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High-throughput Multimodal Automated Phenotyping (MAP) with Application to PheWAS [article]

Katherine P. Liao, Jiehuan Sun, Tianrun A. Cai, Nicholas Link, Chuan Hong, Jie Huang, Jennifer E. Huffman, Jessica Gronsbell, Yichi Zhang, Yuk-Lam Ho, Victor Castro, Vivian Gainer (+8 others)
<span title="2019-03-23">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The objective of this study was to develop an automated high-throughput phenotyping method integrating International Classification of Diseases (ICD) codes and narrative data extracted using natural language  ...  The PheWAS results suggest that the MAP approach detected previously validated associations with higher power when compared to the standard PheWAS method based on ICD codes.ConclusionThe MAP approach increased  ...  In this paper, we propose an unsupervised multimodal automated phenotyping (MAP) method with application in PheWAS.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/587436">doi:10.1101/587436</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gn773e7dkbdmhm43gseq2ez6v4">fatcat:gn773e7dkbdmhm43gseq2ez6v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501180533/https://www.biorxiv.org/content/biorxiv/early/2019/03/23/587436.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/0a/f0/0af0e8b7df90c50088a8c61d799a90f5356485da.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/587436"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Pharmacogenomics in the Age of GWAS, Omics Atlases, and PheWAS [article]

Ari Allyn-Feuer, Gerald A. Higgins, Brian D. Athey
<span title="2018-08-28">2018</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We conclude with a vision for a pharmacophenomic atlas, in which omics atlas data, PheWAS associations, and biobank data would be used with AI to design thousands of genetic tests for clinical deployment  ...  in an automated parallel process.  ...  of Hi-C: high throughput chromatin conformation capture.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1808.09481v1">arXiv:1808.09481v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7tys2l3qlfgifjxtgjq4jejoma">fatcat:7tys2l3qlfgifjxtgjq4jejoma</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191020034939/https://arxiv.org/pdf/1808.09481v1.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/77/67/7767f19dfeea783b1576901cad5acb3e354a95f3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1808.09481v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius
<span title="2020-06-05">2020</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;
Here, we present a customizable workflow (PS4DR) which not only integrates high-throughput data such as genome-wide association study (GWAS) data and gene expression signatures from disease and drug perturbations  ...  We showcase PS4DR with applications demonstrating how this tool can be used for repositioning and identifying new drugs as well as proposing drugs that can simulate disease dysregulations.  ...  Acknowledgments We would like to thank Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03568-5">doi:10.1186/s12859-020-03568-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32503412">pmid:32503412</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/72oupapphzcntipdawrhkgyqgm">fatcat:72oupapphzcntipdawrhkgyqgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106124913/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03568-5" 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/04/fe/04fe457d3a02876a7b01e0aa4dfc9bc755fcf0dc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03568-5"> <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>

Semi-supervised Calibration of Risk with Noisy Event Times (SCORNET) Using Electronic Health Record Data [article]

Yuri Ahuja, Liang Liang, Sicong Huang, Tianxi Cai
<span title="2021-01-09">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Current status labels -- binary indicators of phenotype status during follow up -- are significantly more efficient and feasible to compile, enabling more precise survival curve estimation given limited  ...  In this paper we propose Semi-supervised Calibration of Risk with Noisy Event Times (SCORNET), which yields a consistent and efficient survival curve estimator by leveraging a small size of current status  ...  High-throughput multimodal automated phenotyping (map) with application of phewas. Journal of the American Medical Informatics Association 26(11), 2019).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.01.08.425976">doi:10.1101/2021.01.08.425976</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7j7vkvbbfzaerp6o5wmjeyo5ri">fatcat:7j7vkvbbfzaerp6o5wmjeyo5ri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428201859/https://www.biorxiv.org/content/biorxiv/early/2021/01/09/2021.01.08.425976.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/d9/b1/d9b1139f5275993bd3cbcb29950641904312b8b9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.01.08.425976"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The anatomy of phenotype ontologies: principles, properties and applications

Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
<span title="2017-04-06">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional.  ...  The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration  ...  Funding The National Science Foundation (IOS:1340112 to G.V.G.), the European Commission H2020 (grant agreement number 731075) to G.V.G. and the King Abdullah University of Science and Technology (to R.H  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbx035">doi:10.1093/bib/bbx035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28387809">pmid:28387809</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eouajqukvncvfjlazgmsnmyxbe">fatcat:eouajqukvncvfjlazgmsnmyxbe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502070420/https://repository.kaust.edu.sa/bitstream/handle/10754/629373/bbx035.pdf;jsessionid=802B2548C445530082AF49528DBA75E8?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/17/57/175751b5cdf87fcfd27f66d397f237ae152deb42.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbx035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Informatics and Computational Methods in Natural Product Drug Discovery: A Review and Perspectives

Joseph D. Romano, Nicholas P. Tatonetti
<span title="2019-04-30">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;
Finally, we conclude with a "road map" of research priorities that seeks to realize this goal.  ...  We also explore the current informatics knowledge gaps and other barriers that need to be overcome to fully leverage these compounds for drug discovery.  ...  Multi-omics and high-throughput sequencing are also major areas within bioinformatics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2019.00368">doi:10.3389/fgene.2019.00368</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31114606">pmid:31114606</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6503039/">pmcid:PMC6503039</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hf5mvhwqbja5zdvlmfyrba753a">fatcat:hf5mvhwqbja5zdvlmfyrba753a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200214075112/https://fjfsdata01prod.blob.core.windows.net/articles/files/442506/pubmed-zip/.versions/1/.package-entries/fgene-10-00368/fgene-10-00368.pdf?sv=2015-12-11&amp;sr=b&amp;sig=eYbXi5oBik1ZtIZS5XijIcR2dju55PkCK9yz%2BMszjxk%3D&amp;se=2020-02-14T07%3A51%3A41Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-10-00368.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/85/c0/85c0db7f98d7cbd92780ecaa166c019b0f9a5a4e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2019.00368"> <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/PMC6503039" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Linking brain structure, activity and cognitive function through computation

Katrin Amunts, Javier DeFelipe, Cyriel Pennartz, Alain Destexhe, Michele Migliore, Philippe Ryvlin, Steve Furber, Alois Knoll, Lise Bitsch, Jan G. Bjaalie, Yannis Ioannidis, Thomas Lippert (+3 others)
<span title="2022-02-25">2022</span> <i title="Society for Neuroscience"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rjgmscj365bdfijeu26tkpn4xa" style="color: black;">eNeuro</a> </i> &nbsp;
In 2013 the European Union launched the Human Brain Project (HBP) with the mission to integrate spatial and temporal scales of brain sciences within a common framework, ultimately leading to the digital  ...  community of researchers united by the quest to understand the brain, with fascinating insights and perspectives for societal benefits.Significance statementTheoretical and methodological integration  ...  It links data from high resolution brain mapping to brain avatars, running on high-performance computers to simulate the spread of individual seizure activity along cortical and subcortical surfaces (  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1523/eneuro.0316-21.2022">doi:10.1523/eneuro.0316-21.2022</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35217544">pmid:35217544</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8925650/">pmcid:PMC8925650</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k7obyuqb5vcenossdwrlcbg4eu">fatcat:k7obyuqb5vcenossdwrlcbg4eu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220427035301/https://www.eneuro.org/content/eneuro/9/2/ENEURO.0316-21.2022.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/1b/d9/1bd9d7657a7d15ae56d491ca49e69a09e4a67260.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1523/eneuro.0316-21.2022"> <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/PMC8925650" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

50th European Mathematical Genetics Meeting (EMGM) 2022

<span title="2022-04-20">2022</span>
Numerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions.  ...  Thus, inherited plasticity in recombination rate is hypothesized to be a superior evolutionary strategy in changing environments. Previous theoretical models proceeded from the  ...  PANCAIM Project (https://pancaim.eu/) During the last years, a plethora of cancerspecific data generated by high-throughput biotechnological platforms along with clinicopathological information are being  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1159/000524615">doi:10.1159/000524615</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35443248">pmid:35443248</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/teoklss77zg7fkvnqrimm6ez3e">fatcat:teoklss77zg7fkvnqrimm6ez3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220423205640/https://www.karger.com/Article/Pdf/524615" 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/a9/72/a9725fb2247f86bca5185d1a988381f3d99d685f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1159/000524615"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Surrogate Assisted Semi-supervised Inference for High Dimensional Risk Prediction [article]

Jue Hou, Zijian Guo, Tianxi Cai
<span title="2021-05-04">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Risk modeling with EHR data is challenging due to a lack of direct observations on the disease outcome, and the high dimensionality of the candidate predictors.  ...  In this paper, we develop a surrogate assisted semi-supervised-learning (SAS) approach to risk modeling with high dimensional predictors, leveraging a large unlabeled data on candidate predictors and surrogates  ...  High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. Journal of the American Medical Informatics Association 26 (11), 1255-1262. Ma, R., T. T. Cai, and H. Li (2020).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2105.01264v1">arXiv:2105.01264v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eonzxzeeefelbh3gjpm6ifdfq4">fatcat:eonzxzeeefelbh3gjpm6ifdfq4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210506025451/https://arxiv.org/pdf/2105.01264v1.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/fa/bb/fabbb0afc126e9d1d5a6cfeb1508cb596c68f861.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2105.01264v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Romano_columbia_0054D_15271.pdf [article]

<span title="2019-05-28">2019</span>
VenomSeq is a biotechnology workflow that is designed to generate new high-throughput sequencing data for incorporation into VenomKB.  ...  To provide a platform for structuring, representing, retrieving, and integrating venom data relevant to drug discovery, VenomKB provides a database-backed web application and knowledge base for computational  ...  A particular application that has experienced rapid growth and major methodological advancements in drug discovery is linking new types of high-throughput sequencing (HTS) data to clinically-meaningful  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7916/d8-spcd-yh22">doi:10.7916/d8-spcd-yh22</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qj4yn44c6nd7jj3fegklasfrua">fatcat:qj4yn44c6nd7jj3fegklasfrua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200218220353/https://academiccommons.columbia.edu/doi/10.7916/d8-spcd-yh22/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/67/f5/67f5ed14c7d1e1d9537e752bd2606705ef2e860f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7916/d8-spcd-yh22"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>