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Browsing Research Articles (University of Pretoria) by UP Author "Van de Peer, Yves"
Now showing items 1-20 of 153
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Phoma, Sandra; Vikram, Surendra; Jansson, Janet K.; Ansorge, Isabelle J.; Cowan, Don A.; Van de Peer, Yves; Makhalanyane, Thulani Peter (Nature Publising Group, 2018-07-12)Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas ...
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Vanneste, Kevin; Baele, Guy; Maere, Steven; Van de Peer, Yves (Cold Spring Harbor Laboratory Press, 2014-08)Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary ...
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Hakala, Kai; Van Landeghem, Sofie; Salakoski, Tapio; Van de Peer, Yves; Ginter, Filip (BioMed Central, 2015-10-30)BACKGROUND : Modern methods for mining biomolecular interactions from literature typically make predictions based solely on the immediate textual context, in effect a single sentence. No prior work has been published ...
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Vermeirssen, Vanessa; De Clercq, Inge; Van Parys, Thomas; Van Breusegem, Frank; Van de Peer, Yves (American Society of Plant Biologists, 2014-12)The abiotic stress response in plants is complex and tightly controlled by gene regulation. We present an abiotic stress gene regulatory network of 200,014 interactions for 11,938 target genes by integrating four complementary ...
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Mushthofa, Mushthofa; Torres, Gustavo; Van de Peer, Yves; Marchal, Kathleen; De Cock, Martine; Valencia, Alfonso (Oxford University Press, 2014-07-15)MOTIVATION : Boolean network models are suitable to simulate gene regulatory networks (GRNs) in the absence of detailed kinetic information. However, reducing the biological reality implies making assumptions on how ...
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Heydari, Mahdi; Miclotte, Giles; Van de Peer, Yves; Fostier, Jan (BioMed Central, 2018-09-04)BACKGROUND : Aligning short reads to a reference genome is an important task in many genome analysis pipelines. This task is computationally more complex when the reference genome is provided in the form of a de Bruijn ...
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Kaewphan, Suwisa; Van Landeghem, Sofie; Ohta, Tomoko; Van de Peer, Yves; Ginter, Filip; Pyysalo, Sampo (Oxford University Press, 2016-01)MOTIVATION : The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the ...
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Ma, Xiao; Vaistij, Fabian 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. (Wiley, 2021-05)Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over-reliant on a small number of internation ...
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Yang, Fu-Sheng; Nie, Shuai; Liu, Hui; Shi, Tian-Le; Tian, Xue-Chan; Zhou, Shan-Shan; Bao, Yu-Tao; Jia, Kai-Hua; Guo, Jing-Fang; Zhao, Wei; An, Na; Zhang, Ren-Gang; Yun, Quan-Zheng; Wang, Xin-Zhu; Mannapperuma, Chanaka; Porth, Ilga; El-Kassaby, Yousry Aly; Street, Nathaniel Robert; Wang, Xiao-Ru; Van de Peer, Yves; Mao, Jian-Feng (Nature Publising Group, 2020-10-19)Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of ...
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Chang, Jiyang; Marczuk-Rojas, Juan Pablo; Waterman, Carrie; Garcia-Llanos, Armando; Chen, Shiyu; Ma, Xiao; Hulse-Kemp, Amanda; Van Deynze, Allen; Van de Peer, Yves; Carretero-Paulet, Lorenzo (Wiley Open Access, 2022-09)The African Orphan Crops Consortium (AOCC) selected the highly nutritious, fast growing and drought tolerant tree crop moringa (Moringa oleifera Lam.) as one of the first of 101 plant species to have its genome sequenced ...
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Tzfadia, Oren; Diels, Tim; De Meyer, Sam; Vandepoele, Klaas; Aharoni, Asaph; Van de Peer, Yves (Frontiers Research Foundation, 2016-01-05)MOTIVATION : Comparative transcriptomics is a common approach in functional gene discovery efforts. It allows for finding conserved co-expression patterns between orthologous genes in closely related plant species, suggesting ...
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Ranade, Sonali Sachin; Lin, Yao-Cheng; Zuccolo, Andrea; Van de Peer, Yves; García-Gil, María del Rosario (BioMed Central, 2014)BACKGROUND: Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and ...
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Ranade, Sonali Sachin; Lin, Yao-Cheng; Van de Peer, Yves; García-Gil, María Rosario (BioMed Central, 2015-12-26)BACKGROUND : Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1–6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic ...
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Thi Le, Phuong; Makhalanyane, Thulani Peter; Guerrero, Leandro D.; Vikram, Surendra; Van de Peer, Yves; Cowan, Don A. (Oxford University Press, 2016)Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ...
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Jelen, Vid; De Jonge, Ronnie; Van de Peer, Yves; Javornik, Branka; Jakse, Jernej (Public Library of Science, 2016-02-03)Verticillium nonalfalfae is a fungal plant pathogen that causes wilt disease by colonizing the vascular tissues of host plants. The disease induced by hop isolates of V. nonalfalfae manifests in two different forms, ...
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Ngoc, Phuong Cao Thi; Greenhalgh, Robert; Dermauw, Wannes; Rombauts, Stephane; Bajda, Sabina; Zhurov, Vladimir; Grbic, Miodrag; Van de Peer, Yves; Van Leeuwen, Thomas; Rouze, Pierre (Oxford University Press, 2016-10-26)While mechanisms to detoxify plant produced, anti-herbivore compounds have been associated with plant host use by herbivores, less is known about the role of chemosensory perception in their life histories. This is ...
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Verhelst, Bram; Van de Peer, Yves; Rouze, Pierre (Oxford University Press, 2013-11)Genes in pieces and spliceosomal introns are a landmark of eukaryotes, with intron invasion usually assumed to have happened early on in evolution. Here, we analyze the intron landscape of Micromonas, a unicellular green ...
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De La Torre, Amanda R.; Li, Zhen; Van de Peer, Yves; Ingvarsson, Par K. (Oxford University Press, 2017)The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for ...
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Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization Guo, Liangyu; Wang, Shuo; Jiao, Xi; Ye, Xiaoxue; Deng, Deyin; Liu, Hua; Li, Yan; Van de Peer, Yves; Wu, Wenwu (Wiley, 2024-05)Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging ...
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Zhang, Ticao; Qiao, Qin; Du, Xiao; Zhang, Xiao; Hou, Yali; Wei, Xin; Sun, Chao; Zhang, Rengang; Yun, Quanzheng; Crabbe, M. James C.; Van de Peer, Yves; Dong, Wenxuan (Wiley, 2022-08)Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosomelevel genome sequence ...
Now showing items 1-20 of 153