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

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 Venkatakrishnan1,
  • Arjun Puranik1,
  • Akash Anand2,
  • David Zemmour1,
  • Xiang Yao3,
  • Xiaoying Wu3,
  • Ramakrishna Chilaka2,
  • Dariusz K. Murakowski1,
  • Kristopher Standish3,
  • Bharathwaj Raghunathan4,
  • Tyler Wagner1,
  • Enrique Garcia-Rivera1,
  • Hugo Solomon1,
  • Abhinav Garg2,
  • Rakesh Barve2,
  • Anuli Anyanwu-Ofili3,
  • Najat Khan3,
  • Venky Soundararajan1*
  • 1nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA.
  • 2nference Labs, pvt. ltd., Wind Tunnel Road, Murugesh Palaya, Bengaluru 560017, India.
  • 3Janssen Research & Development LLC, USA.
  • 4nference, 111 Peter St, Toronto, ON M5V 2G9, Canada.
  • Correspondence:
  • Affiliations:
  • Timeline:
  • Received: April 18, 2020
  • Accepted: May 27, 2020
  • Published: May 28, 2020 (v1)
  • 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.
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  • Affiliations:
  • Media coverage:
  • Timeline:
  • Received: April 18, 2020
  • Accepted: May 27, 2020
  • Published: May 28, 2020 (v1)
  • 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.
  • Related Tweets:
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