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Article
To do no harm — and the most good — with AI in health care
Drawing from real-life scenarios and insights shared at the RAISE (Responsible AI for Social and Ethical Healthcare) conference, we highlight the critical need for AI in health care (AIH) to primarily benefit ...
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Article
Open AccessFrozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma
Omics characterization of pancreatic adenocarcinoma tissue is complicated by the highly heterogeneous and mixed populations of cells. We evaluate the feasibility and potential benefit of using a coring method ...
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Article
Open AccessA comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of develo** effective and saf...
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Article
Open AccessInternational electronic health record-derived post-acute sequelae profiles of COVID-19 patients
The risk profiles of post-acute sequelae of COVID-19 (PASC) have not been well characterized in multi-national settings with appropriate controls. We leveraged electronic health record (EHR) data from 277 inte...
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Article
Open AccessInternational comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality
Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare sys...
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Protocol
Personal Dense Dynamic Data Clouds Connect Systems Biomedicine to Scientific Wellness
The dramatic convergence of molecular biology, genomics, proteomics, metabolomics, bioinformatics, and artificial intelligence has provided a substrate for deep understanding of the biological basis of health ...
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Article
Open AccessMultinational characterization of neurological phenotypes in patients hospitalized with COVID-19
Neurological complications worsen outcomes in COVID-19. To define the prevalence of neurological conditions among hospitalized patients with a positive SARS-CoV-2 reverse transcription polymerase chain reactio...
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Article
Open AccessA high-stringency blueprint of the human proteome
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate an...
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Article
Open AccessUntargeted longitudinal analysis of a wellness cohort identifies markers of metastatic cancer years prior to diagnosis
We analyzed 1196 proteins in longitudinal plasma samples from participants in a commercial wellness program, including samples collected pre-diagnosis from ten cancer patients and 69 controls. For three indivi...
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Article
Open AccessInternational electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium
We leveraged the largely untapped resource of electronic health record data to address critical clinical and epidemiological questions about Coronavirus Disease 2019 (COVID-19). To do this, we formed an intern...
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Article
Open AccessCIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis
The Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, and analysis.
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Article
Blood metabolome predicts gut microbiome α-diversity in humans
Depleted gut microbiome α-diversity is associated with several human diseases, but the extent to which this is reflected in the host molecular phenotype is poorly understood. We attempted to predict gut microb...
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Article
Open AccessGenetic Predisposition Impacts Clinical Changes in a Lifestyle Coaching Program
Both genetic and lifestyle factors contribute to an individual’s disease risk, suggesting a multi-omic approach is essential for personalized prevention. Studies have examined the effectiveness of lifestyle co...
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Article
Reply to "Precision medicine in the clouds"
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Article
Open AccessMap** genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework
The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are pred...
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Article
A wellness study of 108 individuals using personal, dense, dynamic data clouds
Longitudinal clinical and multi-omics data from 108 healthy individuals are analyzed to identify putative biomarkers and diagnostics of early disease states.
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Protocol
Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks
Tens of thousands of splice isoforms of proteins have been catalogued as predicted sequences from transcripts in humans and other species. Relatively few have been characterized biochemically or structurally. ...
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Article
Linking MedDRA®-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors
A translational bioinformatics challenge exists in connecting population and individual clinical phenotypes in various formats to biological mechanisms. The Medical Dictionary for Regulatory Activities (MedDRA®) ...
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Article
Strategies for Genomic and Proteomic Profiling of Cancers
Omics-based technology platforms have made new kinds of cancer profiling tests feasible. There are several valuable examples in clinical practice, and many more under development. A concerted, transparent proc...
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Article
Open AccessA Network of Splice Isoforms for the Mouse
The laboratory mouse is the primary mammalian species used for studying alternative splicing events. Recent studies have generated computational models to predict functions for splice isoforms in the mouse. Ho...
