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Updates to HCOP: the HGNC comparison of orthology predictions tool

Bethan Yates, Kristian A Gray, Tamsin E M Jones, Elspeth A Bruford
<span title="2021-05-06">2021</span> <i title="Oxford University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The HGNC Comparison of Orthology Predictions (HCOP) search tool integrates and displays data from multiple ortholog prediction resources for a specified human gene or set of genes.  ...  The HCOP pipeline used to fetch and integrate the information from the disparate ortholog and nomenclature data resources has recently been rewritten, both to enable the inclusion of new data and to take  ...  for their input into the development of the HCOP tool.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbab155">doi:10.1093/bib/bbab155</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33959747">pmid:33959747</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8574622/">pmcid:PMC8574622</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/meot4jf5hzhbne24n2plo6dtiq">fatcat:meot4jf5hzhbne24n2plo6dtiq</a> </span>
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HCOP: a searchable database of human orthology predictions

T. A. Eyre, M. W. Wright, M. J. Lush, E. A. Bruford
<span title="2006-05-26">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The HUGO Gene Nomenclature Committee (HGNC) Comparison of Orthology Predictions (HCOP) search tool combines the human, mouse, rat and chicken orthology assertions made by PhIGs, HomoloGene, Ensembl, Inparanoid  ...  The HCOP resource provides a useful method to integrate, compare and access a variety of disparate sources of human orthology data.  ...  Acknowledgements Many thanks to the other members of the HGNC team, especially Prof. Sue Povey and Fabrice Ducluzeau. This work was funded by the Wellcome Trust as part of the HUMOT Project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbl030">doi:10.1093/bib/bbl030</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16951416">pmid:16951416</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z2uvgaskxfbbpfeirazhd7mllu">fatcat:z2uvgaskxfbbpfeirazhd7mllu</a> </span>
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Genenames.org: the HGNC resources in 2015

Kristian A. Gray, Bethan Yates, Ruth L. Seal, Mathew W. Wright, Elspeth A. Bruford
<span title="2014-10-31">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;
more powerful search, a vastly improved HCOP tool and a REST service to increase the number of ways users can retrieve our data.  ...  To date the HGNC have assigned over 39 000 gene names and, representing an increase of over 5000 entries in the past two years.  ...  ACKNOWLEDGEMENT The authors would like to thank their former colleagues, specialist advisors and other researchers who have provided invaluable contributions to this project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1071">doi:10.1093/nar/gku1071</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25361968">pmid:25361968</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4383909/">pmcid:PMC4383909</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6bgwdrhfizcmtfnls2i7s3iwly">fatcat:6bgwdrhfizcmtfnls2i7s3iwly</a> </span>
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Genenames.org: the HGNC and VGNC resources in 2019

Bryony Braschi, Paul Denny, Kristian Gray, Tamsin Jones, Ruth Seal, Susan Tweedie, Bethan Yates, Elspeth Bruford
<span title="2018-10-10">2018</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;
Our HGNC website https://www.genenames.org has undergone a major design update, simplifying the homepage to provide easy access to our search tools and making the site more mobile friendly.  ...  The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes.  ...  Our naming strategy uses a subset of data from our HCOP (HGNC Comparison of Orthology Predictions) tool (24) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky930">doi:10.1093/nar/gky930</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30304474">pmid:30304474</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fhml3cnddvgcrjz54mjwoczc2e">fatcat:fhml3cnddvgcrjz54mjwoczc2e</a> </span>
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The HGNC Database in 2008: a resource for the human genome

E. A. Bruford, M. J. Lush, M. W. Wright, T. P. Sneddon, S. Povey, E. Birney
<span title="2007-12-23">2007</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;
resources, such as the HCOP orthology search tool and manually curated gene family webpages.  ...  The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique and ideally meaningful name and symbol to every human gene.  ...  We would like to thank all of our collaborators and past members of the HGNC, in particular Fabrice Ducluzeau, for their invaluable help.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkm881">doi:10.1093/nar/gkm881</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17984084">pmid:17984084</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2238870/">pmcid:PMC2238870</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xej5gy3szzdkvjq255g6rvu7uq">fatcat:xej5gy3szzdkvjq255g6rvu7uq</a> </span>
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genenames.org: the HGNC resources in 2011

R. L. Seal, S. M. Gordon, M. J. Lush, M. W. Wright, E. A. Bruford
<span title="2010-10-06">2010</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 site provides a public access portal to our database with no restrictions imposed on access or the use of the data.  ...  Within this article, we review our online resources and data with particular emphasis on the updates to our website.  ...  ACKNOWLEDGEMENTS The authors would like to thank all of their past HGNC colleagues for their invaluable contributions to this project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq892">doi:10.1093/nar/gkq892</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20929869">pmid:20929869</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013772/">pmcid:PMC3013772</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qhlso4wnfzgz3jiyet2fatlhau">fatcat:qhlso4wnfzgz3jiyet2fatlhau</a> </span>
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Genenames.org: the HGNC resources in 2013

Kristian A. Gray, Louise C. Daugherty, Susan M. Gordon, Ruth L. Seal, Mathew W. Wright, Elspeth A. Bruford
<span title="2012-11-17">2012</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 site provides a public access portal to our database with no restrictions imposed on access or the use of the data.  ...  Within this article, we review our online resources and data with particular emphasis on the updates to our website.  ...  ACKNOWLEDGEMENTS The authors would like to thank all of their past HGNC colleagues for their invaluable contributions to this project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1066">doi:10.1093/nar/gks1066</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23161694">pmid:23161694</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3531211/">pmcid:PMC3531211</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yz7p6tqwszdxziq5jd2kywjw3y">fatcat:yz7p6tqwszdxziq5jd2kywjw3y</a> </span>
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The chicken gene nomenclature committee report

David W Burt, Wilfrid Carrë, Mark Fell, Andy S Law, Parker B Antin, Donna R Maglott, Janet A Weber, Carl J Schmidt, Shane C Burgess, Fiona M McCarthy
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
However comparative biology both within avian species and within amniotes is hampered due to the difficulty of recognising functional orthologs.  ...  Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species.  ...  Acknowledgements The authors wish to thank members of the HGNC for their support and guidance, particularly Elspeth Bruford.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-10-s2-s5">doi:10.1186/1471-2164-10-s2-s5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19607656">pmid:19607656</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2966335/">pmcid:PMC2966335</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s4fi2ljoijhbdkmcxtstekk4nu">fatcat:s4fi2ljoijhbdkmcxtstekk4nu</a> </span>
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Orthology for comparative genomics in the mouse genome database

Mary E. Dolan, Richard M. Baldarelli, Susan M. Bello, Li Ni, Monica S. McAndrews, Carol J. Bult, James A. Kadin, Joel E. Richardson, Martin Ringwald, Janan T. Eppig, Judith A. Blake
<span title="2015-07-30">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2wcheulsyvd7bott7zn35dhoti" style="color: black;">Mammalian Genome</a> </i> &nbsp;
Over the past 25 years, novel algorithms and addition of orthologs from other model organisms have enriched comparative genomics in MGD data, extending the use of orthology data to support the laboratory  ...  Here, we describe current comparative data in MGD and review the history and refinement of orthology representation in this resource.  ...  Acknowledgments This work is funded through NIH grants HG000330 to MGD, HG002273 to the Gene Ontology Consortium, and HD062499 to GXD.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00335-015-9588-5">doi:10.1007/s00335-015-9588-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26223881">pmid:26223881</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4534493/">pmcid:PMC4534493</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gsj5nwfyj5b4jkwsku72xkysve">fatcat:gsj5nwfyj5b4jkwsku72xkysve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808001813/https://link.springer.com/content/pdf/10.1007%2Fs00335-015-9588-5.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/df/9d/df9d1503e9a90107ad943ef2c73116449af65b52.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00335-015-9588-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534493" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Mouse genome database 2016

Carol J. Bult, Janan T. Eppig, Judith A. Blake, James A. Kadin, Joel E. Richardson
<span title="2015-11-17">2015</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;
Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of  ...  the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine.  ...  We draw primarily on external sources for homology assertions including Homologene (21, 22) and the HGNC Comparison of Orthology Predictions (HCOP) (23) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1211">doi:10.1093/nar/gkv1211</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26578600">pmid:26578600</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702860/">pmcid:PMC4702860</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ufv3jxfe55fdljxozjt6gzuayi">fatcat:ufv3jxfe55fdljxozjt6gzuayi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223200217/http://pdfs.semanticscholar.org/4aa1/b4acb82761509d71207e99c1ebc1d794182d.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/4a/a1/4aa1b4acb82761509d71207e99c1ebc1d794182d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1211"> <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/PMC4702860" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An integrative approach to ortholog prediction for disease-focused and other functional studies

Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E Mohr
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt), for rapid identification of orthologs.  ...  Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward.  ...  Acknowledgements and Funding The authors would like to thank members of the Perrimon lab and Lizabeth Perkins for helpful suggestions and discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-357">doi:10.1186/1471-2105-12-357</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21880147">pmid:21880147</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3179972/">pmcid:PMC3179972</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jtvaobinn5dzrgyl4omxu73spi">fatcat:jtvaobinn5dzrgyl4omxu73spi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830102410/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-357?site=http://bmcbioinformatics.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/df/cc/dfcc9e82e1b3cc472c221b4aadae0fa454c62def.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-357"> <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/PMC3179972" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Quest for Orthologs benchmark service and consensus calls in 2020

Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José M Fernández, Laia Codó, Josep Ll Gelpi (+11 others)
<span title="2020-05-06">2020</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;
To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org).  ...  Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.  ...  Several meta-prediction resources have been developed, including HGNC Comparison of Orthology Predictions (HCOP) (31), Drosophila Integrative Ortholog Prediction Tool (DIOPT) (32), OrthoList (33) , and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa308">doi:10.1093/nar/gkaa308</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32374845">pmid:32374845</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7319555/">pmcid:PMC7319555</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fuzbeoshlvegddgzcylkiwvqpu">fatcat:fuzbeoshlvegddgzcylkiwvqpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427081155/https://ora.ox.ac.uk/objects/uuid:c9c28bd9-e404-4264-bfa8-713245fb314e/download_file?safe_filename=The%2520Quest%2520for%2520Orthologs%2520benchmark%2520service%2520and%2520consensus%2520calls%2520in%25202020.pdf&amp;type_of_work=Journal+article" 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/d0/45/d0450647a1b79e5aecd4757f0f85b9a5dc900eaf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa308"> <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/PMC7319555" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks

Zhongzhong Chen, Tianhong Zhang, Jun Lin, Zidan Yan, Yongren Wang, Weiqiang Zheng, Kevin C. Weng
<span title="2014-03-26">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
As an increasing number of PPIs are identified and vast amount of information accumulated, researchers are finding different ways to interrogate the data and understand the interactions in context.  ...  However, it is widely recognized that a significant portion of the data is scattered, redundant, not considered high quality, and not readily accessible to researchers in a systematic fashion.  ...  A group of homology-related links, including TreeFam 23 , mouse genome informatics (MGI) 24 , rat genome databases (RGD) 25 , and HGNC comparison of orthology predictions (HCOP) 26 are used to specify  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep04474">doi:10.1038/srep04474</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24667292">pmid:24667292</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3966033/">pmcid:PMC3966033</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2uj7x6vzyrgordjc3vfch3epku">fatcat:2uj7x6vzyrgordjc3vfch3epku</a> </span>
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The quest for orthologs: finding the corresponding gene across genomes

Arnold Kuzniar, Roeland C.H.J. van Ham, Sándor Pongor, Jack A.M. Leunissen
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/alw4ab5u3vdqlgfh3smvbfnjqu" style="color: black;">Trends in Genetics</a> </i> &nbsp;
Acknowledgements The authors are grateful to Jack Franklin and Simon Fisher for their help in shaping the manuscript and to the anonymous reviewers for their valuable comments.  ...  The examples of integrated databases include HUGO gene nomenclature committee (HGNC) Comparison of Orthology Predictions (HCOP; http://www.genenemas.org/) and Eukaryotic Orthology (YOGY; http://www.sanger.ac.uk  ...  Cons: Ortholuge predictions of orthologs are incomplete in the presence of single gene loss. Ortholuge is limited to pair-wise proteome comparisons.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2008.08.009">doi:10.1016/j.tig.2008.08.009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18819722">pmid:18819722</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4w6qrixl7naw7aoqko73vruavq">fatcat:4w6qrixl7naw7aoqko73vruavq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813044430/http://pongor.itk.ppke.hu/library/Group-Publications/PAPERS%20PDF%20ONLY/238_Kuzniar_etal2008.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/b7/c7b794d850bbc4cbfbe0ebd8cd74651c07aed802.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2008.08.009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Some Algorithmic Challenges in Genome-Wide Ortholog Assignment

Tao Jiang
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5acgllsvrbf5dar4dbo3vyrz2a" style="color: black;">Journal of Computer Science and Technology</a> </i> &nbsp;
We will also discuss some possible extensions of the approach to the simultaneous comparison of multiple genomes.  ...  In this article, we consider the recently proposed parsimony approach for assigning orthologs between closely related genomes based on genome rearrangement, which essentially attempts to transform one  ...  The HGNC Comparison of Orthology Predictions (HCOP) [26] is a tool maintained by HUGO Gene Nomenclature Committee that integrates and displays the human-mouse orthology assertions made by six methods  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11390-010-9304-6">doi:10.1007/s11390-010-9304-6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tx2q42pgafgh3c53i5x5bzix6m">fatcat:tx2q42pgafgh3c53i5x5bzix6m</a> </span>
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