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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)
2019 bioRxiv   pre-print
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.  ... 
doi:10.1101/587436 fatcat:gn773e7dkbdmhm43gseq2ez6v4

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

Ari Allyn-Feuer, Gerald A. Higgins, Brian D. Athey
2018 arXiv   pre-print
in an automated parallel process.  ...  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  ...  The construction of tissue files on an automated basis requires a degree of natural language processing.  ... 
arXiv:1808.09481v1 fatcat:7tys2l3qlfgifjxtgjq4jejoma

The anatomy of phenotype ontologies: principles, properties and applications

Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2017 Briefings in Bioinformatics  
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  ... 
doi:10.1093/bib/bbx035 pmid:28387809 fatcat:eouajqukvncvfjlazgmsnmyxbe

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
2020 BMC Bioinformatics  
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.  ...  Programming language: R. Other Requirements: R 3.5.1. License: Apache License 2.0. Any restrictions to use by non-academics: None.  ... 
doi:10.1186/s12859-020-03568-5 pmid:32503412 fatcat:72oupapphzcntipdawrhkgyqgm

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)
2022 eNeuro  
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  ...  Likewise, much work remains to be done to elucidate how the brain interacts with the natural and cultural environment, e.g., how epigenetic mechanisms act on the brain, how genotype-phenotype relationships  ... 
doi:10.1523/eneuro.0316-21.2022 pmid:35217544 pmcid:PMC8925650 fatcat:k7obyuqb5vcenossdwrlcbg4eu

Romano_columbia_0054D_15271.pdf [article]

2019
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  ...  VenomSeq is a biotechnology workflow that is designed to generate new high-throughput sequencing data for incorporation into VenomKB.  ... 
doi:10.7916/d8-spcd-yh22 fatcat:qj4yn44c6nd7jj3fegklasfrua