Filters








132,480 Hits in 3.6 sec

GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms

Emre Guney, Javier Garcia-Garcia, Baldo Oliva
<span title="2014-02-14">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
GUILDify offers a prioritization approach based on the protein-protein interaction network where the initial phenotype-gene associations are retrieved via free text search on biological databases.  ...  Special attention has been paid on using physical interactions between the proteins encoded by the genes to link them with diseases.  ...  For a given phenotype, GUILDify uses descriptive fields in several proteomics and genomics databases in combination with network-based prioritization methods and provides an interactome-wide ranking.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu092">doi:10.1093/bioinformatics/btu092</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24532728">pmid:24532728</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nif7bx2c7re4tolgrdjwognwp4">fatcat:nif7bx2c7re4tolgrdjwognwp4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227152515/http://pdfs.semanticscholar.org/7d41/803eedc48764cd2433c862260bd3ef552a9a.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/7d/41/7d41803eedc48764cd2433c862260bd3ef552a9a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu092"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

GRONS: a comprehensive genetic resource of nicotine and smoking

Zhonghai Fang, Yichen Yang, Yanshi Hu, Ming D Li, Ju Wang
<span title="2017-01-01">2017</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;
genes associated with nicotine addiction.  ...  Moreover, GRONS not only provides tools for data browse, search and graphical presentation of gene prioritization, but also presents the results from comprehensive bioinformatics analyses for the prioritized  ...  Acknowledgement We are grateful to the staff at Information Center of Tianjin Medical University for their support and help on managing the server. We also appreciate Mr. Xinhua Liu and Ms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bax097">doi:10.1093/database/bax097</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vla7ie7jeffvnobcmvou6i6nve">fatcat:vla7ie7jeffvnobcmvou6i6nve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200315065454/https://watermark.silverchair.com/bax097.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAnQwggJwBgkqhkiG9w0BBwagggJhMIICXQIBADCCAlYGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMT_znloZPwb60NZyfAgEQgIICJ8vHhUoy0xSesbZ2gRUkz_2rE7F69O_VoaXl1ESF_RtFhxuSsQCaknxTNaHEjTG_ruqXzOcix8TdZb8Yfg-3Po8Bzfb2CNEYeIljSLcWU3EUDGEW691bgMDgvGXmh3QEjMelYnB2Auz6kueob7l2jL2oCl7b8aZWWv-hr6uPHRjOO46IGSAv3zO9ZYSfiBtIxn_CcbnNFpsB3phYOqaPxc7s4hB9g_C6VDuAVKX3kKXOVQOGWM2M8DfCI9S9Wd_OwfG0SlmKtM2RFsxkJVjMPEEv1rFBybeUd34ONpRQdUegkWLROC-neTW0iWVu2Or0Me0iFL3E6Gb6K0j9aybBb1GSwhribkUrIIRWqZ3hSMNxMOY8eWo4Q0avC7sLi00hv43RZrLj7F7g_VZSg80x0x2TA-SsEj3Dvb3gwWZs7AMOIQFpI-MW5B9aWVR3oRdc-jgHplfydptREqxi7Rnox-OSoLinrRgd0-WzHZg4c9CFKcU6X1-MkrFL6AVFnA7icwXVXyd1nSNaD-H5F0KdhOcyNbrE0jM7VbChoa42infD8mEc_51e5a0cdk2rAYkv-W9MTQ33PsVMO7DJevq0pHmbck877hhFgDLJ1RW9O2VBiqHBAxWHfre1woByRUCcFgXM2HB3hIhs0bNE1HDR2_Muzk38we48Yl3RjXm_WmnhpPwa6ncGjj48VfoIP5wgEDrqWHfL5qURYYlQxb909-aaA5tA855S" 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/4e/70/4e70f814c9b724d3e7a9ecb56d5077ea42bec256.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bax097"> <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>

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

Imane Boudellioua, Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos, Robert Hoehndorf
<span title="2018-10-02">2018</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Information that links patient phenotypes to databases of gene-phenotype associations observed in clinical or non-human model organism research can provide useful information and improve variant prioritization  ...  We have developed OligoPVP, an algorithm that can be used to prioritize causative combinations of variants in digenic and oligogenic diseases, using whole exome or whole genome sequences together with  ...  We have combined PhenomeNET with genome-wide pathogenicity predictions to develop the PhenomeNET Variant Predictor (PVP) 4 as a system that combines information about pathogenicity of variants with known  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-018-32876-3">doi:10.1038/s41598-018-32876-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30279426">pmid:30279426</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6168481/">pmcid:PMC6168481</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5kvtz7pu3zbrtatiooaqz3ick4">fatcat:5kvtz7pu3zbrtatiooaqz3ick4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430083755/https://www.repository.cam.ac.uk/bitstream/handle/1810/285619/s41598-018-32876-3.pdf;jsessionid=78FCAA2EB54BAE394954C8715FDFA8C9?sequence=3" 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/10.1038/s41598-018-32876-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168481" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prioritizing anthropogenic chemicals in drinking water and sources through combined use of mass spectrometry and ToxCast toxicity data

Andrea M. Brunner, Milou M.L. Dingemans, Kirsten A. Baken, Annemarie P. van Wezel
<span title="2018-10-18">2019</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mlgm2lsi2zcufo6cnuvtfy5pym" style="color: black;">Journal of Hazardous Materials</a> </i> &nbsp;
Here, we compare prioritization of chemicals in Dutch water samples based on relative intensities only to prioritization including hazard information based on high-throughput in vitro toxicity data.  ...  The comparison showed that different prioritization strategies resulted in significantly different ranking, with only 2 suspects prioritized based on occurrence among the top 20 in the hazard ranking.  ...  The relative intensities of suspect chemicals were combined with ToxCast toxicity information to calculate a synergistic priority score by dividing the ISeq corrected for the water type by the 5 th percentile  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jhazmat.2018.10.044">doi:10.1016/j.jhazmat.2018.10.044</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30384243">pmid:30384243</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zdom7fcd3ngirkgyqytistkcoq">fatcat:zdom7fcd3ngirkgyqytistkcoq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200311011124/https://dspace.library.uu.nl/bitstream/handle/1874/377444/1_s2.0_S0304389418309531_main_1_.pdf;jsessionid=9EEF2A1A03721AEDEE5445B2E63630C8?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] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3c/85/3c85fcec7fea550147dad5596444cc0074f3d0a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jhazmat.2018.10.044"> <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>

METU-SNP: An Integrated Software System for SNPComplex Disease Association Analysis

Gürkan Üstünkar, Yeşim Aydın Son
<span title="2011-06-01">2011</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
METU-SNP software is a Java based integrated desktop application specifically designed for the prioritization of SNP biomarkers and the discovery of genes and pathways related to diseases via analysis  ...  We believe that the METU-SNP will help researchers with the reliable identification of SNPs that are involved in the etiology of complex diseases, ultimately supporting the development of personalized  ...  Acknowledgements We sincerely thank developers of SNPLogic for helping us with our integrated database structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2011-187">doi:10.1515/jib-2011-187</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uniwvj4jkbgdvlzyb32vwfasb4">fatcat:uniwvj4jkbgdvlzyb32vwfasb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201129162443/https://www.degruyter.com/downloadpdf/journals/jib/8/2/article-p204.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/25/b5/25b51e80433cccbfd3e6f909c93269150fd0fdb0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2011-187"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> degruyter.com </button> </a>

METU-SNP: an integrated software system for SNP-complex disease association analysis

Gürkan Ustünkar, Yeşim Aydın Son
<span title="2011-12-12">2011</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
METU-SNP software is a Java based integrated desktop application specifically designed for the prioritization of SNP biomarkers and the discovery of genes and pathways related to diseases via analysis  ...  We believe that the METU-SNP will help researchers with the reliable identification of SNPs that are involved in the etiology of complex diseases, ultimately supporting the development of personalized  ...  Acknowledgements We sincerely thank developers of SNPLogic for helping us with our integrated database structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2011-187">doi:10.2390/biecoll-jib-2011-187</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22156365">pmid:22156365</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s4ngjm6ffzhndpmm7hrya2pc6u">fatcat:s4ngjm6ffzhndpmm7hrya2pc6u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200225133245/https://www.degruyter.com/downloadpdf/j/jib.2011.8.issue-2/biecoll-jib-2011-187/biecoll-jib-2011-187.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2011-187"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Candidate Gene Predictions: Bioinformatics Significance in Linkage Analysis

<span title="2015-11-05">2015</span> <i title="International Journal of Science and Research"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odv46yibm5gf7evzoopmrrqr3q" style="color: black;">International Journal of Science and Research (IJSR)</a> </i> &nbsp;
The prioritization of target genes are based on their presence in particular disease or phenotype. Gene Wanderer combines two sources of information for candidate gene predictions.  ...  Gene Cards: The Human Gene Database GeneCards is an integrated database that provides information on all annotated and predicted human genes with domain, expression, functions, orthologs , paralogs, localization  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21275/v4i11.sub15940">doi:10.21275/v4i11.sub15940</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bafcil632vhgvg75rftlvijqhi">fatcat:bafcil632vhgvg75rftlvijqhi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220303204707/https://www.ijsr.net/archive/v4i11/SUB15940.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/28/85/2885bad1c182f812cbb6851809db0c32dbee0845.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21275/v4i11.sub15940"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Gene4MND: An Integrative Genetic Database and Analytic Platform for Motor Neuron Disease

Guihu Zhao, Zhen Liu, Mengli Wang, Yanchun Yuan, Jie Ni, Wanzhen Li, Ling Huang, Yiting Hu, Pan Liu, Xiaorong Hou, Jifeng Guo, Hong Jiang (+4 others)
<span title="2021-04-01">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uc7xbcwzljashhncrlsxupx3em" style="color: black;">Frontiers in Molecular Neuroscience</a> </i> &nbsp;
Combined with popular genomic data sources, various functional annotation data were integrated into the database.  ...  Gene Prioritization To identify high-confidence genes by their relevance to MND, gene prioritization (except for C9orf72 and ATXN2) was conducted by combining the different types of genetic evidence as  ...  No use, distribution or reproduction is permitted which does not comply with these terms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fnmol.2021.644202">doi:10.3389/fnmol.2021.644202</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33867934">pmid:33867934</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8047132/">pmcid:PMC8047132</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pehrmgrl5jgd3f7s6s7x4trsvq">fatcat:pehrmgrl5jgd3f7s6s7x4trsvq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210404131705/https://fjfsdata01prod.blob.core.windows.net/articles/files/644202/pubmed-zip/.versions/1/.package-entries/fnmol-14-644202/fnmol-14-644202.pdf?sv=2018-03-28&amp;sr=b&amp;sig=XgXsFVzxkPhc4Ybrc6PmXeZMkZoXEx8j9pu41jkMA%2BM%3D&amp;se=2021-04-04T13%3A17%3A34Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fnmol-14-644202.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/a7/ab/a7ab114bff787157a360dc5dc8cde048085e1ec9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fnmol.2021.644202"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8047132" 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 prioritization using a probabilistic knowledge model

Shuguang Wang, Milos Hauskrecht, Shyam Visweswaran
<span title="">2009</span> <i title="IEEE"> 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop </i> &nbsp;
., genes) and is extracted from a domain database (e.g., protein-protein interaction database).  ...  In this paper, we present a new gene prioritization method that learns a probabilistic knowledge model and exploits it to prioritize candidate genes.  ...  Such information include sequence data [1] , combination of sequence data and biological annotation information [2] , functional information, and gene expression data [3] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/bibmw.2009.5332107">doi:10.1109/bibmw.2009.5332107</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kksaqezh7bf7dipaxu2rhmro74">fatcat:kksaqezh7bf7dipaxu2rhmro74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706040643/http://people.cs.pitt.edu/~milos/research/BIBM_Shuguang_workshop_2009.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/23/fc/23fc4e5b7cd7fbf6287497d3857133385cbd9c03.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/bibmw.2009.5332107"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans

<span title="2020-01-08">2019</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 fill the unmet need, we integrated 580 799 DNMs, including 30 060 coding DNMs detected by WES/WGS from 23 951 individuals across 24 phenotypes and prioritized a list of candidate genes with different  ...  Furthermore, Gene4Denovo provides end-users with limited bioinformatics skills to analyse their own genetic data, perform comprehensive annotation, and prioritize candidate genes using custom parameters  ...  Additionally, users will be able to analyse more DNMs by integrating their own in-house data with our database and then prioritize new candidate genes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz923">doi:10.1093/nar/gkz923</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31642496">pmid:31642496</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145562/">pmcid:PMC7145562</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qw2tpvetirgobd5l4wqmw6b4ke">fatcat:qw2tpvetirgobd5l4wqmw6b4ke</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200512060423/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7145562&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/13/18/13188246dfe33e2fa109f5a7869849e12143bf4d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz923"> <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/PMC7145562" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Improving Disease Gene Prioritization by Comparing the Semantic Similarity of Phenotypes in Mice with Those of Human Diseases

Anika Oellrich, Robert Hoehndorf, Georgios V. Gkoutos, Dietrich Rebholz-Schuhmann, Markus Schuelke
<span title="2012-06-14">2012</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;
In this manuscript, we present a method for disease gene prioritization based on comparing phenotypes of mouse models with those of human diseases.  ...  Our method significantly outperforms previous phenotype-based approaches of prioritizing gene-disease associations.  ...  The OMIM database collects information about human heritable diseases, including genotype and phenotype information and known gene-disease associations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0038937">doi:10.1371/journal.pone.0038937</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22719993">pmid:22719993</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3375301/">pmcid:PMC3375301</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ajsbuifb4bgxjkgqy3cgvotvnu">fatcat:ajsbuifb4bgxjkgqy3cgvotvnu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170930225906/https://core.ac.uk/download/pdf/10184403.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/e2/9e/e29e3e0f23c2fac3f7fd444d24ceab0334ead8c3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0038937"> <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/PMC3375301" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals

Peifeng Ruan, Jing Shen, Regina M. Santella, Shuigeng Zhou, Shuang Wang
<span title="2016-06-14">2016</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 simulation studies, we demonstrate the power gain from using both the prior biological information and variance signals compared to using either of the two or neither information.  ...  Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one  ...  are connected to genes with high gene-level combined signal scores.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw546">doi:10.1093/nar/gkw546</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27302130">pmid:27302130</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5027497/">pmcid:PMC5027497</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4y72sial5raita3yfgfb4o2e7a">fatcat:4y72sial5raita3yfgfb4o2e7a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729015042/https://watermark.silverchair.com/gkw546.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaAwggGcBgkqhkiG9w0BBwagggGNMIIBiQIBADCCAYIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM_8hp8Gqp4SJzgkHiAgEQgIIBU9Zcx_P3D3BpL7fQ1PaCYqAXke7USkEl96r5IsbLGT40zLWp4whvnXWA4372neDIzVkDVG-UZwS6pHhC9iW-ay_m7Nop_hB3dJD9LbDlUnhu2s6FRPyqRxdHf2DH-GxlWk3bS4D-mndqWWHsME-x5KZ2lT4tkhliQeMBd8pycp-Wy6ZAEFPhMDqauNjRnNjVW-isPbXeC0dLdWxePpZ9xGME5JToowMY4o_LbeOmP59wkzQSm0MTLMtjiyvPae9N72e3LzzoDCqR995lscb36KC2kvZlluXetwkpTqTEKHyFBKQCOZGLgnmP-GG6wKTeHOr6Wh86IUNP3G-op6b45-9e4-lfh0OFnn-ovU4nLeIXNHDRrWS4GFLEh_vjpuOM4JC45pGTfrrhK5Skv-GgNOETj22wJ2-pagKp761LnWbvps9PiCsZ4uqkPFW-oVS0PYuJtQ" 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/63/dd/63dd5d35e475cfc743a054b8b1a368d7f429d925.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw546"> <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/PMC5027497" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prioritizing network communities

Marinka Zitnik, Rok Sosič, Jure Leskovec
<span title="2018-06-29">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
CRank can be used with any community detection method. It needs only information provided by the network structure and does not require any additional metadata or labels.  ...  CRank efficiently evaluates robustness and magnitude of structural features of each community and then combines these features into the community prioritization.  ...  In contrast, ranking communities by modularity score gives a poor correspondence with information in the external chemical databases (Fig. 3c ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-018-04948-5">doi:10.1038/s41467-018-04948-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29959323">pmid:29959323</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6026212/">pmcid:PMC6026212</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/57ugmvqa5bfubom7ooiimyfuny">fatcat:57ugmvqa5bfubom7ooiimyfuny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220082555/http://pdfs.semanticscholar.org/20c8/ef1bd47a27cf3d44452d1a0d1a9dbaf67f8f.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/20/c8/20c8ef1bd47a27cf3d44452d1a0d1a9dbaf67f8f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-018-04948-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026212" 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 prioritization for livestock diseases by data integration

Li Jiang, Peter Sørensen, Bo Thomsen, Stefan M. Edwards, Axel Skarman, Christine M. Røntved, Mogens S. Lund, Christopher T. Workman
<span title="">2012</span> <i title="American Physiological Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mqztspprufa63gu3akalkojdd4" style="color: black;">Physiological Genomics</a> </i> &nbsp;
The transcriptome ranks was integrated with the ranks from the prioritizations based on phenome information.  ...  Ortholog information. An important feature of our networkbased gene prioritization approach is that it allow us to combine information from multiple species (cattle, human, and mouse).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1152/physiolgenomics.00047.2011">doi:10.1152/physiolgenomics.00047.2011</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22234994">pmid:22234994</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dt3olo4cdfabpnoguaammdh5g4">fatcat:dt3olo4cdfabpnoguaammdh5g4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218092159/http://pdfs.semanticscholar.org/0a96/c1c0bc04630de908b92a312eafcc8ea9b528.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/0a/96/0a96c1c0bc04630de908b92a312eafcc8ea9b528.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1152/physiolgenomics.00047.2011"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study

S. F. Saccone, R. Bolze, P. Thomas, J. Quan, G. Mehta, E. Deelman, J. A. Tischfield, J. P. Rice
<span title="2010-06-06">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;
Investigators will often incorporate information from biological databases so that biologically relevant SNPs, such as those in genes related to the phenotype or with potentially nonneutral effects on  ...  Users can specify candidate genes or genomic regions with custom levels of prioritization.  ...  METHODS Genomic Information Networks Given a list of SNPs and P-values from a statistical test for genetic association, the goal of the GIN prioritization method (4) is to combine biological information  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq513">doi:10.1093/nar/gkq513</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20529875">pmid:20529875</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2896195/">pmcid:PMC2896195</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/crtot5o3rrc5jgsbuzlf623gpq">fatcat:crtot5o3rrc5jgsbuzlf623gpq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222050117/http://pdfs.semanticscholar.org/340b/12b8ee7b1f2ad6a4c48416a9519af69e91ff.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/34/0b/340b12b8ee7b1f2ad6a4c48416a9519af69e91ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq513"> <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/PMC2896195" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 132,480 results