Search Results - "Winnenburg, Rainer"

Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations by Tomczak, Aurelie, Mortensen, Jonathan M., Winnenburg, Rainer, Liu, Charles, Alessi, Dominique T., Swamy, Varsha, Vallania, Francesco, Lofgren, Shane, Haynes, Winston, Shah, Nigam H., Musen, Mark A., Khatri, Purvesh

“…Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying…”
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SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions by Preissner, Saskia, Kroll, Katharina, Dunkel, Mathias, Senger, Christian, Goldsobel, Gady, Kuzman, Daniel, Guenther, Stefan, Winnenburg, Rainer, Schroeder, Michael, Preissner, Robert

“…Much of the information on the Cytochrome P450 enzymes (CYPs) is spread across literature and the internet. Aggregating knowledge about CYPs into one database…”
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Feasibility of Prioritizing Drug–Drug-Event Associations Found in Electronic Health Records by Banda, Juan M., Callahan, Alison, Winnenburg, Rainer, Strasberg, Howard R., Cami, Aurel, Reis, Ben Y., Vilar, Santiago, Hripcsak, George, Dumontier, Michel, Shah, Nigam Haresh

“…Background and Objective Several studies have demonstrated the ability to detect adverse events potentially related to multiple drug exposure via data mining…”
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A time-indexed reference standard of adverse drug reactions by Harpaz, Rave, Odgers, David, Gaskin, Greg, DuMouchel, William, Winnenburg, Rainer, Bodenreider, Olivier, Ripple, Anna, Szarfman, Ana, Sorbello, Alfred, Horvitz, Eric, White, Ryen W., Shah, Nigam H.

“…Undetected adverse drug reactions (ADRs) pose a major burden on the health system. Data mining methodologies designed to identify signals of novel ADRs are of…”
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Pathogen-Host Interactions Database (PHI-base) Provides Insights into Generic and Novel Themes of Pathogenicity by Baldwin, T.K, Winnenburg, R, Urban, M, Rawlings, C, Koehler, J, Hammond-Kosack, K.E

“…Fungal and oomycete pathogens of plants and animals are a major global problem. In the last 15 years, many genes required for pathogenesis have been determined…”
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Drug repurposing by integrated literature mining and drug–gene–disease triangulation by Sun, Peng, Guo, Jiong, Winnenburg, Rainer, Baumbach, Jan

“…•Computational drug repositioning infers promising new candidates for existing drugs.•Existing approaches differ in the utilized data sources.•Combined…”
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Implementation and relevance of FAIR data principles in biopharmaceutical R&D by Wise, John, de Barron, Alexandra Grebe, Splendiani, Andrea, Balali-Mood, Beeta, Vasant, Drashtti, Little, Eric, Mellino, Gaspare, Harrow, Ian, Smith, Ian, Taubert, Jan, van Bochove, Kees, Romacker, Martin, Walgemoed, Peter, Jimenez, Rafael C., Winnenburg, Rainer, Plasterer, Tom, Gupta, Vibhor, Hedley, Victoria

“…•Biopharma R&D productivity can be improved by implementing the FAIR Data Principles.•FAIR enables powerful new AI analytics to access data for machine…”
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A method for systematic discovery of adverse drug events from clinical notes by Wang, Guan, Jung, Kenneth, Winnenburg, Rainer, Shah, Nigam H

“…Objective Adverse drug events (ADEs) are undesired harmful effects resulting from use of a medication, and occur in 30% of hospitalized patients. The authors…”
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Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature by Winnenburg, Rainer, Shah, Nigam H

“…Identification of associations between marketed drugs and adverse events from the biomedical literature assists drug safety monitoring efforts. Assessing the…”
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A framework for assessing the consistency of drug classes across sources by Winnenburg, Rainer, Bodenreider, Olivier

“…The objective of this study is to develop a framework for assessing the consistency of drug classes across sources, such as MeSH and ATC. Our framework…”
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The OXL format for the exchange of integrated datasets by Taubert, Jan, Sieren, Klaus Peter, Hindle, Matthew, Hoekman, Berend, Winnenburg, Rainer, Philippi, Stephan, Rawlings, Chris, Köhler, Jacob

“…A prerequisite for systems biology is the integration and analysis of heterogeneous experimental data stored in hundreds of life-science databases and millions…”
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Desiderata for an authoritative Representation of MeSH in RDF by Winnenburg, Rainer, Bodenreider, Olivier

“…The Semantic Web provides a framework for the integration of resources on the web, which facilitates information integration and interoperability. RDF is the…”
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Metrics for assessing the quality of value sets in clinical quality measures by Winnenburg, Rainer, Bodenreider, Olivier

“…To assess the quality of value sets in clinical quality measures, both individually and as a population of value sets. The concepts from a given value set are…”
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Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective by Winnenburg, Rainer, Bodenreider, Olivier

“…To investigate the extent to which pharmacoepidemiologic groupings are homogeneous in terms of clinical properties. In our analysis, we classified drug…”
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Leveraging MEDLINE indexing for pharmacovigilance – Inherent limitations and mitigation strategies by Winnenburg, Rainer, Sorbello, Alfred, Ripple, Anna, Harpaz, Rave, Tonning, Joseph, Szarfman, Ana, Francis, Henry, Bodenreider, Olivier

“…[Display omitted] •We demonstrate significant improvement over a baseline approach to identifying ADEs from MEDLINE indexing.•This approach mitigates some of…”
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U-Index, a dataset and an impact metric for informatics tools and databases by Callahan, Alison, Winnenburg, Rainer, Shah, Nigam H

“…Measuring the usage of informatics resources such as software tools and databases is essential to quantifying their impact, value and return on investment. We…”
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Exploring adverse drug events at the class level by Winnenburg, Rainer, Sorbello, Alfred, Bodenreider, Olivier

“…While the association between a drug and an adverse event (ADE) is generally detected at the level of individual drugs, ADEs are often discussed at the class…”
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PHI-base: a new database for pathogen host interactions by Winnenburg, Rainer, Baldwin, Thomas K., Urban, Martin, Rawlings, Chris, Köhler, Jacob, Hammond-Kosack, Kim E.

“…To utilize effectively the growing number of verified genes that mediate an organism's ability to cause disease and/or to trigger host responses, we have…”
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Issues in creating and maintaining value sets for clinical quality measures by Winnenburg, Rainer, Bodenreider, Olivier

“…To develop methods for assessing the validity, consistency and currency of value sets for clinical quality measures, in order to support the developers of…”
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Toward multimodal signal detection of adverse drug reactions by Harpaz, Rave, DuMouchel, William, Schuemie, Martijn, Bodenreider, Olivier, Friedman, Carol, Horvitz, Eric, Ripple, Anna, Sorbello, Alfred, White, Ryen W., Winnenburg, Rainer, Shah, Nigam H.

“…[Display omitted] •Improving signal detection is key to strengthening drug safety surveillance.•Multimodal signal detection (MSD) is based on jointly analyzing…”
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