Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors
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- May 26, 2020
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- 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 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: Venky Soundararajan (venky@nference.net)
- Correspondence:
- Venky Soundararajan (venky@nference.net)
- 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.
- Media coverage:
- Related Tweets:
This article is frickin' weird. It's like the saying about using a Buick to swat a fly, except as far as I can tell they actually missed the fly. Please guilt-trip me later so I'm forced to discuss in more detail.
https://elifesciences.org/articles/58040
This nferX Platform could be very useful to infer associations between entities to obtain #multiomic #networks.
"Knowledge synthesis of 100 million #biomedical documents augments the deep expression profiling of #coronavirus receptors" https://doi.org/10.7554/eLife.58040 Thanks @CyrilPedia !
'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).'
https://elifesciences.org/articles/58040
Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors
https://elifesciences.org/articles/58040
Fantastic article by @sxbegle and @statnews on the multi-organ damage potential for SARS-CoV-2 infection in #COVID19
Excellent quotes from Founder & CSO Venky Soundararajan (@in4ence) on our @eLife paper published last month (https://elifesciences.org/articles/58040) and @MayoClinic partnership
For a 'respiratory' virus, #SARSCoV2 attacks an astonishing array of organs, from nose to toes. Video by @sayhitohyacinth & words by me explains why docs say, 'wait a minute; it's doing this, too?!' https://www.statnews.com/2020/06/26/from-nose-to-toe-covid19-virus-attacks-like-no-other-respiratory-infection/
- 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:
This article is frickin' weird. It's like the saying about using a Buick to swat a fly, except as far as I can tell they actually missed the fly. Please guilt-trip me later so I'm forced to discuss in more detail.
https://elifesciences.org/articles/58040
This nferX Platform could be very useful to infer associations between entities to obtain #multiomic #networks.
"Knowledge synthesis of 100 million #biomedical documents augments the deep expression profiling of #coronavirus receptors" https://doi.org/10.7554/eLife.58040 Thanks @CyrilPedia !
'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).'
https://elifesciences.org/articles/58040
Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors
https://elifesciences.org/articles/58040
Fantastic article by @sxbegle and @statnews on the multi-organ damage potential for SARS-CoV-2 infection in #COVID19
Excellent quotes from Founder & CSO Venky Soundararajan (@in4ence) on our @eLife paper published last month (https://elifesciences.org/articles/58040) and @MayoClinic partnership
For a 'respiratory' virus, #SARSCoV2 attacks an astonishing array of organs, from nose to toes. Video by @sayhitohyacinth & words by me explains why docs say, 'wait a minute; it's doing this, too?!' https://www.statnews.com/2020/06/26/from-nose-to-toe-covid19-virus-attacks-like-no-other-respiratory-infection/