Works matching AU Van de Peer, Yves

Results: 258

Opinion: Re-evaluating prokaryotic species.

Published in:

Nature Reviews Microbiology, 2005, v. 3, n. 9, p. 733, doi. 10.1038/nrmicro1236

By:

Gevers, Dirk;
Cohan, Frederick M.;
Lawrence, Jeffrey G.;
Spratt, Brian G.;
Coenye, Tom;
Feil, Edward J.;
Stackebrandt, Erko;
Van de Peer, Yves;
Vandamme, Peter;
Thompson, Fabiano L.;
Swings, Jean

Publication type:

Article

OMSim: a simulator for optical map data.

Published in:

Bioinformatics, 2017, v. 33, n. 17, p. 2740, doi. 10.1093/bioinformatics/btx293

By:

Miclotte, Giles;
Audenaert, Pieter;
Fostier, Jan;
Rombauts, Stephane;
de Peer, Yves Van;
Plaisance, Stéphane

Publication type:

Article

A Cytoscape app for motif enumeration with ISMAGS.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 461, doi. 10.1093/bioinformatics/btw626

By:

Van Parys, Thomas;
Melckenbeeck, Ine;
Houbraken, Maarten;
Audenaert, Pieter;
Colle, Didier;
Pickavet, Mario;
Demeester, Piet;
de Peer, Yves Van

Publication type:

Article

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

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 276, doi. 10.1093/bioinformatics/btv570

By:

Kaewphan, Suwisa;
Van Landeghem, Sofie;
Ohta, Tomoko;
Van de Peer, Yves;
Ginter, Filip;
Pyysalo, Sampo

Publication type:

Article

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

Published in:

Bioinformatics, 2014, v. 30, n. 21, p. 3086, doi. 10.1093/bioinformatics/btu481

By:

Mushthofa, Mushthofa;
Torres, Gustavo;
Van de Peer, Yves;
Marchal, Kathleen;
De Cock, Martine

Publication type:

Article

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

Published in:

Bioinformatics, 2011, v. 27, n. 11, p. 1587, doi. 10.1093/bioinformatics/btr182

By:

Audenaert, Pieter;
Van Parys, Thomas;
Brondel, Florian;
Pickavet, Mario;
Demeester, Piet;
Van de Peer, Yves;
Michoel, Tom

Publication type:

Article

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

Published in:

Bioinformatics, 2011, v. 27, n. 6, p. 749, doi. 10.1093/bioinformatics/btr008

By:

Fostier, Jan;
Proost, Sebastian;
Dhoedt, Bart;
Saeys, Yvan;
Demeester, Piet;
Van de Peer, Yves;
Vandepoele, Klaas

Publication type:

Article

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

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. i638, doi. 10.1093/bioinformatics/btq395

By:

Bonnet, Eric;
Michoel, Tom;
Van de Peer, Yves

Publication type:

Article

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

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. i554, doi. 10.1093/bioinformatics/btq381

By:

Van Landeghem, Sofie;
Abeel, Thomas;
Saeys, Yvan;
Van de Peer, Yves

Publication type:

Article

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

Published in:

Bioinformatics, 2010, v. 26, n. 12, p. 1566, doi. 10.1093/bioinformatics/btq233

By:

Bonnet, Eric;
Ying He;
Billiau, Kenny;
Van De Peer, Yves

Publication type:

Article

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods.

Published in:

Bioinformatics, 2010, v. 26, n. 3, p. 392, doi. 10.1093/bioinformatics/btp630

By:

Abeel, Thomas;
Helleputte, Thibault;
Van De Peer, Yves;
Dupont, Pierre;
Saeys, Yvan

Publication type:

Article

Toward a gold standard for promoter prediction evaluation.

Published in:

Bioinformatics, 2009, v. 25, n. 12, p. i313, doi. 10.1093/bioinformatics/btp191

By:

Thomas Abeel;
Yves Van de Peer;
Yvan Saeys

Publication type:

Article

Module networks revisited: computational assessment and prioritization of model predictions.

Published in:

Bioinformatics, 2009, v. 25, n. 4, p. 490, doi. 10.1093/bioinformatics/btn658

By:

Anagha Joshi;
Riet De Smet;
Kathleen Marchal;
Yves Van de Peer;
Tom Michoel

Publication type:

Article

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

Published in:

Bioinformatics, 2008, v. 24, n. 13, p. i24, doi. 10.1093/bioinformatics/btn172

By:

Thomas Abeel;
Yvan Saeys;
Pierre Rouzé;
Yves Van de Peer

Publication type:

Article

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

Published in:

Bioinformatics, 2008, v. 24, n. 13, p. 1532, doi. 10.1093/bioinformatics/btn225

By:

Michiel Van Bel;
Yvan Saeys;
Yves Van de Peer

Publication type:

Article

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

Published in:

Bioinformatics, 2008, v. 24, n. 2, p. 176, doi. 10.1093/bioinformatics/btm562

By:

Anagha Joshi;
Yves Van de Peer;
Tom Michoel

Publication type:

Article

MANTIS: a phylogenetic framework for multi-species genome comparisons.

Published in:

Bioinformatics, 2008, v. 24, n. 2, p. 151, doi. 10.1093/bioinformatics/btm567

By:

Athanasia C. Tzika;
RaphaÃ«l Helaers;
Yves Van de Peer;
Michel C. Milinkovitch

Publication type:

Article

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

Published in:

Bioinformatics, 2008, v. 24, n. 1, p. 127, doi. 10.1093/bioinformatics/btm449

By:

Cedric Simillion;
Koen Janssens;
Lieven Sterck;
Yves Van de Peer

Publication type:

Article

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

Published in:

Bioinformatics, 2007, v. 23, n. 13, p. i418, doi. 10.1093/bioinformatics/btm177

By:

Yvan Saeys;
Thomas Abeel;
Sven Degroeve;
Yves Van de Peer

Publication type:

Article

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

Published in:

Bioinformatics, 2007, v. 23, n. 4, p. 414

By:

Pierre Rouzé;
Yves Van de Peer

Publication type:

Article

Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production.

Published in:

Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02697-8

By:

Song, Chi;
Fu, Fangfang;
Yang, Lulu;
Niu, Yan;
Tian, Zhaoyang;
He, Xiangxiang;
Yang, Xiaoming;
Chen, Jie;
Sun, Wei;
Wan, Tao;
Zhang, Han;
Yang, Yicheng;
Xiao, Tian;
Dossa, Komivi;
Meng, Xiangxiao;
Cao, Fuliang;
Van de Peer, Yves;
Wang, Guibin;
Chen, Shilin

Publication type:

Article

Erratum to: Polyploidy: an evolutionary and ecological force in stressful times.

Published in:

Plant Cell, 2021, v. 33, n. 8, p. 2899, doi. 10.1093/plcell/koab149

By:

Peer, Yves Van de;
Ashman, Tia-Lynn;
Soltis, Pamela S.;
Soltis, Douglas E.

Publication type:

Article

Polyploidy: an evolutionary and ecological force in stressful times.

Published in:

Plant Cell, 2021, v. 33, n. 1, p. 11, doi. 10.1093/plcell/koaa015

By:

Peer, Yves Van de;
Ashman, Tia-Lynn;
Soltis, Pamela S;
Soltis, Douglas E

Publication type:

Article

Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana.

Published in:

Plant Cell, 2017, v. 29, n. 11, p. 2786, doi. 10.1105/tpc.17.00531

By:

Smet, Riet De;
Sabaghian, Ehsan;
Li, Zhen;
Saeys, Yvan;
Peer, Yves Van de

Publication type:

Article

Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance Sensitivity.

Published in:

Plant Cell, 2017, v. 29, n. 11, p. 2766, doi. 10.1105/tpc.17.00313

By:

Tasdighian, Setareh;
Bel, Michiel Van;
Li, Zhen;
Peer, Yves Van de;
Carretero-Paulet, Lorenzo;
Maere, Steven

Publication type:

Article

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.

Published in:

Plant Cell, 2016, v. 28, n. 2, p. 326, doi. 10.1105/tpc.15.00877

By:

Li, Zhen;
Defoort, Jonas;
Tasdighian, Setareh;
Maere, Steven;
Peer, Yves Van de;
Smet, Riet De

Publication type:

Article

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.

Published in:

Plant Cell, 2015, v. 27, n. 6, p. 1595, doi. 10.1105/tpc.114.135848

By:

Zhang, Zhonghua;
Mao, Linyong;
Chen, Huiming;
Bu, Fengjiao;
Li, Guangcun;
Sun, Jinjing;
Li, Shuai;
Sun, Honghe;
Jiao, Chen;
Blakely, Rachel;
Pan, Junsong;
Cai, Run;
Luo, Ruibang;
Peer, Yves Van de;
Jacobsen, Evert;
Fei, Zhangjun;
Huang, Sanwen

Publication type:

Article

Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum.

Published in:

Plant Cell, 2015, v. 27, n. 6, p. 1567, doi. 10.1105/tpc.15.00157

By:

Vanneste, Kevin;
Sterck, Lieven;
Myburg, Alexander Andrew;
Peer, Yves Van de;
Mizrachi, Eshchar

Publication type:

Article

Arabidopsis Ensemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress.

Published in:

Plant Cell, 2014, v. 26, n. 12, p. 4656, doi. 10.1105/tpc.114.131417

By:

Vermeirssen, Vanessa;
Clercq, Inge De;
Parys, Thomas Van;
Breusegem, Frank Van;
Peer, Yves Van de

Publication type:

Article

Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks.

Published in:

Plant Cell, 2014, v. 26, n. 3, p. 929, doi. 10.1105/tpc.113.122242

By:

Morreel, Kris;
Saeys, Yvan;
Dima, Oana;
Lu, Fachuang;
Peer, Yves Van de;
Vanholme, Ruben;
Ralph, John;
Vanholme, Bartel;
Boerjan, Wout

Publication type:

Article

Membrane-Bound NAC Transcription Factor ANAC013 Functions in Mitochondrial Retrograde Regulation of the Oxidative Stress Response in Arabidopsis.

Published in:

Plant Cell, 2013, v. 25, n. 9, p. 3472, doi. 10.1105/tpc.113.117168

By:

Clercq, Inge De;
Vermeirssen, Vanessa;
Aken, Olivier Van;
Vandepoele, Klaas;
Murcha, Monika W.;
Law, Simon R.;
Inzé, Annelies;
Ng, Sophia;
Ivanova, Aneta;
Rombaut, Debbie;
van de Cotte, Brigitte;
Jaspers, Pinja;
Peer, Yves Van de;
Kangasjärvi, Jaakko;
Whelan, James;
Breusegem, Frank Van

Publication type:

Article

Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis.

Published in:

Plant Cell, 2013, v. 25, n. 3, p. 794, doi. 10.1105/tpc.112.108753

By:

Landeghem, Sofie Van;
Bodt, Stefanie De;
Drebert, Zuzanna J.;
Inzé, Dirk;
Peer, Yves Van de

Publication type:

Article

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants.

Published in:

Plant Cell, 2009, v. 21, n. 12, p. 3718, doi. 10.1105/tpc.109.071506

By:

Proost, Sebastian;
Bel, Michiel Van;
Sterck, Lieven;
Billiau, Kenny;
Parys, Thomas Van;
Peer, Yves Van de;
Vandepoele, Klaas

Publication type:

Article

Evolution of NLR Resistance Genes in Magnoliids: Dramatic Expansions of CNLs and Multiple Losses of TNLs.

Published in:

Frontiers in Plant Science, 2021, v. 12, p. 1, doi. 10.3389/fpls.2021.777157

By:

Wu, Jia-Yi;
Xue, Jia-Yu;
Van de Peer, Yves

Publication type:

Article

Genomic Resources to Guide Improvement of the Shea Tree.

Published in:

Frontiers in Plant Science, 2021, v. 12, p. 1, doi. 10.3389/fpls.2021.720670

By:

Hale, Iago;
Ma, Xiao;
Melo, Arthur T. O.;
Padi, Francis Kwame;
Hendre, Prasad S.;
Kingan, Sarah B.;
Sullivan, Shawn T.;
Chen, Shiyu;
Boffa, Jean-Marc;
Muchugi, Alice;
Danquah, Agyemang;
Barnor, Michael Teye;
Jamnadass, Ramni;
Van de Peer, Yves;
Van Deynze, Allen

Publication type:

Article

Insights Into the Mechanisms Implicated in Pinus pinaster Resistance to Pinewood Nematode.

Published in:

Frontiers in Plant Science, 2021, v. 12, p. 1, doi. 10.3389/fpls.2021.690857

By:

Modesto, Inês;
Sterck, Lieven;
Arbona, Vicent;
Gómez-Cadenas, Aurelio;
Carrasquinho, Isabel;
Van de Peer, Yves;
Miguel, Célia M.

Publication type:

Article

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris.

Published in:

Plant Journal, 2025, v. 121, n. 2, p. 1, doi. 10.1111/tpj.17220

By:

Liu, Si‐Jie;
Liu, Zhengtai;
Shao, Bing‐Yan;
Li, Tao;
Zhu, Xinning;
Wang, Ren;
Shi, Lei;
Xu, Sheng;
Van de Peer, Yves;
Xue, Jia‐Yu

Publication type:

Article

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris.

Published in:

Plant Journal, 2025, v. 121, n. 1, p. 1, doi. 10.1111/tpj.17220

By:

Liu, Si‐Jie;
Liu, Zhengtai;
Shao, Bing‐Yan;
Li, Tao;
Zhu, Xinning;
Wang, Ren;
Shi, Lei;
Xu, Sheng;
Van de Peer, Yves;
Xue, Jia‐Yu

Publication type:

Article

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

Published in:

Plant Journal, 2023, v. 113, n. 5, p. 1021, doi. 10.1111/tpj.16097

By:

Xue, Jia‐Yu;
Li, Zhen;
Hu, Shuai‐Ya;
Kao, Shu‐Min;
Zhao, Tao;
Wang, Jie‐Yu;
Wang, Yue;
Chen, Min;
Qiu, Yichun;
Fan, Hai‐Yun;
Liu, Yang;
Shao, Zhu‐Qing;
Van de Peer, Yves

Publication type:

Article

The genome of the king protea, Protea cynaroides.

Published in:

Plant Journal, 2023, v. 113, n. 2, p. 262, doi. 10.1111/tpj.16044

By:

Chang, Jiyang;
Duong, Tuan A.;
Schoeman, Cassandra;
Ma, Xiao;
Roodt, Danielle;
Barker, Nigel;
Li, Zhen;
Van de Peer, Yves;
Mizrachi, Eshchar

Publication type:

Article

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

Published in:

Plant Journal, 2022, v. 112, n. 3, p. 830, doi. 10.1111/tpj.15984

By:

Zhang, Yue;
Yang, Xingyu;
Van de Peer, Yves;
Chen, Jinming;
Marchal, Kathleen;
Shi, Tao

Publication type:

Article

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

Published in:

Plant Journal, 2022, v. 111, n. 1, p. 217, doi. 10.1111/tpj.15788

By:

Xu, Zhichao;
Li, Zhen;
Ren, Fengming;
Gao, Ranran;
Wang, Zhe;
Zhang, Jinlan;
Zhao, Tao;
Ma, Xiao;
Pu, Xiangdong;
Xin, Tianyi;
Rombauts, Stephane;
Sun, Wei;
Van de Peer, Yves;
Chen, Shilin;
Song, Jingyuan

Publication type:

Article

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

Published in:

Plant Journal, 2022, v. 110, n. 1, p. 129, doi. 10.1111/tpj.15660

By:

Xu, Hui;
Li, Zhen;
Jiang, Peng‐Fei;
Zhao, Li;
Qu, Chang;
Van de Peer, Yves;
Liu, Yan‐Jing;
Zeng, Qing‐Yin

Publication type:

Article

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.

Published in:

Plant Journal, 2021, v. 107, n. 2, p. 613, doi. 10.1111/tpj.15298

By:

Ma, Xiao;
Vaistij, Fabián E.;
Li, Yi;
Jansen van Rensburg, Willem S.;
Harvey, Sarah;
Bairu, Michael W.;
Venter, Sonja L.;
Mavengahama, Sydney;
Ning, Zemin;
Graham, Ian A.;
Van Deynze, Allen;
Van de Peer, Yves;
Denby, Katherine J.

Publication type:

Article

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

Published in:

Plant Journal, 2021, v. 105, n. 4, p. 1072, doi. 10.1111/tpj.15088

By:

Liu, Hui;
Lyu, Hai‐Meng;
Zhu, Kaikai;
Van de Peer, Yves;
(Max) Cheng, Zong‐Ming

Publication type:

Article

The ‘TranSeq’ 3′‐end sequencing method for high‐throughput transcriptomics and gene space refinement in plant genomes.

Published in:

Plant Journal, 2018, v. 96, n. 1, p. 223, doi. 10.1111/tpj.14015

By:

Tzfadia, Oren;
Bocobza, Samuel;
Defoort, Jonas;
Almekias‐Siegl, Efrat;
Panda, Sayantan;
Levy, Matan;
Storme, Veronique;
Rombauts, Stephane;
Jaitin, Diego Adhemar;
Keren‐Shaul, Hadas;
Van de Peer, Yves;
Aharoni, Asaph

Publication type:

Article

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

Published in:

Journal of Experimental Botany, 2015, v. 66, n. 17, p. 5257, doi. 10.1093/jxb/erv346

By:

Ghorbani, Sarieh;
Yao-Cheng Lin;
Parizot, Boris;
Fernandez, Ana;
Njo, Maria Fransiska;
de Peer, Yves Van;
Beeckman, Tom;
Hilson, Pierre

Publication type:

Article

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

Published in:

Journal of Experimental Botany, 2014, v. 65, n. 17, p. 4731, doi. 10.1093/jxb/eru233

By:

Pajoro, Alice;
Biewers, Sandra;
Dougali, Evangelia;
Leal Valentim, Felipe;
Mendes, Marta Adelina;
Porri, Aimone;
Coupland, George;
Van de Peer, Yves;
van Dijk, Aalt D. J.;
Colombo, Lucia;
Davies, Brendan;
Angenent, Gerco C.

Publication type:

Article

Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis).

Published in:

Genes, 2020, v. 11, n. 1, p. 27, doi. 10.3390/genes11010027

By:

Sahu, Sunil Kumar;
Liu, Min;
Yssel, Anna;
Kariba, Robert;
Muthemba, Samuel;
Jiang, Sanjie;
Song, Bo;
Hendre, Prasad S.;
Muchugi, Alice;
Jamnadass, Ramni;
Kao, Shu-Min;
Featherston, Jonathan;
Zerega, Nyree J. C.;
Xu, Xun;
Yang, Huanming;
Van Deynze, Allen;
de Peer, Yves Van;
Liu, Xin;
Liu, Huan

Publication type:

Article

ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes.

Published in:

Genes, 2019, v. 10, n. 12, p. 950, doi. 10.3390/genes10120950

By:

Yssel, Anna E. J.;
Kao, Shu-Min;
Van de Peer, Yves;
Sterck, Lieven

Publication type:

Article