Filters








6 Hits in 12.0 sec

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

Adrian M. Altenhoff, Nives Škunca, Natasha Glover, Clément-Marie Train, Anna Sueki, Ivana Piližota, Kevin Gori, Bartlomiej Tomiczek, Steven Müller, Henning Redestig, Gaston H. Gonnet, Christophe Dessimoz
<span title="2014-11-15">2014</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;
In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes  ...  and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML  ...  ACKNOWLEDGEMENT We thank three anonymous referees for their comments on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1158">doi:10.1093/nar/gku1158</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25399418">pmid:25399418</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4383958/">pmcid:PMC4383958</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zwz6zab5lfetzej7saase2ztyy">fatcat:zwz6zab5lfetzej7saase2ztyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303030403/http://pdfs.semanticscholar.org/ae1e/7dc003feed4d01c09c403cd153a1900de4aa.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/ae/1e/ae1e7dc003feed4d01c09c403cd153a1900de4aa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1158"> <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/PMC4383958" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ensembl comparative genomics resources

Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha (+2 others)
<span title="">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate  ...  Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views.  ...  We also thank the rest of the Ensembl team, especially the members of Ensembl Outreach for supporting the users and helping with the documentation and tutorials.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw053">doi:10.1093/database/baw053</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27141089">pmid:27141089</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4852398/">pmcid:PMC4852398</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sluvrnnct5dpxmd7grm3z76m3y">fatcat:sluvrnnct5dpxmd7grm3z76m3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224163701/http://pdfs.semanticscholar.org/5ad9/a4e6972b742a93fccc17e8ef995d3d8139d1.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/5a/d9/5ad9a4e6972b742a93fccc17e8ef995d3d8139d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw053"> <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/PMC4852398" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors

Simon R. Foster, Alexander S. Hauser, Line Vedel, Ryan T. Strachan, Xi-Ping Huang, Ariana C. Gavin, Sushrut D. Shah, Ajay P. Nayak, Linda M. Haugaard-Kedström, Raymond B. Penn, Bryan L. Roth, Hans Bräuner-Osborne (+1 others)
<span title="2019-10-31">2019</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iwommhyo5bdk7c3u37mhjzexfe" style="color: black;">Cell</a> </i> &nbsp;
This integrated computational and multifaceted experimental approach expands the peptide-GPCR network and opens the way for studies to elucidate the roles of these signaling systems in human physiology  ...  The peptidergic system is the most abundant network of ligand-receptor-mediated signaling in humans.  ...  ,Redestig, H., et al. (2015). The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cell.2019.10.010">doi:10.1016/j.cell.2019.10.010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31675498">pmid:31675498</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6838683/">pmcid:PMC6838683</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/usfzdv75rvc55pqiyh65ikq44a">fatcat:usfzdv75rvc55pqiyh65ikq44a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200505233537/https://curis.ku.dk/ws/files/236371021/1_s2.0_S0092867419311262_main.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/2f/cb/2fcbd42ef3faeb21f05eeca88af74b1fb255aaca.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cell.2019.10.010"> <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/PMC6838683" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Gene-tree reconciliation with MUL-trees to resolve polyploidy events [article]

Gregg W.C. Thomas, S. Hussain Ather, Matthew W. Hahn
<span title="2016-06-10">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants.  ...  auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees.  ...  The OMA orthology 549 database in 2015: Function predictions, better plant support, synteny view, and 550 other improvement.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/058149">doi:10.1101/058149</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4tgprlzc6vewxlbbmgdhiov3vq">fatcat:4tgprlzc6vewxlbbmgdhiov3vq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502143134/https://www.biorxiv.org/content/biorxiv/early/2017/03/21/058149.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/d5/9a/d59aaba4fcb7c90e8a6209531cd067fd56ff85b8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/058149"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A study of protein coding genes in Enterobacteriaceae family: essentiality of genes and orthology [article]

Fatemeh Ashari Ghomi, University Of Canterbury
<span title="2018-10-12">2018</span>
We then compare the accuracy of this tool with other well-known models and discuss ways for improving the accuracy of the method.  ...  We compare it with other methods and showcase its uniqueness in presenting multi-layer networks.  ...  The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Research, 43(Database issue):D240-249.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.26021/7562">doi:10.26021/7562</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hbqvdo2kwvbwphum3t37xfwkzm">fatcat:hbqvdo2kwvbwphum3t37xfwkzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190201054120/https://ir.canterbury.ac.nz/bitstream/handle/10092/16109/Ashari-Ghomi,%20Fatemeh_Final%20PhD%20Thesis.pdf?sequence=1" 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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.26021/7562"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors

D.E. Gloriam, A.S. Hauser, B.L. Roth, L.M. Haugaard-Kedström, S.R. Foster, L. Vedel, A.C. Gavin, R.B. Penn, R.T. Strachan, A.P. Nayak, H. Bräuner-Osborne, X.-P. Huang (+1 others)
<span title="">2019</span>
Video Abstract: Features learned from comparative sequence and structural analyses enabled prediction of peptide ligands for orphan GPCRs that, when coupled with functional validation, expose physiologically  ...  This integrated computational and multifaceted experimental approach expands the peptide-GPCR network and opens the way for studies to elucidate the roles of these signaling systems in human physiology  ...  ,Redestig, H., et al. (2015). The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17615/9xfr-er83">doi:10.17615/9xfr-er83</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oom6zoo3znfm5opelpxiimqayq">fatcat:oom6zoo3znfm5opelpxiimqayq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201212215010/https://cdr.lib.unc.edu/downloads/nk322m039" 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/fb/e5/fbe5ebadadb0cf811dc95d25c4ffebcd3f979223.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17615/9xfr-er83"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>