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The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork, Lars J. Jensen, Christian von Mering
<span title="2016-10-18">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;
The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms.  ...  The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful.  ...  ACKNOWLEDGEMENTS The authors are indebted to Yan P. Yuan (EMBL Heidelberg) for IT support, and to Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw937">doi:10.1093/nar/gkw937</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27924014">pmid:27924014</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5210637/">pmcid:PMC5210637</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3y6esccgnrc4tbzudtgsowov4a">fatcat:3y6esccgnrc4tbzudtgsowov4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304153648/http://pdfs.semanticscholar.org/c8aa/7efd11ff4c2b2f1ac34fa1c80ecd45650a8c.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/c8/aa/c8aa7efd11ff4c2b2f1ac34fa1c80ecd45650a8c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw937"> <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/PMC5210637" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork, Lars J Jensen, Christian Von Mering
<span title="">2016</span>
The STRING resource is available online, at http://string-db.org/. Christian (2016). The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.  ...  The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms.  ...  ACKNOWLEDGEMENTS The authors are indebted to Yan P. Yuan (EMBL Heidelberg) for IT support, and to Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5167/uzh-144858">doi:10.5167/uzh-144858</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ivii3eqk7rfy7pxmumrncfsttq">fatcat:ivii3eqk7rfy7pxmumrncfsttq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200223175519/https://www.zora.uzh.ch/id/eprint/144858/1/gkw937.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/8c/20/8c203c4dc63f8bc90cb30ef6501c638a411f1b91.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5167/uzh-144858"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Duchenne Muscular Dystrophy (DMD) Protein-Protein Interaction Mapping

Mostafa Rezaei Tavirani, Farshad OkHOVATIAN, Mona Zamanian Azodi, Majid Rezaei Tavirani
<span title="">2017</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/x2cqekkvavgyrngaxvf6ajbg2e" style="color: black;">Iranian journal of child neurology</a> </i> &nbsp;
Applying Cytoscape and String Database, the protein-protein interaction network was constructed and the gene ontology of the constructed network was analyzed for biological process, molecular function,  ...  Among 100 proteins related to DMD, dystrophin, utrophin, caveolin 3, and myogenic differentiation 1 play key roles in DMD network.  ...  The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res 2016: gkw937. 14.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29201118">pmid:29201118</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5703623/">pmcid:PMC5703623</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/62cvh7i6mvdihlghxmpve6oxmm">fatcat:62cvh7i6mvdihlghxmpve6oxmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210192738/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5703623&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/f3/07/f30768848e2f2e059dd5ffc37a5bb34f2896600b.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/PMC5703623" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities

John D Lapek, Patricia Greninger, Robert Morris, Arnaud Amzallag, Iulian Pruteanu-Malinici, Cyril H Benes, Wilhelm Haas
<span title="2017-09-11">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t2bqrmk7orfmxpqzqwiiyjwide" style="color: black;">Nature Biotechnology</a> </i> &nbsp;
We expect that IMAHP can be broadly used to gain insight into how changing landscapes of protein-protein associations affect the phenotype of biological systems.  ...  in specific cell lines from the consensus network impacts to cellular fitness.  ...  Acknowledgements We thank Steven Gygi, Harvard Medical School, for access to computational software and facilities to process the proteomics data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt.3955">doi:10.1038/nbt.3955</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28892078">pmid:28892078</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5683351/">pmcid:PMC5683351</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pntvfyza6zg23kl4p3omjoo5ei">fatcat:pntvfyza6zg23kl4p3omjoo5ei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724005022/https://dash.harvard.edu/bitstream/handle/1/35982072/5683351.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3c/8d/3c8d3b43349c1f92fa13c809bd7c9d03a18d3212.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt.3955"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5683351" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioinformatics in translational drug discovery

Sarah K. Wooller, Graeme Benstead-Hume, Xiangrong Chen, Yusuf Ali, Frances M.G. Pearl
<span title="2017-05-09">2017</span> <i title="Portland Press Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6l6pmcnczjcrlbo3znqgtyvpqa" style="color: black;">Bioscience Reports</a> </i> &nbsp;
Competing interests The authors declare that there are no competing interests associated with the manuscript.  ...  break repair; SSL, synthetically sensitive or lethal; TCGA, The Cancer Genome Atlas.  ...  This illustrates the protein-protein interaction network of proteins (derived from the STRING database [114] ) involved in the DNA damage response as described in [46] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1042/bsr20160180">doi:10.1042/bsr20160180</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28487472">pmid:28487472</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iffd7elku5b5fbnrggvpwzbqn4">fatcat:iffd7elku5b5fbnrggvpwzbqn4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427113929/http://sro.sussex.ac.uk/id/eprint/77617/1/BSR20160180.full-2.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/a2/dc/a2dc23b30d24f18d9ff497e692fbc99cd469e4a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1042/bsr20160180"> <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>

Presentation A. de Brouwer [article]

De Sl
<span title="2019-07-15">2019</span> <i title="Figshare"> Figshare </i> &nbsp;
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362-D8.  ...  The universal protein resource (UniProt).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.8869892.v1">doi:10.6084/m9.figshare.8869892.v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/efmvoagwxrdjllizargtldhyjy">fatcat:efmvoagwxrdjllizargtldhyjy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200214050120/https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/16261598/Brouwerde_AFMJoubertSyndromeFinalPresentation.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/63/9f/639fada8f45fefad78943d006b68ee801f49eecd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.8869892.v1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium

Woncheoul Park, Deivendran Rengaraj, Dong-Yong Kil, Heebal Kim, Hak-Kyo Lee, Ki-Duk Song
<span title="2017-09-18">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
The symptoms of severe hypocalcaemia are associated with the loss/weakness of muscle and nerve function, milk fever in cows, and tetany in lactating cows, pigs, and dogs.  ...  Quality screening and annotation of the RNA-seq reads revealed several differentially expressed genes (DEGs) in the kidney samples between 0.8 and 1.0% Ca intake, 0.8 and 1.2% Ca intake, and 1.0 and 1.2%  ...  Protein/protein interaction network and Co-occurrence analysis. We used the STRING database 80 to construct the protein/protein interaction network.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-11379-7">doi:10.1038/s41598-017-11379-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28924246">pmid:28924246</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5603577/">pmcid:PMC5603577</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wvpmpqh5nbbwfmgayugfvylnfa">fatcat:wvpmpqh5nbbwfmgayugfvylnfa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191026162654/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5603577&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/37/1c/371cad88a182fcb96de2c36888bc8713c7e208bc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-11379-7"> <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/PMC5603577" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies

Medha L. Upasani, Bhakti M. Limaye, Gayatri S. Gurjar, Sunitha M. Kasibhatla, Rajendra R. Joshi, Narendra Y. Kadoo, Vidya S. Gupta
<span title="2017-08-10">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
protein especially for the majority of the vegetarian population in the Indian sub-continent.  ...  Moreover, the pathogen can survive in soil for up to six years even in the absence of the host, which makes its control very difficult 2 .  ...  STRING database), were used to construct an interaction network (Fig. 2) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-07114-x">doi:10.1038/s41598-017-07114-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28798320">pmid:28798320</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5552786/">pmcid:PMC5552786</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a2wn3ztkh5gp5kpa7spzamnxbi">fatcat:a2wn3ztkh5gp5kpa7spzamnxbi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191028223517/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5552786&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/65/39/65392823a89e950769b51fab19afe060efbe5567.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-07114-x"> <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/PMC5552786" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Report of the Executive Committee for 2017

A. T. Ashcroft
<span title="2019-01-01">2019</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rd3cuh2n4rfezc6sy4igtb5jci" style="color: black;">Acta Crystallographica Section A: Foundations and Advances</a> </i> &nbsp;
The report of the Executive Committee for 2017 is presented.  ...  Other important events for the crystal-growth community in 2017 were: 7th Asian Conference on Crystal Growth and Crystal Technology (CGCT-7)  ...  Members and consultants of the CCGCM are strongly involved in the work of the Programme and Advisory Committees of this meeting.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s205327331801330x">doi:10.1107/s205327331801330x</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h3ivhkyr7fg7xopm54ns7zxcqm">fatcat:h3ivhkyr7fg7xopm54ns7zxcqm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430040036/https://journals.iucr.org/a/issues/2019/01/00/es5004/es5004.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/ec/4b/ec4bdf59cd02d5495d720b3fd39360b58a70be31.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s205327331801330x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Community standards to facilitate development and address challenges in metabolic modeling [article]

Maureen A. Carey, Andreas Dräger, Jason A. Papin, James T. Yurkovich
<span title="2019-07-14">2019</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We anticipate that this community-driven outline will help the long-term development of community-inspired resources as well as produce high-quality, accessible models.  ...  As a result, the amount, quality, and format of the information contained within systems biology models are not consistent and therefore present challenges for widespread use and communication.  ...  Acknowledgements The authors would like to thank those who con- Conflict of interest The authors declare that they have no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/700112">doi:10.1101/700112</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2itizjyjuncvlhjsphrrpdkbey">fatcat:2itizjyjuncvlhjsphrrpdkbey</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427161851/https://backend.orbit.dtu.dk/ws/files/235833948/msb.20199235_1.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/0d/2b/0d2b0029f0dbabbb40eb40f44d2b96963f34e2f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/700112"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Finance and Development, September 2017

International Monetary Fund
<span title="">2017</span> <i title="International Monetary Fund (IMF)"> Finance &amp; Development </i> &nbsp;
F&D: Who is least likely to have access to financial services in Tanzania or the region more broadly? BN: First, it is the rural population.  ...  Outside the system Among the factors outside the formal health system that determine well-being are access to clean water and sanitation; air quality; access to and use of toilets, soap, and condoms; walkability  ...  Women who have control over their income are likely to work harder and longer. Women also support the economy through unpaid labor, particularly at home.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5089/9781484315972.022">doi:10.5089/9781484315972.022</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/66y2p4xv4vbmbaiouqxkqfnu7q">fatcat:66y2p4xv4vbmbaiouqxkqfnu7q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200506185953/https://www.elibrary.imf.org/doc/IMF022/24551-9781484315972/24551-9781484315972/Other_formats/Source_PDF/24551-9781484316023.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/0c/a5/0ca5d67fa1c4b7c50236e3030960142eadab1087.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5089/9781484315972.022"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data

En-Yu Lai, Yi-Hau Chen, Kun-Pin Wu, Jacquelyn S. Fetrow
<span title="2017-06-16">2017</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
The covariance matrix used in the test statistic is constructed by the confidence scores retrieved from the STRING database or the HitPredict database.  ...  Consequently, these methods often underestimate the associations among biomolecules and cause false positives in practice.  ...  Acknowledgments We thank Fang-Yi Su and Ning Tsao for helping us to describe the pathway mechanisms of original publications. Author Contributions Conceptualization: EYL.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005601">doi:10.1371/journal.pcbi.1005601</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28622336">pmid:28622336</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5493430/">pmcid:PMC5493430</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j2s2cdm55zdkrhqg5curnewyv4">fatcat:j2s2cdm55zdkrhqg5curnewyv4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725003542/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005601&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/fe/91/fe910a6443bad754dbc2511f96c46fd01ae4ea0f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005601"> <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/PMC5493430" 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 multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle

Pablo Augusto de Souza Fonseca, Samir Id-Lahoucine, Antonio Reverter, Juan F Medrano, Marina S Fortes, Joaquim Casellas, Filippo Miglior, Luiz Brito, Maria Raquel S Carvalho, Flávio S Schenkel, Loan T Nguyen, Laercio R Porto-Neto (+2 others)
<span title="2018-10-18">2018</span> <i title="Public Library of Science"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Furthermore, data-mining analyses were performed using the Cattle QTL database (CattleQTLdb) to identify the QTL category annotated in the regions around the genes shared among breeds.  ...  These genes will be further investigated to better understand the biological processes involved in the expression of complex traits and assist in the identification of functional variants associated with  ...  The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic acids research. 2016:gkw937. 26. Csardi G, Nepusz T.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0205295">doi:10.1371/journal.pone.0205295</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30335783">pmid:30335783</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6193631/">pmcid:PMC6193631</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dkj3sxvobfgqtfhik26lt5cz4i">fatcat:dkj3sxvobfgqtfhik26lt5cz4i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222131749/http://pdfs.semanticscholar.org/36c6/c3d31b36d9f225a2dfa4dc2ffb300400f185.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/36/c6/36c6c3d31b36d9f225a2dfa4dc2ffb300400f185.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0205295"> <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/PMC6193631" 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 screening of potential glioma-related genes and drugs based on analysis of GEO dataset and text mining

Zhengye Jiang, Yanxi Shi, Guowei Tan, Zhanxiang Wang, Edwin Wang
<span title="2021-02-26">2021</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;
We also constructed the protein interaction network of common genes through STRING, and selected the important modules for further drug-gene analysis.  ...  Methods Eight glioma samples and twelve control samples were analyzed on the GSE31095 datasets, and differentially expressed genes (DEGs) were obtained via the R software.  ...  The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0247612">doi:10.1371/journal.pone.0247612</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33635875">pmid:33635875</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/52xjjtovybfi3p3t5dqhll7xlu">fatcat:52xjjtovybfi3p3t5dqhll7xlu</a> </span>
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Infrastructures of systems biology that facilitate functional genomic study in rice

Woo-Jong Hong, Yu-Jin Kim, Anil Kumar Nalini Chandran, Ki-Hong Jung
<span title="2019-03-14">2019</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fgcfkzf2dvaxxktrnomuue24ki" style="color: black;">Rice</a> </i> &nbsp;
Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems  ...  We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions  ...  The latest version of STRING contains Cytoscape app integration, programmatic access to the protein network, statistical analyses of the network, and user-provided interactome analyses.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12284-019-0276-z">doi:10.1186/s12284-019-0276-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30874968">pmid:30874968</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6419666/">pmcid:PMC6419666</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zfqydgycnrahxjftpyg6cxd2v4">fatcat:zfqydgycnrahxjftpyg6cxd2v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429051543/https://thericejournal.springeropen.com/track/pdf/10.1186/s12284-019-0276-z" 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/e2/9d/e29db65f4a807823af7252b2a9c3da2ed1d8b73d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12284-019-0276-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/PMC6419666" 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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