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Answering biological questions: querying a systems biology database for nutrigenomics

Chris T. Evelo, Kees van Bochove, Jahn-Takeshi Saito
<span title="2010-10-30">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cm37q7fk2zhc7nbgwhszqpwzd4" style="color: black;">Genes &amp; Nutrition</a> </i> &nbsp;
The nutritional phenotype database When fully developed, the nutritional phenotype database, (dbNP, van Ommen et al. [18]) will be a research and collaboration tool and a publicly available data and knowledge  ...  A particularly urgent objective in coping with the data avalanche is making biologically meaningful information accessible to the researcher.  ...  Similarly, a query covers a list of compounds with certain values and a treatment with a specific dosage, e.g., 1 microgram of Vitamin B12.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12263-010-0190-x">doi:10.1007/s12263-010-0190-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21437033">pmid:21437033</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3040802/">pmcid:PMC3040802</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uu6wyjshdnb65kk7z6ow6h3vwy">fatcat:uu6wyjshdnb65kk7z6ow6h3vwy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171014065421/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/6fe/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjEwMDcvczEyMjYzLTAxMC0wMTkwLXgucGRm.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/3a/8d/3a8d6adbecabec1b2f877f7d83c7c20d685c6b16.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12263-010-0190-x"> <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/PMC3040802" 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 pathway approach to investigate the function and regulation of SREBPs

Sabine Daemen, Martina Kutmon, Chris T. Evelo
<span title="2013-03-21">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cm37q7fk2zhc7nbgwhszqpwzd4" style="color: black;">Genes &amp; Nutrition</a> </i> &nbsp;
This allows a more extensive study of the pathway through reviewing these links.  ...  SREBPs has been well described; however, a rapidly growing number of studies reveal the complex regulation of these SREBP transcription factors at multiple levels.  ...  The C-terminal domain is a hydrophilic region of 546 amino acids containing 4 repeats of a tryptophan-aspartate repeat, WD.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12263-013-0342-x">doi:10.1007/s12263-013-0342-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23516131">pmid:23516131</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3639327/">pmcid:PMC3639327</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oq55usrepfh2pfavj4c5p3ymz4">fatcat:oq55usrepfh2pfavj4c5p3ymz4</a> </span>
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A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

Elisa Cirillo, Laurence D. Parnell, Chris T. Evelo
<span title="2017-11-07">2017</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis.  ...  Tool evaluation was performed using a computational epistatic dataset of gene-gene interactions for obesity risk.  ...  The association of a SNP to a particular gene is normally evaluated using a cutoff for SNP significance in a specific gene neighborhood region.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2017.00174">doi:10.3389/fgene.2017.00174</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29163640">pmid:29163640</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5681904/">pmcid:PMC5681904</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i2j3u2a7lfhzlbfo6d5trmfvxu">fatcat:i2j3u2a7lfhzlbfo6d5trmfvxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302011128/http://pdfs.semanticscholar.org/ad10/0fbe00520edac7c0587129c947c7ab65df44.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/ad/10/ad100fbe00520edac7c0587129c947c7ab65df44.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2017.00174"> <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/PMC5681904" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CyTargetLinker app update: A flexible solution for network extension in Cytoscape

Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. Coort
<span title="2018-06-14">2018</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
CyTargetLinker provides a simple interface to extend networks with links to relevant data and/or knowledge extracted from so-called linksets.  ...  We first extend a protein-protein interaction network created with the stringApp, with compound-target interactions and disease-gene annotations.  ...  Formal Analysis, Validation, Writing -Original Draft Preparation, Writing - Ehrhart F Review & Editing; : Data Curation, Writing -Review & Editing; : Conceptualization, Supervision; : Willighagen EL Evelo  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.14613.1">doi:10.12688/f1000research.14613.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31489175">pmid:31489175</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6707396/">pmcid:PMC6707396</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/34tzrw6jwveelgms6znbbi7vwa">fatcat:34tzrw6jwveelgms6znbbi7vwa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430102336/https://f1000researchdata.s3.amazonaws.com/manuscripts/15902/0dcc1af8-040e-493b-bba7-4a86431857e2_14613_-_martina_summer-kutmon.pdf?doi=10.12688/f1000research.14613.1&amp;numberOfBrowsableCollections=17&amp;numberOfBrowsableGateways=23" 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/f3/7d/f37db575bc364b75d646176c5a633036345fffb2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.14613.1"> <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/PMC6707396" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CyTargetLinker app update: A flexible solution for network extension in Cytoscape

Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. Coort
<span title="2019-08-13">2019</span> <i title="F1000 ( Faculty of 1000 Ltd)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
CyTargetLinker provides a simple interface to extend networks with links to relevant data and/or knowledge extracted from so-called linksets.  ...  We first extend a protein-protein interaction network created with the stringApp, with compound-target interactions and disease-gene annotations.  ...  Formal Analysis, Validation, Writing -Original Draft Preparation, Writing - Ehrhart F Review & Editing; : Data Curation, Writing -Review & Editing; : Conceptualization, Supervision; : Willighagen EL Evelo  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.14613.2">doi:10.12688/f1000research.14613.2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qr654mccujeavnmmdb5jyzfilq">fatcat:qr654mccujeavnmmdb5jyzfilq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200718224223/https://f1000researchdata.s3.amazonaws.com/manuscripts/22256/4b9ef3d0-a334-46e5-86d2-81b4dd92b7e9_14613_-_martina_summer-kutmon_v2.pdf?doi=10.12688/f1000research.14613.2&amp;numberOfBrowsableCollections=24&amp;numberOfBrowsableInstitutionalCollections=5&amp;numberOfBrowsableGateways=24" 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/78/36/7836145dc997bef26ac83a4b238b9b50d0738120.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.14613.2"> <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>

ComMet: A method for comparing metabolic states in genome-scale metabolic models [article]

Chaitra Sarathy, Marian Breuer, Martina Kutmon, Michiel E. Adriaens, Chris T. Evelo, Ilja C. W. Arts
<span title="2020-09-15">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Being a comprehensive knowledge bases of cellular metabolism, Genome-scale metabolic models (GEMs) serve as mathematical tools for studying cellular flux states in various organisms.  ...  In this study, we introduce a model-based method, ComMet (Comparison of Metabolic states), for comprehensive analysis of large metabolic flux spaces and comparison of various metabolic states.  ...  Each node represents a reaction and the connections indicate shared metabolites (either a reactant or a product).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.09.14.296145">doi:10.1101/2020.09.14.296145</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qz6j7zaqlfaufnvwutjgmntpvy">fatcat:qz6j7zaqlfaufnvwutjgmntpvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718051220/https://www.biorxiv.org/content/biorxiv/early/2021/01/19/2020.09.14.296145.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/75/dd/75dd62e5405e874fbf85bdca8812e188432e2005.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.09.14.296145"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A network biology workflow to study transcriptomics data of the diabetic liver

Martina Kutmon, Chris T Evelo, Susan L Coort
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Results: A publicly available dataset comparing the liver transcriptome from lean and healthy vs. obese and insulin-resistant subjects was selected after a thorough analysis.  ...  downstream which might interfere with the action or efficiency of a drug.  ...  HNF4A is a nuclear receptor (NR), which is a key regulator of the liver cell function, is a sensor of inflammation and is known to regulate genes in lipid and glucose metabolism [34] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-971">doi:10.1186/1471-2164-15-971</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25399255">pmid:25399255</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4246458/">pmcid:PMC4246458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r4cn4ondozfafijichixigjbtu">fatcat:r4cn4ondozfafijichixigjbtu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830124543/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-15-971?site=http://bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/60/87/6087549984e8d848c48b237df1aa64d155caa022.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-971"> <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/PMC4246458" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

History of rare diseases and their genetic causes - a data driven approach [article]

Friederike Ehrhart, Egon L. Willighagen, Martina Kutmon, Max van Hoften, Nasim Bahram Sangani, Leopold G.M. Curfs, Chris T. Evelo
<span title="2019-04-01">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The data is available as a spreadsheet and as RDF in a semantic model modified from DisGeNET.This dataset relies on publicly available data and publications with a PubMed IDs but this is to our knowledge  ...  the first time this data has been linked and made available for further study under a liberal license.  ...  "http://www.wikidata.org/prop/direct/P3331") figshare = factory.createURI("https://doi.org/10.6084/m9.figshare.7718537.v1") def text = new File(input).getText() def data = parseCsv(text, separator: '\t'  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/595819">doi:10.1101/595819</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zvd3s77ltjh7nbyi2ntgjhwyr4">fatcat:zvd3s77ltjh7nbyi2ntgjhwyr4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429144928/https://www.biorxiv.org/content/biorxiv/early/2019/04/01/595819.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bc/31/bc31cc1ac8b86f0a7faa916e1e2bd229c507c363.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/595819"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Overlap of vitamin A and vitamin D target genes with CAKUT-related processes

Ozan Ozisik, Friederike Ehrhart, Chris T Evelo, Alberto Mantovani, Anaı̈s Baudot
<span title="2021-05-18">2021</span> <i title="F1000 Research Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
CAKUT patients display a large clinical variability as well as a complex aetiology, as only 5% to 20% of the cases have a monogenic origin.  ...  be relevant to a broad range of urogenital abnormalities.  ...  These results are expected due to the recognized role of vitamin A in differentiation. 43, 44 t should be noted that all overlapping CAKUT causal genes except NRIP1 are also part of the kidney development  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.51018.1">doi:10.12688/f1000research.51018.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35528959">pmid:35528959</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC9051587/">pmcid:PMC9051587</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pnppvanxdzhhfjaizi7t7m5e2m">fatcat:pnppvanxdzhhfjaizi7t7m5e2m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210519030247/https://f1000researchdata.s3.amazonaws.com/manuscripts/54123/1dfeb7f9-c936-431b-a559-377121f7a5f4_51018_-_ozan_ozisik.pdf?doi=10.12688/f1000research.51018.1&amp;numberOfBrowsableCollections=27&amp;numberOfBrowsableInstitutionalCollections=4&amp;numberOfBrowsableGateways=25" 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/26/44/26440e86fb6180198d771e4c79e86485d1dd1504.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.51018.1"> <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/PMC9051587" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis

Martina Kutmon, Thomas Kelder, Pooja Mandaviya, Chris T. A. Evelo, Susan L. Coort, Julio Vera
<span title="2013-12-05">2013</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;
and predicted microRNAs, (ii) enriching a molecular interaction network, containing DNA repair genes, with ENCODE transcription factor and (iii) building a regulatory meta-network in which a biological  ...  Visualization options enable biological interpretation of complex regulatory networks in a graphical way.  ...  While CluePedia is also available as a Cytoscape 3.x app, it requires a license key.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0082160">doi:10.1371/journal.pone.0082160</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24340000">pmid:24340000</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3855388/">pmcid:PMC3855388</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q2seyn4vibfrlkbtr5na5tm624">fatcat:q2seyn4vibfrlkbtr5na5tm624</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171009093000/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0082160&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/82/85/828559f7748b0c1229f20bd3c281146e5830bdec.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.0082160"> <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/PMC3855388" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bilberries potentially alleviate stress-related retinal gene expression induced by a high-fat diet in mice

Otto T Mykkänen, Giedrius Kalesnykas, Michiel Adriaens, Chris T Evelo, Riitta Törrönen, Kai Kaarniranta
<span title="2012-09-07">2012</span> <i title="Molecular Vision"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gctorfv4vzfc7b3sj56nhr24hq" style="color: black;">Molecular Vision</a> </i> &nbsp;
Mice (n=6 per group, four groups) were fed ad libitum a normal control diet (NCD), a HFD, or a diet with 5% bilberries (NCD+BB, HFD+BB) for 12 weeks.  ...  Despite minor effects in the phenotype, a diet rich in bilberries mitigates the upregulation of crystallins otherwise induced by HFD.  ...  expression of Tnf-α, intercellular adhesion molecule 1 (Icam-1), interleukin-6, and interleukin-1-beta in the retina [46] , and network analyses of two mouse models centered on p38MAPK (Ins2 Akita ) and T  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22993483">pmid:22993483</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3444297/">pmcid:PMC3444297</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uscdxzic5jetzbgk422oftm6oq">fatcat:uscdxzic5jetzbgk422oftm6oq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210203540/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3444297&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/e3/af/e3af42008b2969680d483e10bfa6e08a191e5891.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3444297" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

Ryan A. Miller, Friederike Ehrhart, Lars M. T. Eijssen, Denise N. Slenter, Leopold M. G. Curfs, Chris T. Evelo, Egon L. Willighagen, Martina Kutmon
<span title="2019-02-21">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
In conclusion, using pathway models for classical enrichment and more advanced network analysis enables a more comprehensive analysis of gene expression data and provides novel results.  ...  Our active module analysis provided a valuable extension of the analysis prominently showing the regulatory mechanism of MECP2, especially on DNA maintenance, cell cycle, transcription, and translation  ...  The samples were taken postmortem from human frontal and temporal cortex of three Rett syndrome patients (MECP2 mutations c.378-2A>G, c.763C>T, c.451G>T) and three age-, gender-, and ethnicitymatched controls  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2019.00059">doi:10.3389/fgene.2019.00059</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30847002">pmid:30847002</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6393361/">pmcid:PMC6393361</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pdvpmwegevc67kgyoeqzreqiza">fatcat:pdvpmwegevc67kgyoeqzreqiza</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200212075545/https://fjfsdata01prod.blob.core.windows.net/articles/files/436196/pubmed-zip/.versions/1/.package-entries/fgene-10-00059/fgene-10-00059.pdf?sv=2015-12-11&amp;sr=b&amp;sig=S9Kuw3ipfa6haPeBiYvQZDpkDf3V9x%2Fq1lH7vg9lmR8%3D&amp;se=2020-02-12T07%3A56%3A15Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-10-00059.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/f3/0f/f30f4fcfcd534417adfd13570c14eb40f2170c3a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2019.00059"> <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/PMC6393361" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Effect of Vitamin E on Glutathione-Dependent Enzymes

Rachel I. M. van Haaften, Guido R. M. M. Haenen, Chris T. A. Evelo, Aalt Bast
<span title="">2003</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g377oj2ubbauxfyhaqzc5yf4ye" style="color: black;">Drug metabolism reviews (Softcover ed.)</a> </i> &nbsp;
A submitted manuscript is the version of the article upon submission and before peer-review.  ...  Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1081/dmr-120024086">doi:10.1081/dmr-120024086</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12959415">pmid:12959415</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bjzobgdownhqzlaycrekm7f7hq">fatcat:bjzobgdownhqzlaycrekm7f7hq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428183735/https://cris.maastrichtuniversity.nl/portal/files/1404452/guid-742a2e7a-cc26-462f-ae13-73d959cea78c-ASSET1.0.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/3d/0c/3d0c6b3332646709e82039783707a9a664a570fe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1081/dmr-120024086"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A resource to explore the discovery of rare diseases and their causative genes

Friederike Ehrhart, Egon L. Willighagen, Martina Kutmon, Max van Hoften, Leopold M. G. Curfs, Chris T. Evelo
<span title="2021-05-04">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a577b42d4nfhddl7kurxnuyzem" style="color: black;">Scientific Data</a> </i> &nbsp;
AbstractHere, we describe a dataset with information about monogenic, rare diseases with a known genetic background, supplemented with manually extracted provenance for the disease itself and the discovery  ...  The data are available under CC0 license as spreadsheet and as RDF in a semantic model modified from DisGeNET, and was added to Wikidata.  ...  For importing in R we recommend to disable quoting and enabling headers (read.table(file = "Gene-RD-Provenance_V2.1.txt", quote = "", sep = '\t' , header = TRUE).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41597-021-00905-y">doi:10.1038/s41597-021-00905-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33947870">pmid:33947870</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hcexmrswzrf7fjq4v2nrdqbniy">fatcat:hcexmrswzrf7fjq4v2nrdqbniy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718082802/https://www.nature.com/articles/s41597-021-00905-y.pdf?error=cookies_not_supported&amp;code=39f5f921-9ff7-4649-93cd-eb245627954f" 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/3e/cb/3ecbb5071e4b6484648ee115deae51d3b4e1a760.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41597-021-00905-y"> <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>

Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus–A Co-expression Network Based Analysis

Amnah Siddiqa, Elisa Cirillo, Samar H. K. Tareen, Amjad Ali, Martina Kutmon, Lars M. T. Eijssen, Jamil Ahmad, Chris T. Evelo, Susan L. Coort
<span title="2018-12-21">2018</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/evju7ot335gbrctgmomg4gg6je" style="color: black;">Frontiers in Physiology</a> </i> &nbsp;
In the current study, the analysis of a transcriptomic data set was performed for functional assessment of ANGPTL8 in liver.  ...  Angiopoietin like protein 8 (ANGPTL8) is a newly identified hormone with unique nature due to its ability to regulate both glucose and lipid metabolic pathways.  ...  It is a key signaling component of B-and T-cell activation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphys.2018.01841">doi:10.3389/fphys.2018.01841</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30627105">pmid:30627105</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6309236/">pmcid:PMC6309236</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/52jhtbbl4vduvlv6spnrmszm4a">fatcat:52jhtbbl4vduvlv6spnrmszm4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302225733/http://pdfs.semanticscholar.org/ab1a/5f2bc749d2a67eb950ca8aa2face4a754bed.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/ab/1a/ab1a5f2bc749d2a67eb950ca8aa2face4a754bed.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphys.2018.01841"> <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/PMC6309236" 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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