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1دورية أكاديمية
المؤلفون: Nilsson, R. Henrik, Hyde, Kevin D., Pawłowska, Julia, Ryberg, Martin, Tedersoo, Leho, Aas, Anders Bjørnsgard, Alias, Siti A., Alves, Artur, Anderson, Cajsa Lisa, Antonelli, Alexandre, Arnold, A. Elizabeth, Bahnmann, Barbara, Bahram, Mohammad, Bengtsson-Palme, Johan, Berlin, Anna, Branco, Sara, Chomnunti, Putarak, Dissanayake, Asha, Drenkhan, Rein, Friberg, Hanna, Frøslev, Tobias Guldberg, Halwachs, Bettina, Hartmann, Martin, Henricot, Beatrice, Jayawardena, Ruvishika, Jumpponen, Ari, Kauserud, Håvard, Koskela, Sonja, Kulik, Tomasz, Liimatainen, Kare, Lindahl, Björn D., Lindner, Daniel, Liu, Jian-Kui, Maharachchikumbura, Sajeewa, Manamgoda, Dimuthu, Martinsson, Svante, Neves, Maria Alice, Niskanen, Tuula, Nylinder, Stephan, Pereira, Olinto Liparini, Pinho, Danilo Batista, Porter, Teresita M., Queloz, Valentin, Riit, Taavi, Sánchez-García, Marisol, de Sousa, Filipe, Stefańczyk, Emil, Tadych, Mariusz, Takamatsu, Susumu, Tian, Qing, Udayanga, Dhanushka, Unterseher, Martin, Wang, Zheng, Wikee, Saowanee, Yan, Jiye, Larsson, Ellen, Larsson, Karl-Henrik, Kõljalg, Urmas, Abarenkov, Kessy
المصدر: Fungal Diversity: An International Journal of Mycology. July 2014 67(1):11-19
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المؤلفون: Michael Levine, Chandra L. Theesfeld, Aaron K. Wong, João Raimundo, Olga G. Troyanskaya, Yuji Yamazaki, Evan M. Cofer, Alicja Tadych
مصطلحات موضوعية: 0303 health sciences, biology, business.industry, Deep learning, fungi, Danio, Computational biology, biology.organism_classification, Chromatin, 03 medical and health sciences, Annotation, 0302 clinical medicine, Histone, biology.protein, Artificial intelligence, Drosophila melanogaster, business, Transcription factor, 030217 neurology & neurosurgery, Caenorhabditis elegans, 030304 developmental biology
الوصف: To enable large-scale analyses of regulatory logic in model species, we developed DeepArk (https://DeepArk.princeton.edu), a set of deep learning models of the cis-regulatory codes of four widely-studied species: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, and Mus musculus. DeepArk accurately predicts the presence of thousands of different context-specific regulatory features, including chromatin states, histone marks, and transcription factors. In vivo studies show that DeepArk can predict the regulatory impact of any genomic variant (including rare or not previously observed), and enables the regulatory annotation of understudied model species.
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bf271ee8824c3642091ed721110b2d6b
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المؤلفون: Ellen Larsson, Sajeewa S. N. Maharachchikumbura, Asha J. Dissanayake, Alexandre Antonelli, Marisol Sánchez-García, Olinto Liparini Pereira, Kevin D. Hyde, Tomasz Kulik, Dhanushka Udayanga, Hanna Friberg, Valentin Queloz, Ari Jumpponen, Zheng Wang, Anna Berlin, Karl-Henrik Larsson, Martin Hartmann, Rein Drenkhan, Leho Tedersoo, B. Henricot, Putarak Chomnunti, Jiye Yan, Anders Bjørnsgard Aas, Qing Tian, Björn D. Lindahl, Mariusz Tadych, Urmas Kõljalg, Taavi Riit, Tuula Niskanen, Sonja Koskela, Filipe de Sousa, Saowanee Wikee, Kessy Abarenkov, Stephan Nylinder, Susumu Takamatsu, R. Henrik Nilsson, Jian-Kui Liu, Maria Alice Neves, Teresita M. Porter, Julia Pawłowska, Cajsa Lisa Anderson, Martin Ryberg, Barbara Bahnmann, Artur Alves, Bettina Halwachs, Kare Liimatainen, Dimuthu S. Manamgoda, Håvard Kauserud, Siti Aisyah Alias, Mohammad Bahram, Sara Branco, Danilo Batista Pinho, A. Elizabeth Arnold, Daniel L. Lindner, Emil Stefańczyk, Ruvishika S. Jayawardena, Johan Bengtsson-Palme, Martin Unterseher, Svante Martinsson, Tobias Guldberg Frøslev
المصدر: Fungal Diversity
LOCUS Repositório Institucional da UFV
Universidade Federal de Viçosa (UFV)
instacron:UFV
Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAPمصطلحات موضوعية: Genetics, 0303 health sciences, Ecology, Annotation, mothur, Computational biology, 15. Life on land, Biology, Ribosomal RNA, DNA sequencing, 030308 mycology & parasitology, 03 medical and health sciences, Taxon, Mycology, GenBank, Molecular identification, Internal transcribed spacer, ITS, Phytopathogenic fungi, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Taxonomy
الوصف: Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
وصف الملف: application/pdf