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Using literature-based discovery to identify disease candidate genes

Dimitar Hristovski, Borut Peterlin, Joyce A. Mitchell, Susanne M. Humphrey
<span title="">2005</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jyf7co46pvdybh6jhdipt5d3im" style="color: black;">International Journal of Medical Informatics</a> </i> &nbsp;
We present BITOLA, an interactive literature-based biomedical discovery support system.  ...  To make the system more suitable for disease candidate gene discovery and to decrease the number of candidate relations, we integrate background knowledge about the chromosomal location of the starting  ...  In addition, we would like to thank Tom Rindflesch and Neil Smalheiser for providing valuable comments and insights.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijmedinf.2004.04.024">doi:10.1016/j.ijmedinf.2004.04.024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15694635">pmid:15694635</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gaxffooxwnbjxaycy5y74ebjmm">fatcat:gaxffooxwnbjxaycy5y74ebjmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100620153803/http://arrowsmith.psych.uic.edu/arrowsmith_uic/tutorial/hristovski_ijmi_2005.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/78/4c/784cabefdbec47261f6e48c7c6bc6fdb1cefe521.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijmedinf.2004.04.024"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Mining disease associated biomarker networks from PubMed

Zhong Huang
<span title="">2013</span> <i title="IEEE"> 2013 7th International Conference on Systems Biology (ISB) </i> &nbsp;
Top ranked neurology diseases were then used to extract associated genes from PubMed using context sensitive information retrieval methods.  ...  Associated genes were then integrated into pathways and subject to network biomarker analysis. Our approach identifies both known and potential biomarkers for 3 neurodegenerative diseases.  ...  Biomarker candidates discovery is considered as discovery of hidden semantic relations between diseases and genes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/isb.2013.6623786">doi:10.1109/isb.2013.6623786</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ayjdkiiplve7flgwezljr6aoji">fatcat:ayjdkiiplve7flgwezljr6aoji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811221033/http://www.aporc.org/ISB/2013/Proceedings/Papers/ISB2013F04.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/2e/1b/2e1b453d48954277c03c7a88c1154888f20be3fd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/isb.2013.6623786"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Using the BITOLA system to identify candidate genes for Parkinson's disease

Amela Karić, Alen Karić
<span title="2011-08-20">2011</span> <i title="Association of Basic Medical Sciences of FBIH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iwi24as26rg4hbblqpqi3aerjq" style="color: black;">Bosnian Journal of Basic Medical Sciences</a> </i> &nbsp;
Th e main goal of this research was to identify the potential candidate genes for idiopathic PD by using biomedical discovery support system (BITOLA).  ...  Discovering the novel candidate genes for multifactiorial diseases by using specially mentioned bioinformatics tool BITOLA could off er the new opportunity for researching genetics base of PD without using  ...  From this reason it is need to develop sophisticated techniques and tool to identify key candidates from gene list generated by disease gene discovery methods [] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17305/bjbms.2011.2572">doi:10.17305/bjbms.2011.2572</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21875422">pmid:21875422</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4362554/">pmcid:PMC4362554</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/izdjcd2stzdyrnmyw7tq7ui4fm">fatcat:izdjcd2stzdyrnmyw7tq7ui4fm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206153142/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4362554&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/9d/03/9d0319b233b1242e19fe0293954dbf443dc34baa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17305/bjbms.2011.2572"> <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/PMC4362554" 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 Drug Repositioning: Current Progress and Challenges

Younhee Ko
<span title="2020-07-23">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/smrngspzhzce7dy6ofycrfxbim" style="color: black;">Applied Sciences</a> </i> &nbsp;
Drug repositioning is a strategy to identify a new indication of existing or already approved drugs, beyond the scope of their original use.  ...  Novel drug discovery is time-consuming, costly, and a high-investment process due to the high attrition rate.  ...  These mechanisms allow us to identify candidate drugs and alternative targets of drugs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/app10155076">doi:10.3390/app10155076</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ine7jafxofdwticfwsqr7ipyz4">fatcat:ine7jafxofdwticfwsqr7ipyz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200806114905/https://res.mdpi.com/d_attachment/applsci/applsci-10-05076/article_deploy/applsci-10-05076-v2.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/57/8b/578b69ee24358edeba53e1ef5c1ed32b8eac04f4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/app10155076"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Beegle:from literature mining to disease-gene discovery

Sarah ElShal, Léon-Charles Tranchevent, Alejandro Sifrim, Amin Ardeshirdavani, Jesse Davis, Yves Moreau
<span title="2015-09-17">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;
a genomic model and rank a set of candidate genes to generate novel hypotheses.  ...  Typically, this process involves both finding genes known to be associated with the disease (through literature search) and carrying out preliminary experiments or screens (e.g. linkage or association  ...  First, we evaluated its ability to identify known disease-gene associations from the literature.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv905">doi:10.1093/nar/gkv905</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26384564">pmid:26384564</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4737179/">pmcid:PMC4737179</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6qongohyqfgzdbjdoswg6qbcye">fatcat:6qongohyqfgzdbjdoswg6qbcye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223062426/http://pdfs.semanticscholar.org/4318/0fa16c16accf4966ed4728cc3f5f8dc259a5.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/43/18/43180fa16c16accf4966ed4728cc3f5f8dc259a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv905"> <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/PMC4737179" 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 discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q2rzh4rosrd2rhrlmpfocas4qa" style="color: black;">Drug Discovery Today</a> </i> &nbsp;
Acknowledgements We wish to thank Dr Pavel Pospisil and Dr Lakshmanan K. Iyer for their helpful discussions in this project.  ...  Further, the literature-based angiogenesis network was refined using the retrieved gene expression profiles through a multivariate selection procedure, based on the hypothesis that literature-co-cited  ...  Applications to target discovery Identification of disease-associated entities Text mining has been broadly applied to identify disease-associated entities (genes/proteins) and to understand their roles  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2011.12.006">doi:10.1016/j.drudis.2011.12.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22178890">pmid:22178890</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c7k3puzntbhcrmzjlw6uvgxhny">fatcat:c7k3puzntbhcrmzjlw6uvgxhny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808202230/http://csmres.co.uk/cs.public.upd/article-downloads/Yang%20Adelstein%20and%20Kassis_a3138.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/7c/56/7c564b1985a81655e63ac7cfc1ced2a4789fff3e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2011.12.006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q2rzh4rosrd2rhrlmpfocas4qa" style="color: black;">Drug Discovery Today</a> </i> &nbsp;
Acknowledgements We wish to thank Dr Pavel Pospisil and Dr Lakshmanan K. Iyer for their helpful discussions in this project.  ...  Further, the literature-based angiogenesis network was refined using the retrieved gene expression profiles through a multivariate selection procedure, based on the hypothesis that literature-co-cited  ...  Applications to target discovery Identification of disease-associated entities Text mining has been broadly applied to identify disease-associated entities (genes/proteins) and to understand their roles  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2008.12.005">doi:10.1016/j.drudis.2008.12.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19135549">pmid:19135549</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/plsts2psuvclneuhgd5tlianwi">fatcat:plsts2psuvclneuhgd5tlianwi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808202230/http://csmres.co.uk/cs.public.upd/article-downloads/Yang%20Adelstein%20and%20Kassis_a3138.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/7c/56/7c564b1985a81655e63ac7cfc1ced2a4789fff3e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2008.12.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Computational drug repositioning through heterogeneous network clustering

Chao Wu, Ranga C Gudivada, Bruce J Aronow, Anil G Jegga
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
We clustered this weighted network to identify modules and then assembled all possible drug-disease pairs (putative drug repositioning candidates) from these modules.  ...  Results: Using known disease-gene and drug-target relationships from the KEGG database, we built a weighted disease and drug heterogeneous network.  ...  Figure 1 1 Workflow for identifying drug repositioning candidates using gene-and feature-based disease and drug heterogeneous network.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-7-s5-s6">doi:10.1186/1752-0509-7-s5-s6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564976">pmid:24564976</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4029299/">pmcid:PMC4029299</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uslocydzkfhfpfiwnnfeerm3se">fatcat:uslocydzkfhfpfiwnnfeerm3se</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830075802/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-7-S5-S6?site=http://bmcsystbiol.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/9c/17/9c17e978f16b94f37138795a2849d1a5a18222b4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-7-s5-s6"> <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/PMC4029299" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Evidence based computational drug repositioning candidate screening pipeline design: Case Study

Qian Zhu, Hongfang Liu, Yuji Zhang, Jiabei Wang
<span title="">2014</span> <i title="IEEE"> 2014 8th International Conference on Systems Biology (ISB) </i> &nbsp;
To demonstrate usability and evaluate efficacy of this novel pipeline, we successfully conducted a case study by identifying potential drug repositioning candidates for Alzheimer's disease (AD) based on  ...  In this paper, we introduce a novel computational pipeline designed for drug repositioning candidate screening based on existing phenotypical association (disease-disease association) discovery and pathway  ...  repositioning candidate discovery.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/isb.2014.6990757">doi:10.1109/isb.2014.6990757</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4m4mv3laurhgrmcia7oxk4mwg4">fatcat:4m4mv3laurhgrmcia7oxk4mwg4</a> </span>
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'RE:fine drugs': an interactive dashboard to access drug repurposing opportunities

Soheil Moosavinasab, Jeremy Patterson, Robert Strouse, Majid Rastegar-Mojarad, Kelly Regan, Philip R. O. Payne, Yungui Huang, Simon M. Lin
<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;
'RE:fine Drugs' demonstrates the possibilities to identify and prioritize novelty of candidates for drug repurposing based on the theory of transitive Drug-Gene-Disease triads.  ...  Here, we introduce 'RE:fine Drugs', a freely available interactive website for integrated search and discovery of drug repurposing candidates from GWAS and PheWAS repurposing datasets constructed using  ...  at the Research Institute at Nationwide Children s Hospital for their help to set up the host and domain.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw083">doi:10.1093/database/baw083</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27189611">pmid:27189611</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4869799/">pmcid:PMC4869799</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lz6s7m7o6jamxhy2ebfp52mfnm">fatcat:lz6s7m7o6jamxhy2ebfp52mfnm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207043109/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4869799&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/81/a6/81a602a84ca7767a42c42b60f889a5db60f47fcb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw083"> <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/PMC4869799" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Assessing the Need of Discourse-Level Analysis in Identifying Evidence of Drug-Disease Relations in Scientific Literature

Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Dingcheng Li, Hongfang Liu
<span title="">2015</span> <i title="IOS Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4ju2ftoebbcvrjj6lqnnbh42wq" style="color: black;">Studies in Health Technology and Informatics</a> </i> &nbsp;
We used multiple resources such as Semantic Medline, a literature based resource, and Medline search (for filtering spurious results) and inferred 8,772 potential drug-disease pairs.  ...  In this study, we investigated the significance of extracting information from multiple sentences specifically in the context of drug-disease relation discovery.  ...  Literature-based discovery Literature-based discovery (LBD) aims to find a connection/correlation between concepts using scientific literature.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26262109">pmid:26262109</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5859928/">pmcid:PMC5859928</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yyqiawkunzebxlaawpmagcnsku">fatcat:yyqiawkunzebxlaawpmagcnsku</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200513203401/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5859928&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/2e/66/2e66d746425e0b97de1cfe623a95582b93dddcd6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859928" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A 2.5-year snapshot of Mendelian discovery

Benjamin D. Solomon, Teresa Lee, Anh-Dao Nguyen, Tyra G. Wolfsberg
<span title="2016-04-03">2016</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5ni2bzmxbzaxhbmzgymoywe6ym" style="color: black;">Molecular Genetics &amp; Genomic Medicine</a> </i> &nbsp;
Discovery methods related to the 445 genes (representing 492 studies) newly identified as involved in human Mendelian disease within the selected~2.5-year period.  ...  We would predict that over time, the use of genomic sequencing methods will eclipse other methods of identifying disease genes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/mgg3.221">doi:10.1002/mgg3.221</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27468415">pmid:27468415</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4947858/">pmcid:PMC4947858</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2bni3ntwqjhqpnqoba7yvccium">fatcat:2bni3ntwqjhqpnqoba7yvccium</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208134023/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4947858&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/98/fd/98fd0fa746bc0dc98a0080c1338e3c224fa0c48f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/mgg3.221"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947858" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Using literature-based discovery to identify candidate genes for the interaction between myocardial infarction and depression

Zhenguo Dai, Qian Li, Guang Yang, Yini Wang, Yang Liu, Zhilei Zheng, Yingfeng Tu, Shuang Yang, Bo Yu
<span title="2019-06-11">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/woj2utb4kre43jh3bxegmfxgvm" style="color: black;">BMC Medical Genetics</a> </i> &nbsp;
The main purpose of this study was to identify potential candidate genes for the interaction between the two diseases.  ...  Some researchers have used the text mining tools to identify candidate genes for diseases [13] , such as multiple sclerosis and bilateral polymicrogyria [12, 14, 15] .  ...  By mining the Medline database, new information from the literature can be explored to identify new potential candidate genes linked to both MI and depression, and the potential new relationships can be  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12881-019-0841-8">doi:10.1186/s12881-019-0841-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31185929">pmid:31185929</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6560897/">pmcid:PMC6560897</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ll7xdyccwjeqnefcdtvwrownsy">fatcat:ll7xdyccwjeqnefcdtvwrownsy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209135445/https://bmcmedgenet.biomedcentral.com/track/pdf/10.1186/s12881-019-0841-8" 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/66/de/66dec71eedbce9fa8e4a6fc108a460773493c2f4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12881-019-0841-8"> <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/PMC6560897" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease

Yang Chen, Xiaoshu Cai, Rong Xu
<span title="2015-11-05">2015</span> <i title="American Medical Informatics Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g6q27b56yzeupjryv6lby2r2pa" style="color: black;">AMIA Annual Symposium Proceedings</a> </i> &nbsp;
First, we identified PD-specific mouse phenotypes using well-studied human disease genes. Then we searched all FDA-approved drugs for candidates that share similar mouse phenotype profiles with PD.  ...  Comparison of gene expression profiles between PD and top-ranked drug candidates indicates that quetiapine has the potential to treat PD.  ...  We used the GEO2R software 36 to identify the significantly differential expressed genes (adjusted p value <0.05) for the disease and drugs, respectively.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26958284">pmid:26958284</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4765695/">pmcid:PMC4765695</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/losiupjfsfgezcmmdg5qx54d2q">fatcat:losiupjfsfgezcmmdg5qx54d2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191026190000/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4765695&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/4a/d0/4ad03aada6d3a19164e2fb5a1178d1bbffeb5fb5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765695" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease

Ashutosh Malhotra, Erfan Younesi, Shweta Bagewadi, Martin Hofmann-Apitius
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odidfbcgarekjpyyfxpdptajxa" style="color: black;">Genome Medicine</a> </i> &nbsp;
A number of compelling candidate Alzheimer's biomarkers remain buried within the literature.  ...  Information about putative, highly speculative AD biomarkers was harvested from the literature using a semantic framework and was put into a functional context through disease-and stage-specific models  ...  Acknowledgements The authors would also like to thank "Alpha Tom Kodamullil" for her useful suggestions in setting up BEL framework used in this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-014-0097-z">doi:10.1186/s13073-014-0097-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25484918">pmid:25484918</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4256903/">pmcid:PMC4256903</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/urquki5eq5g3zefuxrydjgi3wi">fatcat:urquki5eq5g3zefuxrydjgi3wi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830034806/https://genomemedicine.biomedcentral.com/track/pdf/10.1186/s13073-014-0097-z?site=genomemedicine.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/ce/ed/ceeda4297192fe1598bb35f6c6f474b85ca83a8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-014-0097-z"> <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/PMC4256903" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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