Filters








584 Hits in 3.4 sec

Cloud-based genomics pipelines for ophthalmology: reviewed from research to clinical practice

David C.S. Wong, Maximiliano Olivera, Jing Yu, Anita Szabo, Ismail Moghul, Konstantinos Balaskas, Robert Luben, Anthony P. Khawaja, Nikolas Pontikos, Pearse A. Keane
<span title="2021-09-17">2021</span> <i title="Kugler Publications"> Modeling and Artificial Intelligence in Ophthalmology </i> &nbsp;
the potential for cloud-based genomic pipelines in eye hospitals.Methods: Narrative review of the literature relevant to clinical genomics and cloud computing, using PubMed and Google Scholar.  ...  research teams.  ...  These open datasets can be a first step towards prototyping cloud-based clinical genomics pipelines.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.35119/maio.v3i1.115">doi:10.35119/maio.v3i1.115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wjxxoar6kfhufmrkw6tj53spna">fatcat:wjxxoar6kfhufmrkw6tj53spna</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210919004630/https://www.maio-journal.com/index.php/MAIO/article/download/115/237" 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/c5/e1/c5e1a6f9acb4cb4b7ef0d460eb7858a796aa2001.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.35119/maio.v3i1.115"> <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>

RICOPILI: Rapid Imputation for COnsortias PIpeLIne [article]

Max Lam, Swapnil Awasthi, Hunna J. Watson, Jackie Goldstein, Georgia Panagiotaropoulou, Vassily Trubetskoy, Robert Karlsson, Oleksander Frei, Chun-Chieh Fan, Ward De Witte, Nina R. Mota, Niamh Mullins (+7 others)
<span title="2019-04-11">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
A comprehensive meta-analysis of simulated GWAS data has been incorporated demonstrating each step of the pipeline.  ...  Simulated GWAS datasets are also packaged with the pipeline for user training tutorials and developer work.Availability and ImplementationRICOPILI has a flexible architecture to allow for ongoing development  ...  Acknowledgments Computing and network infrastructure was provided by various sources, including SURFsara (Genetic Cluster Computer; LISA cluster) and the Stanley Center for Psychiatric Research at the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/587196">doi:10.1101/587196</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cu3uvag25jdbva7inzw6caqlz4">fatcat:cu3uvag25jdbva7inzw6caqlz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503224452/https://www.biorxiv.org/content/biorxiv/early/2019/04/11/587196.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/5d/3e/5d3e9cebd87381328d5c5c929c97c93a88423fa4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/587196"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance

Aquillah M. Kanzi, James Emmanuel San, Benjamin Chimukangara, Eduan Wilkinson, Maryam Fish, Veron Ramsuran, Tulio de Oliveira
<span title="2020-10-23">2020</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;
Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations.  ...  In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying  ...  Cloud-based genomic analysis platforms such as Terra 31 and Seven Bridges are 32 have been developed to accelerate biomedical research including NGS analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.544162">doi:10.3389/fgene.2020.544162</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33193618">pmid:33193618</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7649788/">pmcid:PMC7649788</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dkcsrkvggbbkvhg32l2a4ejlky">fatcat:dkcsrkvggbbkvhg32l2a4ejlky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201026132522/https://fjfsdata01prod.blob.core.windows.net/articles/files/544162/pubmed-zip/.versions/1/.package-entries/fgene-11-544162/fgene-11-544162.pdf?sv=2018-03-28&amp;sr=b&amp;sig=itda%2BVlf44c94i0XBK4q5pkldE6vqhEsaal8fWJ2MdA%3D&amp;se=2020-10-26T13%3A25%3A51Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-11-544162.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/ee/e8/eee8049718a926efe01e331a2e3eb5c8b2c23457.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.544162"> <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/PMC7649788" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

'Next-generation' sequencing becomes 'now-generation'

Daniel E Neafsey, Brian J Haas
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Acknowledgements We thank David Jaffe, Joshua Levin, and Carsten Russ (Broad Institute) for sharing with us their impressions of the meeting and this report.  ...  Toby Bloom (Broad Institute) described her experiences in migrating the Broad Institute's nextgeneration sequence analysis pipeline to the Amazon cloud.  ...  Richard Weinshilboum (Mayo Clinic, Rochester, USA) described functional validation of genomewide association study (GWAS) signals, in this case for breast cancer.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2011-12-3-303">doi:10.1186/gb-2011-12-3-303</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21457529">pmid:21457529</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3129669/">pmcid:PMC3129669</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yx4hlmvzn5envaotzduwxqswt4">fatcat:yx4hlmvzn5envaotzduwxqswt4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719085724/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2011-12-3-303?site=genomebiology.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/bb/79/bb79939c686cee82ec1d7ce0f315f463bbc5c836.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2011-12-3-303"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129669" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations [article]

Bohdan B Khomtchouk, Kasra A Vand, Christopher S Nelson, Salvator Palmisano, Robert L Grossman
<span title="2020-10-21">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
HeartBioPortal2.0 is structured as a cloud-based computing platform and knowledge portal that consolidates a multitude of CVD-relevant next-generation sequencing data modalities into a single powerful  ...  query and browsing interface between data and user via a user-friendly web application publicly available to the scientific research community.  ...  datasets/publications, and providing the tools/infrastructure to do so, effectively leveraging for secondary analysis existing clinical and genetic datasets from federally funded NIH/NSF research grants  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.19.346445">doi:10.1101/2020.10.19.346445</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4xwafve2dngxfd4zrfimuwppla">fatcat:4xwafve2dngxfd4zrfimuwppla</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201213115423/https://www.biorxiv.org/content/biorxiv/early/2020/10/21/2020.10.19.346445.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/77/75/7775b4a3c55c8d551a77bbb33a95e96a977bedbc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.19.346445"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Bioinformatics services for analyzing massive genomic datasets

Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Ho-Yeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byunghee Kang (+10 others)
<span title="2020-03-31">2020</span> <i title="Korea Genome Organization"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/acfgmfmleze4rfuugy66fpl4ky" style="color: black;">Genomics &amp; Informatics</a> </i> &nbsp;
Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data.  ...  Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets.  ...  Web servers for gene-set, pathway, and pharmacogenomic data analysis Namhee Yu: https://orcid.org/0000-0003-3967-0813 Seokjin Ham: https://orcid.org/0000-0002-6950-2848 Insoon Jang: https://orcid.org/0000  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2020.18.1.e8">doi:10.5808/gi.2020.18.1.e8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32224841">pmid:32224841</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7120352/">pmcid:PMC7120352</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/upd22fio7rfqrc3ffaepatxeee">fatcat:upd22fio7rfqrc3ffaepatxeee</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200401024456/https://genominfo.org/upload/pdf/gi-2020-18-1-e8.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/aa/17/aa171140210e7412c4d7a57cbade3fd24ba19e49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2020.18.1.e8"> <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/PMC7120352" 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 services for analyzing massive genomic datasets

Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Ho-Yeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byunghee Kang (+10 others)
<span title="2020-03-31">2020</span> <i title="Korea Genome Organization"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/acfgmfmleze4rfuugy66fpl4ky" style="color: black;">Genomics &amp; Informatics</a> </i> &nbsp;
Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data.  ...  Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets.  ...  Web servers for gene-set, pathway, and pharmacogenomic data analysis Namhee Yu: https://orcid.org/0000-0003-3967-0813 Seokjin Ham: https://orcid.org/0000-0002-6950-2848 Insoon Jang: https://orcid.org/0000  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2020.18.1.e8">doi:10.5808/gi.2020.18.1.e8</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s6adhmxa4vamlpreykcejc3hcy">fatcat:s6adhmxa4vamlpreykcejc3hcy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428052100/https://scholarworks.unist.ac.kr/bitstream/201301/48357/1/gi-2020-18-1-e8.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/54/df543060c161fdefd84a523afc3fb08a5c7f4ba2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2020.18.1.e8"> <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>

MOMIC: A Multi-Omics Pipeline for Data Analysis, Integration and Interpretation

Laura Madrid-Márquez, Cristina Rubio-Escudero, Beatriz Pontes, Antonio González-Pérez, José C. Riquelme, Maria E. Sáez
<span title="2022-04-14">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/smrngspzhzce7dy6ofycrfxbim" style="color: black;">Applied Sciences</a> </i> &nbsp;
Conclusions: MOMIC offers a complete analysis environment for analysing and integrating multi-omics data in a single, easy-to-use platform.  ...  Results: The proposed pipeline is developed as a collection of Jupyter notebooks, easily editable, reproducible and well documented.  ...  , specially for performing a GWAS analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/app12083987">doi:10.3390/app12083987</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wnztfl2tz5dytpihlun7ltjulm">fatcat:wnztfl2tz5dytpihlun7ltjulm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220423103518/https://mdpi-res.com/d_attachment/applsci/applsci-12-03987/article_deploy/applsci-12-03987-v2.pdf?version=1650271413" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/61/df618da2efac7ed4596c01435b5d0e804268098e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/app12083987"> <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>

Migrating a research data warehouse to a public cloud: challenges and opportunities

Michael G Kahn, Joyce Y Mui, Michael J Ames, Anoop K Yamsani, Nikita Pozdeyev, Nicholas Rafaels, Ian M Brooks
<span title="2021-12-17">2021</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/aapnwtybrvghlc35hfimbtdlom" style="color: black;">JAMIA Journal of the American Medical Informatics Association</a> </i> &nbsp;
Objective Clinical research data warehouses (RDWs) linked to genomic pipelines and open data archives are being created to support innovative, complex data-driven discoveries.  ...  New RDWs are migrating to cloud platforms for the scalability and flexibility needed to meet these challenges. We describe our experience in migrating a multi-institutional RDW to a public cloud.  ...  We also thank our partners at Google Cloud for Higher Education and Research for their unfailing support and expert guidance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/jamia/ocab278">doi:10.1093/jamia/ocab278</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34919694">pmid:34919694</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8922165/">pmcid:PMC8922165</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d4xflguhyvbmze2necxfmzpmsa">fatcat:d4xflguhyvbmze2necxfmzpmsa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211227145446/https://watermark.silverchair.com/ocab278.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAt8wggLbBgkqhkiG9w0BBwagggLMMIICyAIBADCCAsEGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMBEMUGIFoPbSZ-3stAgEQgIICktncOh_LYpmtKUyGT1Aht2L_-0pBeBohY4uJ0pSZN1S_vmo30nD_AgJemJM_VFHHZCv-jec9GXcxsdj_9RUua_1sIR0U1hteE0Nl2DrG3VfEYw2-8io-pSWIqEj8-kqbwx6nC0g7nGQwwRMzVh5mmNpbzsp5otGI12npK_33AvxtgC7mRsRo68a9qRPCzznWBVbnuLfft-KmzzMt0uIvhYblqtv4FeBB4-vFA8zBDAarSuy9QVboRTuFvyf5ll0HPSHrPCGl9FqUSjGxAVhB_bnwknlQYtHKJxQQU3fU4hB43HFuyNT2pKN8fWIAO2MY4yT_wBVv8HTAavoTimCH4bE9SXCeAefIueZLLE8Tg_u0cIvUCBJj3oz1AkV_lOIumHYRKeNqRVdDHckx4Qw1H5CrI3PQxD2qPS8rHXc0zCLNnS9_JAJowwK1Dr-WCfoOcWzaZYeQh9sT8GKZEcX975ax7nm2t7y7WXDYp7oQkJzd-xFFSVj47UZSmron4CF57ZN3VSh0XZbb5TR49zN9mW0kE_k9mvby0ge-42FNU2daSkcgjkER0rxxbrxI5bownfoeM8aGfnNRfehx1LcT0ugsM3pcAuh6EDum5su-CmvrfmkB2dYJ-apWAzG4VEUROLYsDxxwckHvgZbn7MUWdPXSepMjBSO79EyH2jmusFKmvpdwvLW6r8ysvtzbVUc6OJoqtipr-hRdx5ZiHofNmTnucZGX5xuxsVrRR3cKSMkjF1GTEo9IXhV9br3AOdJX3JECMXI8CrkC1WkWC62gjG46TFOW6e0lqC0MqV03sPxcUg5eBRoyoKYPq8qQh4gy0u464TJaTutNQI5C3KdPI2L4Zwnt_NE3gqE_93BWtoWa6-4" 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/bf/90/bf9023bb02187cbb7d0929da4b52057bfee65b5b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/jamia/ocab278"> <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/PMC8922165" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson (+25 others)
<span title="2018-12-31">2018</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tsaumnzpkvdmvdi3blhl5clb24" style="color: black;">PLoS Biology</a> </i> &nbsp;
A personalized approach based on a patient's or pathogen's unique genomic sequence is the foundation of precision medicine.  ...  principles for collaborative open standards development."  ...  The complex UVP BCO captures a validated whole genome sequencing (WGS) analysis pipeline, for The Relational Sequencing Tuberculosis (ReSeqTB) knowledge base.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.3000099">doi:10.1371/journal.pbio.3000099</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30596645">pmid:30596645</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6338479/">pmcid:PMC6338479</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dh5fphvtazd5xlzu3vtl6cata4">fatcat:dh5fphvtazd5xlzu3vtl6cata4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190506030827/https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3000099&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/f6/9f/f69f1764a58d4b9ac4471ba74c69f34b320497fd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.3000099"> <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/PMC6338479" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets

Luca Nanni, Pietro Pinoli, Arif Canakoglu, Stefano Ceri
<span title="2019-11-08">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Outsourced processing can address cloud-based installations of the GMQL engine. PyGMQL is an effective and innovative tool for supporting tertiary data extraction and analysis pipelines.  ...  We present PyGMQL, a novel software for the manipulation of region-based genomic files and their relative metadata, built on top of the GMQL genomic big data management system.  ...  Acknowledgements We thank all the members of the Data-Driven Genomic Computing research group at Politecnico di Milano for their continuous support and useful discussion.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-019-3159-9">doi:10.1186/s12859-019-3159-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31703553">pmid:31703553</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6842186/">pmcid:PMC6842186</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zajbfoyq5jgphpxg2ozyrbfhzu">fatcat:zajbfoyq5jgphpxg2ozyrbfhzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209235626/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3159-9" 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/79/aa/79aa9bcae8c8deb719a027b6e79d0bf2506c615a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-019-3159-9"> <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/PMC6842186" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Open Targets Platform: supporting systematic drug–target identification and prioritisation

David Ochoa, Andrew Hercules, Miguel Carmona, Daniel Suveges, Asier Gonzalez-Uriarte, Cinzia Malangone, Alfredo Miranda, Luca Fumis, Denise Carvalho-Silva, Michaela Spitzer, Jarrod Baker, Javier Ferrer (+20 others)
<span title="2020-11-16">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
based upon underlying evidence.  ...  The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery  ...  Sometimes, more detailed analysis is required to extract the relevant information or adjust the available data to a clinical setup.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1027">doi:10.1093/nar/gkaa1027</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33196847">pmid:33196847</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3qrm5q5turgulbvyj2kj6oy5c4">fatcat:3qrm5q5turgulbvyj2kj6oy5c4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211027094833/https://watermark.silverchair.com/gkaa1027.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsYwggLCBgkqhkiG9w0BBwagggKzMIICrwIBADCCAqgGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMw1a_I4naItixgTZnAgEQgIICeYa0UQQYSjO6VJWS3tOER4X14AFVYvHzsf5T_bLZV1BhLKC_C4O2Y70EvgWf-cGw6ARXsSc6Sc1PwXD2ah_3MkH8GxAYu2f05KGcRvdPAmRy6yJlw6K20B2wovZVKWeHOB1pVg_JtVMkMsK2jOFY-JNai6oHqQCBY0uprv2Na778k2HEebl1xUCIGAAVQKP7JRwRTjOvKRUBGAEVQlOkxQBDNDxOLekcTrtRZaqCA7MTtShtLoFiRxtqABtb_LSVajp3TpWs_gNS6lmTzAsYyppx4KPtvaU2CM3A3-A37XCcN1k1ehy7qktAhfJu9vr0tL03XBvW3HXOnuY9ORkeNSuMdsYsGGNLLvSZuj9amVrLRDGP6htDOxMkzIfNCP0ipbTDTJUqtCU6ZuDUQFOAOUQiM2g9gk-0_VR0PULl1TEPi2WT7P_wuNu-QoBkq0BoYBg6mKorYNbt8pNiM3ZnS0ZU9TnCLSEdE0DAiM6f6BFkEdRUNN2H6vnNILNa61wi9ht8ADZwazgVUZ1jOkbL8-sbLmgMIlARbJ0UYbE6eFd0bvvqGZZTr5wNJXkLpzBi7tNYvKlrV81OEimDPHT2r2m9adkJrf8Ltp9VU1pKnJKUwWOgLuSPxiYDj7bPSVqrr-Co4e559MBigMlnNRzdaPaRfqCzD0teXiNO6cuvofF6l9XNBmYoX3Uw4DCNe0i2Hfyv4fxHRFCrHn57mUNvd4UBML-3kxXntkAqm7-7_nKMP8kUaI5quPKSGh1NC6VACVUgB0TrVHvF70fO6Rf3qn0T4ToOcsPX6BwJMQFXl3uNx-4b83Na7Z0NAK_Wi11lEfubKe9O4Bh64Q" 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/56/0f/560fae1081bf29a7f3068d32922d5f633d11d2ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1027"> <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>

Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results [article]

Gil Alterovitz, Dennis A Dean, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Charles Hadley S King, Dan Taylor, KanakaDurga Addepalli, Elaine Johanson (+23 others)
<span title="2017-09-21">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Precision medicine can be empowered by a personalized approach to patient care based on the patient's or pathogen's unique genomic sequence.  ...  For precision medicine, genomic findings must be robust and reproducible, and experimental data capture should adhere to FAIR guiding principles.  ...  LD Hub, a centralized database of GWAS results for diseases/traits [3] , is another example of success.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/191783">doi:10.1101/191783</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6idjm4omhzasfofouk22akgdqy">fatcat:6idjm4omhzasfofouk22akgdqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502092909/https://www.biorxiv.org/content/biorxiv/early/2018/11/05/191783.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/05/fc/05fc7c40ffa592bf8e9cb96f50fd2e8328983f93.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/191783"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Development of Bioinformatics Infrastructure for Genomics Research

Nicola J. Mulder, Ezekiel Adebiyi, Marion Adebiyi, Seun Adeyemi, Azza Ahmed, Rehab Ahmed, Bola Akanle, Mohamed Alibi, Don L. Armstrong, Shaun Aron, Efejiro Ashano, Shakuntala Baichoo (+33 others)
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nacrwrxp7jcyllxemizdattfxi" style="color: black;">Global Heart</a> </i> &nbsp;
Objectives: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis.  ...  H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa.  ...  For downstream analysis of variants from a genome-wide association study (GWAS) or NGS experiment, we developed ancGWAS [22] and HUMA. ancGWAS is a network-based tool for analysis of GWAS summary statistics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gheart.2017.01.005">doi:10.1016/j.gheart.2017.01.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28302555">pmid:28302555</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5582980/">pmcid:PMC5582980</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/stejxlkz2jbj3klajopc6tyngu">fatcat:stejxlkz2jbj3klajopc6tyngu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200709220928/https://globalheartjournal.com/articles/10.1016/j.gheart.2017.01.005/galley/25/download/" 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/4f/1a/4f1a80018c3f3216c829da9658ba330298378dae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gheart.2017.01.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582980" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bio and health informatics meets cloud : BioVLab as an example

Heejoon Chae, Inuk Jung, Hyungro Lee, Suresh Marru, Seong-Whan Lee, Sun Kim
<span title="2013-02-04">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/x77t7madorg4dax6vvdhcnodwi" style="color: black;">Health Information Science and Systems</a> </i> &nbsp;
As data increases in size, many research organizations start to experience the lack of computing power, which becomes a major hurdle in achieving research goals.  ...  Comparing NGS to the traditional Sanger sequencing technology that was used for the first human genome project, a three billion dollar project over a span of 10 years, the cost and time for sequencing  ...  Acknowledgements This work was supported by the new faculty research support grant from Seoul National University (SNU).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2047-2501-1-6">doi:10.1186/2047-2501-1-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25825658">pmid:25825658</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4336112/">pmcid:PMC4336112</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k3s3fhlv4jcfzdq7nexnpex46u">fatcat:k3s3fhlv4jcfzdq7nexnpex46u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170826020645/https://link.springer.com/content/pdf/10.1186%2F2047-2501-1-6.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/d1/49/d1492647ceed4cc274e37466b391d52f1b0c4ae2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2047-2501-1-6"> <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/PMC4336112" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 584 results