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Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors.
Venkatakrishnan, A J; Puranik, Arjun; Anand, Akash; Zemmour, David; Yao, Xiang; Wu, Xiaoying; Chilaka, Ramakrishna; Murakowski, Dariusz K; Standish, Kristopher; Raghunathan, Bharathwaj; Wagner, Tyler; Garcia-Rivera, Enrique; Solomon, Hugo; Garg, Abhinav; Barve, Rakesh; Anyanwu-Ofili, Anuli; Khan, Najat; Soundararajan, Venky.
  • Venkatakrishnan AJ; nference, Cambridge, United States.
  • Puranik A; nference, Cambridge, United States.
  • Anand A; nference Labs, Bengaluru, India.
  • Zemmour D; nference, Cambridge, United States.
  • Yao X; Janssen pharmaceutical companies of Johnson & Johnson (J&J), Spring House, United States.
  • Wu X; Janssen pharmaceutical companies of Johnson & Johnson (J&J), Spring House, United States.
  • Chilaka R; nference Labs, Bengaluru, India.
  • Murakowski DK; nference, Cambridge, United States.
  • Standish K; Janssen pharmaceutical companies of Johnson & Johnson (J&J), Spring House, United States.
  • Raghunathan B; nference, Toronto, Canada.
  • Wagner T; nference, Cambridge, United States.
  • Garcia-Rivera E; nference, Cambridge, United States.
  • Solomon H; nference, Cambridge, United States.
  • Garg A; nference Labs, Bengaluru, India.
  • Barve R; nference Labs, Bengaluru, India.
  • Anyanwu-Ofili A; Janssen pharmaceutical companies of Johnson & Johnson (J&J), Spring House, United States.
  • Khan N; Janssen pharmaceutical companies of Johnson & Johnson (J&J), Spring House, United States.
  • Soundararajan V; nference, Cambridge, United States.
Elife ; 92020 05 28.
Article in English | MEDLINE | ID: covidwho-401507
Semantic information from SemMedBD (by NLM)
1. keratinocyte PART_OF Tongue
Subject
keratinocyte
Predicate
PART_OF
Object
Tongue
2. Enterocytes PART_OF Intestine
Subject
Enterocytes
Predicate
PART_OF
Object
Intestine
3. keratinocyte PART_OF Tongue
Subject
keratinocyte
Predicate
PART_OF
Object
Tongue
4. Enterocytes PART_OF Intestines, Small
Subject
Enterocytes
Predicate
PART_OF
Object
Intestines, Small
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 over 45 quadrillion possible conceptual associations from unstructured text, and triangulation with insights from single-cell RNA-sequencing, bulk RNA-seq 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.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Receptors, Virus / Coronavirus Infections / Libraries, Medical Limits: Animals / Humans Language: English Year: 2020 Document Type: Article Affiliation country: ELife.58040

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Receptors, Virus / Coronavirus Infections / Libraries, Medical Limits: Animals / Humans Language: English Year: 2020 Document Type: Article Affiliation country: ELife.58040