Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors

March 26,2021

 
May 26, 2020

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. 

Authors:
AJ Venkatakrishnan1Arjun Puranik1Akash Anand2David Zemmour1Xiang Yao3Xiaoying Wu3Ramakrishna Chilaka2Dariusz K. Murakowski1Kristopher Standish3Bharathwaj Raghunathan4Tyler Wagner1Enrique Garcia-Rivera1Hugo Solomon1Abhinav Garg2Rakesh Barve2Anuli Anyanwu-Ofili3Najat Khan3Venky Soundararajan1*
 
1nference, Cambridge, MA 02142, USA.
2nference Labs, Bengaluru, KA 560017, India.
3Janssen Research & Development LLC, USA.
4nference, Toronto, ON M5V 2G9, Canada.
 
Correspondence: Venky Soundararajan (venky@nference.net) 
 
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Copyright:
© 2020, Venkatakrishnan et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.