDS

Substitution rate calibration of nucleotide sequence alignments and application to phylogenetic tree construction

Yves Van de PeerRupert De Wachter

A1 Journal Article in ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY

Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae

Yves Van de PeerStefan A RensingUwe-G MaierRupert De Wachter

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships

Edward RB MooreMargit MauAngelika ArnscheidtErik C BöttgerRoger A HutsonMatthew D CollinsYves Van de PeerRupert de WachterKenneth N Timmis

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

The evolution of stramenopiles and alveolates as derived by 'substitution rate calibration' of small ribosomal subunit RNA

Yves Van de PeerGert Van der AuweraRupert De Wachter

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

1995

An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences

Bart NelissenYves Van de PeerAnnick WilmotteRupert De Wachter

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

CARD : a drawing tool for RNA secondary structure models

Birgitta WinnepenninckxYves Van de PeerThierry BackeljauRupert De Wachter

A1 Journal Article in BIOTECHNIQUES

Evolution according to large ribosomal subunit RNA

Peter De RijkYves Van de PeerIlse Van den BroeckRupert De Wachter

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Investigation of fungal phylogeny on the basis of small ribosomal subunit RNA sequences

Yves Van de PeerRupert De Wachter

Bookchapter in Molecular microbial ecology manual

Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences

Gerhard HaaseL SonntagYves Van de PeerJaap MJ UijthofAndreas PodbielskiBeate Melzer-Krick

A1 Journal Article in ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides

Gert Van der AuweraRaymond De BaereYves Van de PeerPeter De RijkIlse Van den BroeckRupert De Wachter

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

1994

About the order of divergence of the major bacterial taxa during evolution

Yves Van de PeerJean-Marc NeefsPeter De RijkPaul De VosRupert De Wachter

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Database on the structure of large ribosomal subunit RNA

Peter De RijkYves Van de PeerSabine ChapelleRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Database on the structure of small ribosomal subunit RNA

Yves Van de PeerIlse Van den BroeckPeter De RijkRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Molecular genealogy of some nematode taxa as based on cytochrome c and globin amino acid sequences

Jacques VanfleterenYves Van de PeerMark L BlaxterSusan AR TweedieClive TrotmanLiu LuMarie-Louise Van HauwaertLuc Moens

A1 Journal Article in MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of part of the env gene of HIV-1 strains isolated in Côte d'Ivoire

Wouter JanssensLeo HeyndrickxYves Van de PeerAnne BouckaertKatrien FransenJan MotteGuy-Michel Gershy-DametMartine PeetersPeter PiotGuido van der Groen

A1 Journal Article in AIDS

TREECON for Windows : a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment

Yves Van de PeerRupert De Wachter

1993

Compilation of small ribosomal subunit RNA structures

Jean-Marc NeefsYves Van de PeerPeter De RijkSabine ChapelleRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences

Yves Van de PeerJean-Marc NeefsPeter De RijkRupert De Wachter

A1 Journal Article in BIOCHEMICAL SYSTEMATICS AND ECOLOGY

Evolutionary relationships among higher fungi inferred from small ribosomal subunit RNA sequence analysis

Annick WilmotteYves Van de PeerAnne GorisSabine ChapelleRaymond De BaereBart NelissenJean-Marc NeefsGrégoire L HennebertRupert De Wachter

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences : calibration of the molecular clock

Yves Van de PeerJean-Marc NeefsPeter De RijkRupert De Wachter

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Structure of 16S and 23S ribosomal RNA genes in Campylobacter species : phylogenetic analysis of the genus Campylobacter and presence of internal transcribed spacers

Guy Van CampYves Van de PeerStefan NicolaiJean-Marc NeefsPeter VandammeRupert De Wachter

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

TREECON : a software package for the construction and drawing of evolutionary trees

Yves Van de PeerRupert De Wachter

A1 Journal Article in COMPUTER APPLICATIONS IN THE BIOSCIENCES

1992

Compilation of small ribosomal subunit RNA sequences

Peter De RijkJean-Marc NeefsYves Van de PeerRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Evolution of basidiomycetous yeasts as deduced from small ribosomal subunit RNA sequences

Yves Van de PeerLydia HendriksAnne GorisJean-Marc NeefsMarc VancanneytKarel KerstersJean-François BernyGregoire L HennebertRupert De Wachter

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Phylogenetic relationships among ascomycetes and ascomycete-like yeasts as deduced from small ribosomal subunit RNA sequences

Lydia HendriksAnne GorisYves Van de PeerJean-Marc NeefsMarc VancanneytKarel KerstersJean-François BernyGregoire L HennebertRupert De Wachter

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

Phylogenetic study of cyanobacteria on the basis of 1S ribosomal RNA sequences

Bart NelissenAnnick WilmotteRaymond De BaereF HaesYves Van de PeerJean-Marc NeefsRupert De Wachter

A1 Journal Article in BELGIAN JOURNAL OF BOTANY

Ribosomal RNA as a tool for studying evolution

Yves Van de PeerJean-Marc NeefsPeter De RijkRaymond De BaereAnne GorisLydia HendriksRupert De Wachter

A1 Journal Article in BELGIAN JOURNAL OF BOTANY

Structure of the small ribosomal subunit RNA of the pulmonate snail, Lumicolaria kambeul, and phylogenetic analysis of the metazoa

Birgitta WinnepenninckxThierry BackeljauYves Van de PeerRupert De Wachter

A1 Journal Article in FEBS LETTERS

Study of invertebrate and plant globins : templates and evolutionary trees

Birgitta WinnepenninckxYves Van de PeerK PeetersRaymond De BaereLuc Moens

A1 Journal Article in BELGIAN JOURNAL OF BOTANY

Taxonomic study of marine oscillatoriacean strains (Cyanobacteria) with narrow trichomes, 2 : nucleotide sequence analysis of the 16S ribosomal RNA

Annick WilmotteSeán TurnerYves Van de PeerNorman R Pace

A1 Journal Article in JOURNAL OF PHYCOLOGY

The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron

Rupert De WachterJean-Marc NeefsAnne GorisYves Van de Peer

A1 Journal Article in NUCLEIC ACIDS RESEARCH

1991

Compilation of small ribosomal subunit RNA sequences

Jean-Marc NeefsYves Van de PeerPeter De RijkAnne GorisRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Phylogenetic analysis of five medically important Candida species as deduced on the basis of small ribosomal subunit RNA sequences

Lydia HendriksAnne GorisYves Van de PeerJean-Marc NeefsMarc VancanneytKarel KerstersGregoire L HennebertRupert De Wachter

A1 Journal Article in JOURNAL OF GENERAL MICROBIOLOGY

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

Lydia HendriksRaymond De BaereYves Van de PeerJean-Marc NeefsAnne GorisRupert De Wachter

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

1990

5S rRNA sequences of myxobacteria and radioresistant bacteria and implications for eubacterial evolution

Hilde Van den EyndeYves Van de PeerHilde VandenabeeleMark Van BogaertRupert De Wachter

A1 Journal Article in INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY

5S rRNA sequences of representatives of the genera Chlorobium, Prosthecochloris, Thermomicrobium, Cytophaga, Flavobacterium, Flexibacterium and Saprospira and a discussion of the evolution of eubacteria in general

Hilde Van den EyndeYves Van de PeerJerome PerryRupert De Wachter

A1 Journal Article in JOURNAL OF GENERAL MICROBIOLOGY

Compilation of small ribosomal subunit RNA sequences

Jean-Marc NeefsYves Van de PeerLydia HendriksRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Evolution of green plants and their relationship with other photosynthetic eukaryotes as deduced from 5S ribosomal RNA sequences

Yves Van de PeerRaymond De BaereJohan CauwenberghsRupert De Wachter

A1 Journal Article in PLANT SYSTEMATICS AND EVOLUTION

Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins

Yves Van de PeerJean-Marc NeefsRupert De Wachter

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin

Luc MoensMarie-Louise Van HauwaertKoen De SmetKris Ver DonckYves Van de PeerJozef Van BeeumenShoshana WodakPhilippe AlardClive Trotman

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

The 18S ribosomal RNA sequence of the sea anemone Anemonia sulcata and its evolutionary position among other eukaryotes

Lydia HendriksYves Van de PeerMartine Van HerckJean-Marc NeefsRupert De Wachter

A1 Journal Article in FEBS LETTERS

1989

5S Ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium : evolutionary relationships within these genera and among eubacteria in general

Hilde Van den EyndeRaymond De BaereHaroun N ShahSaheer E GharbiaGeorge E FoxJoanna MichalikYves Van de PeerRupert De Wachter

A1 Journal Article in INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY

The nucleotide sequence of the small ribosomal subunit RNA of the yeast Candida albicans and the evolutionary position of the fungi among the Eukaryotes

Lydia HendriksAnne GorisJean-Marc NeefsYves Van de PeerGrégoire HennebertRupert De Wachter

A1 Journal Article in SYSTEMATIC AND APPLIED MICROBIOLOGY

1988

Compilation of small ribosomal subunit RNA sequences

Erna DamsLydia HendriksYves Van de PeerJean-Marc NeefsGeert SmitsIsidore VandenbemptRupert De Wachter

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Inferring eubacterial phylogeny from 5S ribosomal RNA structure analysis

Hilde Van den EyndeYves Van de PeerRupert De Wachter

Bookchapter in Green photosynthetic bacteria

Primary and secondary structure of the 18S ribosomal RNA of the bird spider Eurypelma californica and evolutionary relationships among eukaryotic phyla

Lydia HendriksChristine Van BroeckhovenAntoon VandenbergheYves Van de PeerRupert De Wachter

A1 Journal Article in EUROPEAN JOURNAL OF BIOCHEMISTRY

The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast : implications for the evolution of plastids and cyanobacteria

Hilde Van den EyndeRaymond De BaereEls De RoeckYves Van de PeerAntoon VandenberghePeter WillekensRupert De Wachter

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

The sequence of 5-S rRNA of Deinococcus radiodurans and the evolutionary position of the radioresistant bacteria

Hilde VandenabeeleHilde Van den EyndeYves Van de PeerRupert De Wachter