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

Published in eLife

May 28, 2020

Originally Posted in bioRxiv

March 29, 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 Venkatakrishnan, Arjun Puranik, Akash Anand, David Zemmour, Xiang Yao, Xiaoying Wu, Ramakrishna Chilaka, Dariusz K. Murakowski, Kristopher Standish, Bharathwaj Raghunathan, Tyler Wagner, Enrique Garcia-Rivera, Hugo Solomon, Abhinav Garg, Rakesh Barve, Anuli Anyanwu-Ofili, Najat Khan, Venky Soundararajan

nference, Cambridge, MA 02142, USA.
nference Labs Labs, Bengaluru, KA 560017, India.
Janssen Research & Development LLC, USA.
nference, Toronto, ON M5V 2G9, Canada.
 

Correspondence: Venky Soundararajan (venky@nference.net) 

 
 

Featured in S T A T

Affiliations:
 
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.