Recapitulation and Retrospective Prediction of Biomedical Associations Using Temporally-enabled Word Embeddings
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- May 7, 2019
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- May 7, 2019
Abstract: The recent explosion of biomedical knowledge presents both a major opportunity and challenge for scientists tackling complex problems in healthcare. Here we present an approach for synthesizing biomedical knowledge based on a combination of word-embeddings and select cooccurrences. We evaluated our ability to recapitulate and retrospectively predict disease-gene associations from the Online Mendelian Inheritance in Man (OMIM) resource. Our metrics achieved an area under the curve (AUC) value of 0.981 at the recapitulation task for 2,400 disease-gene associations. At the most stringent cutoff, our metrics predicted 13.89% of these associations before their first cooccurrence in the literature, with a median time of 4 years between prediction and first cooccurrence. Finally, our literature metrics can be combined with human genetics data to retrospectively predict disease-gene associations, IL-6 and Giant Cell Arteritis provided as an example. We believe this framework can provide robust biomedical hypotheses at a much faster pace than current standard practices.
- Authors:
- Jiho Park1,
- Agustin Lopez-Marquez1,
- Arjun Puranik1,
- Ajit Rajasekharan1,
- Murali Aravamudan1,
- Enrique Garcia-Rivera1
- 1nference, Cambridge, MA, 02142, USA
- Correspondence: Enrique Garcia-Rivera (enrique@nference.net)
- Correspondence:
- Enrique Garcia-Rivera (enrique@nference.net)
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Updated #SARSCoV preprint: Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion http://dx.doi.org/10.1101/2020.06.19.161620
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Updated #SARSCoV preprint: Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion http://dx.doi.org/10.1101/2020.06.19.161620
Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion

Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion
The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. Here, we identify 33 distinct 8-mer/9-mer p...
www.biorxiv.org
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- The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
- Related Tweets:
Updated #SARSCoV preprint: Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion http://dx.doi.org/10.1101/2020.06.19.161620
Contribute a rapid review or request one for "Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC ..." (http://dx.doi.org/10.1101/2020.06.19.161620). "Add" or "Request" w/DOI (10.1101/2020.06.19.161620) at https://outbreaksci.prereview.org/ @outbreaksci @PREreview_
Updated #SARSCoV preprint: Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion http://dx.doi.org/10.1101/2020.06.19.161620
Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion

Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion
The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. Here, we identify 33 distinct 8-mer/9-mer p...
www.biorxiv.org