tetano
Editor, Senior Moderator
Elife
. 2020 May 28;9:e58040.
doi: 10.7554/eLife.58040. Online ahead of print.
Knowledge Synthesis of 100 Million Biomedical Documents Augments the Deep Expression Profiling of Coronavirus Receptors
A J Venkatakrishnan[SUP] 1 [/SUP], Arjun Puranik[SUP] 2 [/SUP], Akash Anand[SUP] 3 [/SUP], David Zemmour[SUP] 1 [/SUP], Xiang Yao[SUP] 4 [/SUP], Xiaoying Wu[SUP] 5 [/SUP], Ramakrishna Chilaka[SUP] 6 [/SUP], Dariusz K Murakowski[SUP] 1 [/SUP], Kristopher Standish[SUP] 4 [/SUP], Bharathwaj Raghunathan[SUP] 7 [/SUP], Tyler Wagner[SUP] 1 [/SUP], Enrique Garcia-Rivera[SUP] 1 [/SUP], Hugo Solomon[SUP] 1 [/SUP], Abhinav Garg[SUP] 6 [/SUP], Rakesh Barve[SUP] 8 [/SUP], Anuli Anyanwu-Ofili[SUP] 9 [/SUP], Najat Khan[SUP] 10 [/SUP], Venky Soundararajan[SUP] 1 [/SUP]
Affiliations
Abstract
The COVID-19 pandemic demands assimilation of all biomedical knowledge to decode mechanisms of pathogenesis. Despite the recent renaissance in neural networks, a platform for the real-time synthesis of the exponentially growing biomedical literature and deep omics insights is unavailable. Here, we present the nferX platform for dynamic inference from 45 quadrillion+ possible conceptual associations from unstructured text and triangulation with insights from Single Cell RNA-sequencing, bulk RNAseq and proteomics from diverse tissue types. A hypothesis-free profiling of ACE2 suggests tongue keratinocytes, olfactory epithelial cells, airway club cells and respiratory ciliated cells as potential reservoirs of the SARS-CoV-2 receptor. We find the gut as the putative hotspot of COVID-19, where a maturation correlated transcriptional signature is shared in small intestine enterocytes among coronavirus receptors(ACE2, DPP4, ANPEP). A holistic data science platform triangulating insights from structured and unstructured data holds potential for accelerating the generation of impactful biological insights and hypotheses.
Keywords: human; human biology; medicine.
. 2020 May 28;9:e58040.
doi: 10.7554/eLife.58040. Online ahead of print.
Knowledge Synthesis of 100 Million Biomedical Documents Augments the Deep Expression Profiling of Coronavirus Receptors
A J Venkatakrishnan[SUP] 1 [/SUP], Arjun Puranik[SUP] 2 [/SUP], Akash Anand[SUP] 3 [/SUP], David Zemmour[SUP] 1 [/SUP], Xiang Yao[SUP] 4 [/SUP], Xiaoying Wu[SUP] 5 [/SUP], Ramakrishna Chilaka[SUP] 6 [/SUP], Dariusz K Murakowski[SUP] 1 [/SUP], Kristopher Standish[SUP] 4 [/SUP], Bharathwaj Raghunathan[SUP] 7 [/SUP], Tyler Wagner[SUP] 1 [/SUP], Enrique Garcia-Rivera[SUP] 1 [/SUP], Hugo Solomon[SUP] 1 [/SUP], Abhinav Garg[SUP] 6 [/SUP], Rakesh Barve[SUP] 8 [/SUP], Anuli Anyanwu-Ofili[SUP] 9 [/SUP], Najat Khan[SUP] 10 [/SUP], Venky Soundararajan[SUP] 1 [/SUP]
Affiliations
- PMID: 32463365
- DOI: 10.7554/eLife.58040
Abstract
The COVID-19 pandemic demands assimilation of all biomedical knowledge to decode mechanisms of pathogenesis. Despite the recent renaissance in neural networks, a platform for the real-time synthesis of the exponentially growing biomedical literature and deep omics insights is unavailable. Here, we present the nferX platform for dynamic inference from 45 quadrillion+ possible conceptual associations from unstructured text and triangulation with insights from Single Cell RNA-sequencing, bulk RNAseq and proteomics from diverse tissue types. A hypothesis-free profiling of ACE2 suggests tongue keratinocytes, olfactory epithelial cells, airway club cells and respiratory ciliated cells as potential reservoirs of the SARS-CoV-2 receptor. We find the gut as the putative hotspot of COVID-19, where a maturation correlated transcriptional signature is shared in small intestine enterocytes among coronavirus receptors(ACE2, DPP4, ANPEP). A holistic data science platform triangulating insights from structured and unstructured data holds potential for accelerating the generation of impactful biological insights and hypotheses.
Keywords: human; human biology; medicine.