Research Explorer

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Project

BOF-ZAP-Professorship in phylogeny and comparative analysis

Outputs & Impact

Publications & research data ( 54 )

Bryophytes hold a larger gene family space than vascular plants

Shanshan DongSibo WangLinzhou LiJin YuYongxia ZhangJia-Yu XueHengchi ChenJianchao MaYuying ZengYuqing Cai et al.

A1 Journal Article in NATURE GENETICS

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes

Fabricio De Almeida SilvaYves Van de Peer

A1 Journal Article in PLANT CELL

Rapid establishment of species barriers in plants compared with that in animals

François MonnetZoé PostelPascal TouzetChristelle FraïsseYves Van de PeerXavier VekemansCamille Roux

A1 Journal Article in SCIENCE

Comprehensive sampling from mitochondrial genomes substantiates the Neoproterozoic origin of land plants

Shuaiya HuGongle ShiCheng-Ao YangYves Van de PeerZhen LiJia-Yu Xue

A1 Journal Article in PLANT COMMUNICATIONS

Genome analyses provide insights into Engelhardia’s adaptation to East Asia summer monsoon

Min LiJing-Jing WuRen-Ping SuOu-Yan FangXiang CaiPei-Han HuangXiao-Yang GaoXin-Xing FuXiao-Hui MaLin-Yue He et al.

A1 Journal Article in PLANT DIVERSITY

Polyploid-diploid coexistence in the greater duckweed Spirodela polyrhiza

Frederik MortierYves Van de PeerDries Bonte

A1 Journal Article in JOURNAL OF ECOLOGY

Subgenome partitioning and polyploid genome evolution in the loach family Botiidae (order Cypriniformes)

Yunyun LvJia LiYanping LiYu HuangQiang LaiZhengyong WenJun WangYang HeJinrong ShiZejin Huang et al.

A1 Journal Article in ADVANCED SCIENCE

The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms

Ewout CrombezYves Van de PeerZhen Li

A1 Journal Article in NATURE COMMUNICATIONS

A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava

Luc CornetSyed Shan-e-Ali ZaidiJia LiYvan NgapoutSara ShakirLoic MeunierCaroline CallotWilliam MarandeMarc HanikenneStephane Rombauts et al.

A1 Journal Article in GENOME BIOLOGY

Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

Antoine Van de VloetLucas Prost BoxoenQuinten BafortYunn Thet PaingGriet CasteleynLucile JomatStéphane D. LemaireOlivier De ClerckYves Van de Peer

A1 Journal Article in NEW PHYTOLOGIST

Flavonoids and anthocyanins in seagrasses : implications for climate change adaptation and resilience

Jana BotesXiao MaJiyang ChangYves Van de PeerDave Kenneth Berger

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

doubletrouble : an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

Fabricio De Almeida SilvaYves Van de Peer

A1 Journal Article in BIOINFORMATICS

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

Si‐Jie LiuZhengtai LiuBing‐Yan ShaoTao LiXinning ZhuRen WangLei ShiSheng XuYves Van de PeerJia‐Yu Xue

A1 Journal Article in PLANT JOURNAL

Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Lucas ProstQuinten BafortAntoine Van de VloetFabricio De Almeida SilvaYunn Thet PaingGriet CasteleynSofie D'hondtOlivier De ClerckYves Van de Peer

A1 Journal Article in NEW PHYTOLOGIST

The immediate metabolomic effects of whole‐genome duplication in the greater duckweed, Spirodela polyrhiza

Tian WuQuinten BafortFrederik MortierFabricio De Almeida SilvaAnnelore NatranYves Van de Peer

A1 Journal Article in AMERICAN JOURNAL OF BOTANY

A metabolic perspective on polyploid invasion and the emergence of life histories : insights from a mechanistic model

Silvija MilosavljevićFelipe Kauai PereiraFrederik MortierYves Van de PeerDries Bonte

A1 Journal Article in AMERICAN JOURNAL OF BOTANY

Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms

Tao ShiZhiyan GaoJinming ChenYves Van de Peer

A1 Journal Article in PLANT CELL

Hybridexpress : an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Fabricio De Almeida SilvaLucas Prost BoxoenYves Van de Peer

A1 Journal Article in NEW PHYTOLOGIST

Interspecific transfer of genetic information through polyploid bridges

Felipe Kauai PereiraQuinten BafortFrederik MortierMarc Van MontaguDries BonteYves Van de Peer

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

wgd v2 : a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Hengchi ChenArthur ZwaenepoelYves Van de Peer

A1 Journal Article in BIOINFORMATICS

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Jarkko SalojärviAditi RambaniZhe YuRomain GuyotSusan StricklerMaud LepelleyCui WangSitaram RajaramanPasi RastasChunfang Zheng et al.

A1 Journal Article in NATURE GENETICS

Convergent and/or parallel evolution of RNA‐binding proteins in angiosperms after polyploidization

Liangyu GuoShuo WangXi JiaoXiaoxue YeDeyin DengHua LiuYan LiYves Van de PeerWenwu Wu

A1 Journal Article in NEW PHYTOLOGIST

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Xiao MaSteffen VannesteJiyang ChangLuca AmbrosinoKerrie BarryTill BayerAlexander A. BobrovLoriBeth BostonJustin E. CampbellHengchi Chen et al.

A1 Journal Article in NATURE PLANTS

Understanding polyploid establishment : temporary persistence or stable coexistence?

Frederik MortierQuinten BafortSilvija MilosavljevićFelipe Kauai PereiraLucas ProstYves Van de PeerDries Bonte

A1 Journal Article in OIKOS

Origin and evolution of the triploid cultivated banana genome

Xiuxiu LiSheng YuZhihao ChengXiaojun ChangYingzi YunMengwei JiangXuequn ChenXiaohui WenHua LiWenjun Zhu et al.

A1 Journal Article in NATURE GENETICS

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Jarkko SalojärviAditi RambaniZhe YuRomain GuyotSusan StricklerMaud LepelleyCui WangSitaram RajaramanPasi RastasChunfang Zheng et al.

Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package

Fabricio De Almeida SilvaYves Van de Peer

A1 Journal Article in METHODS IN ECOLOGY AND EVOLUTION

The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil

Mehrshad EbadiQuinten BafortEshchar MizrachiP. AudenaertPieter SimoensMarc Van MontaguDries BonteYves Van de Peer

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

Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of microTom tomato

Jia-Yu XueHai-Yun FanZhen ZengYu-Han ZhouShuai-Ya HuSai-Xi LiYing-Juan ChengXiang-Ru MengFei ChenZhu-Qing Shao et al.

A1 Journal Article in HORTICULTURE RESEARCH

Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms

Fabricio De Almeida SilvaYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Diploid and tetraploid genomes of Acorus and the evolution of monocots

Liang MaKe-Wei LiuZhen LiYu-Yun HsiaoYiying QiTao FuGuang-Da TangDiyang ZhangWei-Hong SunDing-Kun Liu et al.

A1 Journal Article in NATURE COMMUNICATIONS

Genomic insights into adaptation to karst limestone and incipient speciation in East Asian Platycarya spp. (Juglandaceae)

Yu CaoFabricio De Almeida SilvaWei-Ping ZhangYa-Mei DingDan BaiWei-Ning BaiBo-Wen ZhangYves Van de PeerDa-Yong Zhang

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

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.

A1 Journal Article in NATURE COMMUNICATIONS

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

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

Quinten BafortTian WuAnnelore NatranOlivier De ClerckYves Van de Peer

A1 Journal Article in EVOLUTION LETTERS

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

Inference of ancient polyploidy using transcriptome data

Jia LiYves Van de PeerZhen Li

Bookchapter in Polyploidy : methods and protocols

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

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

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

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

Revisiting ancient polyploidy in leptosporangiate ferns

Hengchi ChenYuhan FangArthur ZwaenepoelSanwen HuangYves Van de PeerZhen Li

A1 Journal Article in NEW PHYTOLOGIST

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

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

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

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

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

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

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

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

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

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

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

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