Browsing Research Articles (Genetics) by UP Author "Van de Peer, Yves"

Browsing Research Articles (Genetics) by UP Author "Van de Peer, Yves"

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  • Diffany : an ontology-driven framework to infer, visualise and analyse differential molecular networks 
    Van Landeghem, Sofie; Van Parys, Thomas; Dubois, Marieke; Inze, Dirk; Van de Peer, Yves (BioMed Central, 2016-01-05)
    BACKGROUND : Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such ...
  • Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts 
    Morel, Guillaume; Sterck, Lieven; Swennen, Dominique; Marcet-Houben, Marina; Onesime, Djamila; Levasseur, Anthony; Jacques, Noémie; Mallet, Sandrine; Couloux, Arnaux; Labadie, Karine; Amselem, Joëlle; Beckerich, Jean-Marie; Henrissat, Bernard; Van de Peer, Yves; Wincker, Patrick; Souciet, Jean-Luc; Gabaldón, Toni; Tinsley, Colin R.; Casaregola, Serge (Nature Publishing Group (open access), 2015-06)
    The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships ...
  • Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants 
    Shi, Tao; Rahmani, Razgar Seyed; Gugger, Paul F.; Wang, Muhua H.; Li, Hui; Zhang, Yue; Li, Zhizhong; Wang, Qingfeng; Van de Peer, Yves; Marchal, Kathleen; Chen, Jinming (Oxford University Press, 2020-08)
    For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or ...
  • Draft genome assembly of the false spider mite Brevipalpus yothersi 
    Navia, Denise; Novelli, Valdenice M.; Rombauts, Stephane; Freitas-Astua, Juliana; Santos de Mendonca, Renata; Nunes, Maria Andreia; Machado, Marcos A.; Lin, Yao-Cheng; Le, Phuong; Zhang, Zaichao; Grbic, Miodrag; Wybouw, Nicky; Breeuwer, Johannes A. J.; Van Leeuwen, Thomas; Van de Peer, Yves (American Society for Microbiology, 2019-02-07)
    The false spider mite Brevipalpus yothersi infests a broad host plant range and has become one of the most economically important species within the genus Brevipalpus. This phytophagous mite inflicts damage by both feeding ...
  • Draft genome assembly of the poultry red mite, Dermanyssus gallinae 
    Burgess, Stewart T.G.; Bartley, Kathryn; Nunn, Francesca; Wright, Harry W.; Hughes, Margaret; Gemmell, Matthew; Haldenby, Sam; Paterson, Steve; Rombauts, Stephane; Tomley, Fiona M.; Blake, Damer P.; Pritchard, James; Schicht, Sabine; Strube, Christina; Oines, Oines; Van Leeuwen, Thomas; Van de Peer, Yves; Nisbet, Alasdair J. (American Society for Microbiology, 2018-11-08)
    The poultry red mite, Dermanyssus gallinae, is a major worldwide concern in the egg-laying industry. Here, we report the first draft genome assembly and gene prediction of Dermanyssus gallinae, based on combined PacBio ...
  • Draft genome assembly of the sheep scab mite, Psoroptes ovis 
    Burgess, Stewart T.G.; Bartley, Kathryn; Marr, Edward J.; Wright, Harry W.; Weaver, Robert J.; Prickett, Jessica C.; Hughes, Margaret; Haldenby, Sam; Thi Le, Phuong; Rombauts, Stephane; Van Leeuwen, Thomas; Van de Peer, Yves; Nisbet, Alasdair J. (American Society for Microbiology, 2018-04-19)
    Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene ...
  • Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips 
    Wingfield, Brenda D.; Berger, David Kenneth; Steenkamp, Emma Theodora; Lim, Hye-Jin; Duong, Tuan A.; Bluhm, Burton H.; De Beer, Z. Wilhelm; De Vos, Lieschen; Fourie, Gerda; Naidoo, Kershney; Olivier, Nicholas Abraham; Lin, Yao-Cheng; Van de Peer, Yves; Joubert, Fourie; Crampton, Bridget Genevieve; Swart, Velushka; Soal, Nicole Christine; Tatham, Catherine; Van der Nest, Magrieta Aletta; Van der Merwe, Nicolaas Albertus (Albie); Van Wyk, Stephanie; Wilken, Pieter Markus; Wingfield, Michael J. (International Mycological Association, 2017-11-21)
    The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and ...
  • The draft genomes of five agriculturally important African orphan crops 
    Chang, Yue; Liu, Huan; Liu, Min; Liao, Xuezhu; Sahu, Sunil Kumar; Fu, Yuan; Song, Bo; Cheng, Shifeng; Kariba, Robert; Muthemba, Samuel; Hendre, Prasad S.; Mayes, Sean; Ho, Wai Kuan; Yssel, A.E.J. (Anna); Kendabie, Presidor; Wang, Sibo; Li, Linzhou; Muchugi, Alice; Jamnadass, Ramni; Lu, Haorong; Peng, Shufeng; Van Deynze, Allen; Simons, Anthony; Yana-Shapiro, Howard; Van de Peer, Yves; Xu, Xun; Yang, Huanming; Wang, Jian; Liu, Xin (Oxford University Press, 2019)
    BACKGROUND : The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south ...
  • Draft genomes of two artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis) 
    Sahu, Sunil Kumar; Liu, Min; Yssel, A.E.J. (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; Van de Peer, Yves; Liu, Xin; Liu, Huan (MDPI, 2020)
    Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for ...
  • Dual RNA sequencing of Vitis vinifera during Lasiodiplodia theobromae infection unveils host-pathogen interactions 
    Gonçalves, Micael F.M.; Nunes, Rui B.; Tilleman, Laurentijn; Van de Peer, Yves; Deforce, Dieter; Van Nieuwerburgh, Filip; Esteves, Ana C.; Alves, Artur (MDPI Publishing, 2019-12-03)
    Lasiodiplodia theobromae is one of the most aggressive agents of the grapevine trunk disease Botryosphaeria dieback. Through a dual RNA-sequencing approach, this study aimed to give a broader perspective on the infection ...
  • Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment 
    Yao, Yao; Storme, Veronique; Marchal, Kathleen; Van de Peer, Yves (PeerJ, 2016-12-21)
    We developed a bio-inspired robot controller combining an artificial genome with an agent-based control system. The genome encodes a gene regulatory network (GRN) that is switched on by environmental cues and, following ...
  • Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes 
    Vlastaridis, Panayotis; Kyriakidou, Pelagia; Chaliotis, Anargyros; Van de Peer, Yves; Oliver, Stephen G.; Amoutzias, Grigoris D. (Oxford University Press, 2017)
    BACKGROUND : Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput ...
  • The Euscaphis japonica genome and the evolution of malvids 
    Sun, Wei-Hong; Li, Zhen; Xiang, Shuang; Ni, Lin; Zhang, Diyang; Chen, De-Qiang; Qiu, Meng-Yuan; Zhang, Qi-Gong; Xiao, Lin; Din, Le; Li, Yifan; Liao, Xing-Yu; Liu, Xue-Die; Jiang, Yu-Ting; Zhang, Pei-Lan; Ni, Hui; Wang, Yifan; Yue, Yi-Xun; Wu, Xi; Din, Xiang-Qing; Huang, Wei; Wang, Zhi-Wen; Ma, Xiaokai; Liu, Bobin; Zou, Xiao-Xing; Van de Peer, Yves; Liu, Zhong-Jian; Zou, Shuang-Quan (Wiley, 2021-12)
    Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, ...
  • Evaluation of the impact of Illumina error correction tools on de novo genome assembly 
    Heydari, Mahdi; Miclotte, Giles; Demeester, Piet; Van de Peer, Yves; Fostier, Jan (BioMed Central, 2017-08-18)
    BACKGROUND : Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced ...
  • Evidence for an ancient whole genome duplication in the cycad lineage 
    Roodt, Danielle; Lohaus, Rolf; Sterck, Lieven; Swanepoel, Riaan L.; Van de Peer, Yves; Mizrachi, Eshchar (Public Library of Science, 2017-09-08)
    Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome ...
  • The evolution of gene duplicates in angiosperms and the impact of protein–protein interactions and the mechanism of duplication 
    Defoort, Jonas; Van de Peer, Yves; Carretero-Paulet, Lorenzo (Oxford University Press, 2019-08)
    Gene duplicates, generated through either whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary ...
  • Evolution of NLR resistance genes in magnoliids : dramatic expansions of CNLs and multiple losses of TNLs 
    Wu, Jia-Yi; Xue, Jia-Yu; Van de Peer, Yves (Frontiers Research Foundation, 2021-11-21)
    Magnoliids are the third-largest group of angiosperms and occupy a critical position in angiosperm evolution. In the past years, due to the lack of sequenced genomes, the disease resistance gene (R gene) profile of ...
  • The evolutionary conundrum of whole‐genome duplication 
    Carretero‐Paulet, Lorenzo; Van de Peer, Yves (Wiley, 2020-08)
    Whole‐genome duplication (WGD) is a dramatic, common event in plants. Because of the detrimental effects arising from doubling the entire chromosome set, such as minority cytotype exclusion, genomic instability, mitotic ...
  • Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.) 
    Qiao, Qin; Edger, Patrick P.; Xue, Li; Qiong, La; Lu, Jie; Zhang, Yichen; Cao, Qiang; Yocca, Alan E.; Platts, Adrian E.; Knapp, Steven J.; Van Montagu, Marc; Van de Peer, Yves; Lei, Jiajun; Zhang, Ticao (National Academy of Sciences, 2021-10)
    Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report ...
  • Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays 
    Ghorbani, Sarieh; Lin, Yao-Cheng; Parizot, Boris; Fernandez, Ana; Njo, Maria Fransiska; Van de Peer, Yves; Beeckman, Tom; Hilson, Pierre (Oxford University Press, 2015-08)
    Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this ...