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Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)

R. Balakrishnan
<span title="2004-12-17">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Model Organism BLASTP Best Hits resource displays, for each S.cerevisiae protein, the single most similar protein from several model organisms and presents links to the database pages of those proteins  ...  The Saccharomyces Genome Database (SGD; http:// www.yeastgenome.org/) is a scientific database of gene, protein and genomic information for the yeast Saccharomyces cerevisiae.  ...  The Fungal BLAST and Model Organism BLASTP Best Hits tools, described here, are two new SGD resources that extend the users' reach beyond S.cerevisiae by allowing a variety of sequence comparisons.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki023">doi:10.1093/nar/gki023</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15608219">pmid:15608219</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC539977/">pmcid:PMC539977</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w4oavqa6yfhljfrqwdtv4nqh3u">fatcat:w4oavqa6yfhljfrqwdtv4nqh3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110401160222/http://www.princeton.edu/genomics/botstein/publications/2005_Balakrishnan_Fungal.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b9/6b/b96b46367e1d16d5b546d404aaae571eb6898cf8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki023"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539977" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

Oscar Dias, Andreas K Gombert, Eugénio C Ferreira, Isabel Rocha
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology.  ...  A comparison with KEGG's annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations.  ...  Acknowledgements and funding  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-517">doi:10.1186/1471-2164-13-517</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23025710">pmid:23025710</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3508617/">pmcid:PMC3508617</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eleyuqul5ndlhhdgpwmgnrnyp4">fatcat:eleyuqul5ndlhhdgpwmgnrnyp4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819094021/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-13-517?site=bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f1/47/f147142a9a6197a839a7b23a81b60e5cea5a052a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-517"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3508617" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Page 1226 of Genetics Vol. 174, Issue 3 [page]

<span title="">2006</span> <i title="Genetics Society of America"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_genetics" style="color: black;">Genetics </a> </i> &nbsp;
Dwicur et al., 2005 Fungal BLAST and model organism BLASTP best hits: new comparison resources at the Saccharomy- ces Genome Database (SGD). Nucleic Acids Res. 33: D374—D377. BriRRELL, G. W., J. A.  ...  We also thank the Keck University of New Mexico Genomics Resource facility and the Center for Genetics and Medicine at the University of New Mexico (UNM) School of Medicine for RNA and real-time PCR analyses  ... 
<span class="external-identifiers"> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_genetics_2006-11_174_3/page/1226" title="read fulltext microfilm" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_genetics_2006-11_174_3/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Public Access for Teaching Genomics, Proteomics, and Bioinformatics

A. Malcolm Campbell
<span title="">2003</span> <i title="American Society for Cell Biology (ASCB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xj7hj36mibarzoxaaa7lcar77u" style="color: black;">Cell Biology Education</a> </i> &nbsp;
These online resources provide students with exciting entree into the new fields of genomics, proteomics, and bioinformatics.  ...  I have developed a genomics course that incorporates many of the public-domain databases, research tools, and peer-reviewed journals.  ...  I would like to thank my colleague and coauthor Laurie Heyer for her valuable input as well as the 25 dedicated students who enrolled in my new genomics courses.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1187/cbe.03-02-0007">doi:10.1187/cbe.03-02-0007</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12888845">pmid:12888845</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC162192/">pmcid:PMC162192</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wdljxq2xsnapxnilz4iemtum2i">fatcat:wdljxq2xsnapxnilz4iemtum2i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040223102624/http://www.cellbioed.org:80/articles/vol2no2/pdfs/03-02-0007.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/94/b1/94b130e28e7c8a81865b339ccfa1761a43149b49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1187/cbe.03-02-0007"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC162192" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Phylogenetic diversity of stress signaling pathways in fungi

Elissavet Nikolaou, Ino Agriafioti, Michael Stumpf, Janet Quinn, Ian Stansfield, Alistair JP Brown
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/frh6t5i3jveazlshhan2ekhgcq" style="color: black;">BMC Evolutionary Biology</a> </i> &nbsp;
Putative orthologues of functionally defined signalling components in Saccharomyces cerevisiae were identified by performing reciprocal BLASTP searches, and the percent amino acid identities of these orthologues  ...  The degree of conservation of osmotic, oxidative and cell wall stress signalling pathways amongst the eighteen fungal species was examined.  ...  EN was supported by a studentship from the University of Aberdeen. AB was supported by the Wellcome Trust (080088) and the BBSRC (BB/C510391/1, BB/D009308/1, BB/F00513X/1).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2148-9-44">doi:10.1186/1471-2148-9-44</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19232129">pmid:19232129</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2666651/">pmcid:PMC2666651</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iwtwptis3vckbh5qocfirst6zi">fatcat:iwtwptis3vckbh5qocfirst6zi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150224105859/http://www.biomedcentral.com/content/pdf/1471-2148-9-44.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c7/27/c72797ae79c619e85fee88e37fe278f093584111.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2148-9-44"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666651" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

Li-Jun Ma, Ashraf S. Ibrahim, Christopher Skory, Manfred G. Grabherr, Gertraud Burger, Margi Butler, Marek Elias, Alexander Idnurm, B. Franz Lang, Teruo Sone, Ayumi Abe, Sarah E. Calvo (+21 others)
<span title="2009-07-03">2009</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j6fzfstrmzcj3aeps7bx6tpoy4" style="color: black;">PLoS Genetics</a> </i> &nbsp;
As a representative of the paraphyletic basal group of the fungal kingdom called "zygomycetes," R. oryzae is also used as a model to study fungal evolution.  ...  The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event.  ...  We specially thank Scott Baker and Igor Grigoriev at Joint Genome Institute for sharing their unpublished P. blakesleeanus genomic data for the comparative analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1000549">doi:10.1371/journal.pgen.1000549</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19578406">pmid:19578406</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2699053/">pmcid:PMC2699053</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qoixlvjv55bndn4qh26f72zuja">fatcat:qoixlvjv55bndn4qh26f72zuja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922000519/https://botany.natur.cuni.cz/algo/soubory/publikace/2009_Ma_et_al.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/93/a9/93a9d9e743030fedb256523407a176b265751dfd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1000549"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699053" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational and comparative analyses of 150 full-length cDNA sequences from the oomycete plant pathogen Phytophthora infestans

Joe Win, Thirumala-Devi Kanneganti, Trudy Torto-Alalibo, Sophien Kamoun
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y454jt4zhfesbgeglkpxbo4kum" style="color: black;">Fungal Genetics and Biology</a> </i> &nbsp;
Finally, we identiWed a set of genes that are shared between Phytophthora and fungal phytopathogens but absent in animal fungal pathogens.  ...  Recent genome sequencing eVorts of P. infestans and other Phytophthora species are generating vast amounts of sequence data providing opportunities to unlock the complex nature of pathogenesis.  ...  This work was supported by the NSF Plant Genome Research Program Grant DBI-0211659.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.fgb.2005.10.003">doi:10.1016/j.fgb.2005.10.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16380277">pmid:16380277</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jyw2vygjf5bnnlemoaxalfvz4u">fatcat:jyw2vygjf5bnnlemoaxalfvz4u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810074859/http://kamounlab.dreamhosters.com/pdfs/FGB_06.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/18/f0/18f05773daef50cff44ec345450c88b83710c54d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.fgb.2005.10.003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Genetic Profiling of the Isoprenoid and Sterol Biosynthesis Pathway Genes of Trypanosoma cruzi

Raúl O. Cosentino, Fernán Agüero, Mauricio Martins Rodrigues
<span title="2014-05-14">2014</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Using a number of bioinformatic strategies, we first identified genes that were missing and/or were truncated in the T. cruzi genome.  ...  Based on this analysis we obtained the complete sequence of the ortholog of the yeast ERG26 gene and identified a non-orthologous homolog of the yeast ERG25 gene (sterol methyl oxidase, SMO), and we propose  ...  Acknowledgments We would like to thank Patricio Diosque (Universidad Nacional de Salta, Argentina) for the generous gift of T. cruzi genomic DNA of different reference strains and isolates.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0096762">doi:10.1371/journal.pone.0096762</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24828104">pmid:24828104</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4020770/">pmcid:PMC4020770</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dkrs5hx33fgnfckffoyr34tf2a">fatcat:dkrs5hx33fgnfckffoyr34tf2a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171010002546/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0096762&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/67/ef/67efcb3a49c7a3a1e178a2e841c5cb9fa71ff951.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0096762"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020770" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome Sequence of the Lager Brewing Yeast, an Interspecies Hybrid

Y. Nakao, T. Kanamori, T. Itoh, Y. Kodama, S. Rainieri, N. Nakamura, T. Shimonaga, M. Hattori, T. Ashikari
<span title="2009-01-15">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4htpxjlr6ve2bhmzfom67xy7wu" style="color: black;">DNA Research</a> </i> &nbsp;
The 25 Mb genome comprises two nuclear sub-genomes originating from Saccharomyces cerevisiae and Saccharomyces bayanus and one circular mitochondrial genome originating from S. bayanus.  ...  This work presents the genome sequencing of the lager brewing yeast (Saccharomyces pastorianus) Weihenstephan 34/70, a strain widely used in lager beer brewing.  ...  The expert technical assistance of K. Yasui and H. Toyonaga is gratefully acknowledged. Supplementary data: Supplementary Material is available at www.dnaresearch.oxfordjournals.org.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/dnares/dsp003">doi:10.1093/dnares/dsp003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19261625">pmid:19261625</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2673734/">pmcid:PMC2673734</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t7ll2z2guzeyldoybmjw3tq4ty">fatcat:t7ll2z2guzeyldoybmjw3tq4ty</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170707194924/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/dnaresearch/16/2/10.1093/dnares/dsp003/2/dsp003.pdf?Expires=1499495952&amp;Signature=dnLUMmHVlyAjkq4cGo3qUWDlWGtc97Z2J-JMbj914GJvqk9vBKuoHghokRTcXq-~-rXMEhEFkar6F7eWQqx7fS0qBoCalVXTuaUEx-l6Gzcs0KMT0GL2LHICEBIXKvebS7W8d01K-Q4CEW0gLRri3QE8cVIyr5PrfQc7tVGoJieN3ZOuf20PoiRlZtHNIEVaFEUcTUB2dMLq60wHoRGZm6fHPNlM13K5dmko5LhMUsmC84zPU3qyLo4wt4t9h5gJ3~k7tA4Sbg9dDa5A0TuAQQrcekUUZr5qDVk3M4mS3RN3071JqT1os6fXgQZk~cwb3ffacxTgXCx40KS27TJk5g__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/af/b0/afb0f9aaa43379aa4aa36c98b9e8b985b61728a8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/dnares/dsp003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673734" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis

Daniel Gomes, Tatiana Q Aguiar, Oscar Dias, Eugénio C Ferreira, Lucília Domingues, Isabel Rocha
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Despite the high gene homology and gene order conservation comparatively with Saccharomyces cerevisiae, it presents a lower level of genomic complexity.  ...  Conclusions: This high quality metabolic re-annotation, together with the first membrane transporters annotation and the metabolic comparative analysis, represents a new important tool for the study and  ...  Acknowledgements and funding Research described in this article was financially supported by FEDER and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-810">doi:10.1186/1471-2164-15-810</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25253284">pmid:25253284</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4190384/">pmcid:PMC4190384</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2rwehad4gndyljuqj64dhhh5ua">fatcat:2rwehad4gndyljuqj64dhhh5ua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817202014/http://repositorium.sdum.uminho.pt/bitstream/1822/31640/1/document_18098_1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/29/90/2990385be67c9a2127a3030c53c07e4d403aced1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-810"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190384" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance

T Emri, K Antal, R Riley, Z Karányi, M Miskei, E Orosz, S E Baker, A Wiebenga, R P de Vries, I Pócsi
<span title="2018-10-11">2018</span> <i title="Elsevier"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7vroygzwundttcpoe5a6hql5ze" style="color: black;">Studies in Mycology</a> </i> &nbsp;
We performed a large-scale homology analysis of stress proteins and generated and analysed three stress defence system models based on Saccharomyces cerevisiae, Schizosaccharomyces pombe and Aspergillus  ...  All these multilevel changes are indispensable for the successful adaptation of filamentous fungi to altering environmental conditions, especially when these organisms are entering new ecological niches  ...  ACKNOWLEDGEMENTS The Authors thank the following researchers at the University of Debrecen for their valuable contributions to this project: A Gazdag, R Moh acsi, and LG T oth  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.simyco.2018.10.003">doi:10.1016/j.simyco.2018.10.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30425415">pmid:30425415</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6231086/">pmcid:PMC6231086</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g4q5ottplvcqfkjgi2jcse7zsq">fatcat:g4q5ottplvcqfkjgi2jcse7zsq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200430111912/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6231086&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d6/84/d684f2c35b26227fc743d5b4f19624ae2dcb8b33.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.simyco.2018.10.003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231086" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Target Of Rapamycin pathway in the white-rot fungus Phanerochaete chrysosporium

Duy Vuong Nguyen, Thomas Roret, Antonio Fernandez-Gonzalez, Annegret Kohler, Mélanie Morel-Rouhier, Eric Gelhaye, Rodnay Sormani, Daniel Cullen
<span title="2020-02-20">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
The Target Of Rapamycin (TOR) signaling pathway is known to regulate growth in response to nutrient availability and stress in eukaryotic cells.  ...  Inhibition of TOR activity by rapamycin affects conidia germination and hyphal growth highlighting the conserved mechanism of susceptibility to rapamycin.  ...  We thank Professor Jean-Pierre Jacquot for his help and comments during manuscript preparation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0224776">doi:10.1371/journal.pone.0224776</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32078630">pmid:32078630</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7032718/">pmcid:PMC7032718</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jbesvnpnmfhgjcs7q2dezredoi">fatcat:jbesvnpnmfhgjcs7q2dezredoi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200222204018/https://journals.plos.org/plosone/article/file?id=10.1371%2Fjournal.pone.0224776&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/01/3e/013e6a94d02f055daa4db8b412df239b642133c9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0224776"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7032718" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Patterns of conservation and diversification in the fungal polarization network [article]

Eveline T Diepeveen, Valerie Pourquie, Thies Gehrmann, Thomas Abeel, Liedewij Laan
<span title="2017-06-23">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Here we focus on the polarity network, which is universally essential for cell proliferation and studied in great detail in the model organism, Saccharomyces cerevisiae.  ...  Large-scale comparative studies with high phylogenetic resolution are now feasible through the recent rise in available genomic datasets of both model and non-model species.  ...  Saccharomyces Genome Database (SGD; www.yeastgenome.org; 184 June 2015; Cherry et al. 2011).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/154641">doi:10.1101/154641</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ysbyjt725bh4tfgylozxk4s3yi">fatcat:ysbyjt725bh4tfgylozxk4s3yi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504185638/https://www.biorxiv.org/content/biorxiv/early/2017/06/23/154641.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/c7/fec70b64b82710bfc045d5ad8b0e484daa2cf733.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/154641"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A Human-Curated Annotation of the Candida albicans Genome

Burkhard R. Braun, Marco van het Hoog, Christophe d'Enfert, Mikhail Martchenko, Jan Dungan, Alan Kuo, Diane O. Inglis, M. Andrew Uhl, Hervé Hogues, Matthew Berriman, Michael Lorenz, Anastasia Levitin (+31 others)
<span title="">2005</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j6fzfstrmzcj3aeps7bx6tpoy4" style="color: black;">PLoS Genetics</a> </i> &nbsp;
Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy.  ...  We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained  ...  Ted Jones, Stewart Scherer, and their colleagues at the SGTC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.0010001">doi:10.1371/journal.pgen.0010001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16103911">pmid:16103911</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1183520/">pmcid:PMC1183520</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kqg267k5lvc2ro6yjvgwfwwli4">fatcat:kqg267k5lvc2ro6yjvgwfwwli4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427174931/https://serval.unil.ch/resource/serval:BIB_4CD62D289C63.P001/REF.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8d/23/8d23a9b5e0bb1638da0cbb183cd88b83cc4eceb1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.0010001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1183520" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Target Of Rapamycin pathway in the white-rot fungus Phanerochaete chrysosporium [article]

Vuong Duy Nguyen, Thomas Roret, Antonio Fernández González, Annegret Kohler, Eric Gelhaye, Mélanie Morel-Rouhier, rodnay sormani
<span title="2019-10-23">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The Target Of Rapamycin (TOR) signaling pathway is known to regulate growth in response to nutrient availability and stress in eukaryotic cells.  ...  Inhibition of TOR activity by rapamycin affects conidia germination and hyphal growth highlighting the conserved mechanism of susceptibility to rapamycin.  ...  Using the sequences from S. cerevisiae as bait, two sequences were detected in the genome 242 of P. chrysosporium using BLASTp.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/816447">doi:10.1101/816447</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qg4loa64hvc7bm62sghkutevia">fatcat:qg4loa64hvc7bm62sghkutevia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200310095700/https://www.biorxiv.org/content/biorxiv/early/2019/10/23/816447.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/42/2a/422a0e69ef3f1ed7a4474bbc693fc99e3bdc9a08.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/816447"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>
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