Literature DB >> 35308924

Parsing Immune Correlates of Protection Against SARS-CoV-2 from Biomedical Literature.

Sydney L Foote1,2, Sara Jones1,2, Jane Lockmuller1, Liliana Brown3, Joseph Breen4, Anupama Gururaj4.   

Abstract

After the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, identification of immune correlates of protection (CoPs) have become increasingly important to understand the immune response to SARS-CoV-2. The vast amount of preprint and published literature related to COVID-19 makes it challenging for researchers to stay up to date on research results regarding CoPs against SARS-CoV-2. To address this problem, we developed a machine learning classifier to identify papers relevant to CoPs and a customized named entity recognition (NER) model to extract terms of interest, including CoPs, vaccines, assays, and animal models. A user-friendly visualization tool was populated with the extracted and normalized NER results and associated publication information including links to full-text articles and clinical trial information where available. The goal of this pilot project is to provide a basis for developing real-time informatics platforms that can inform researchers with scientific insights from emerging research. ©2021 AMIA - All rights reserved.

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Year:  2022        PMID: 35308924      PMCID: PMC8861695     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN: 1559-4076


  10 in total

1.  PubTator central: automated concept annotation for biomedical full text articles.

Authors:  Chih-Hsuan Wei; Alexis Allot; Robert Leaman; Zhiyong Lu
Journal:  Nucleic Acids Res       Date:  2019-07-02       Impact factor: 16.971

2.  LitCovid: an open database of COVID-19 literature.

Authors:  Qingyu Chen; Alexis Allot; Zhiyong Lu
Journal:  Nucleic Acids Res       Date:  2020-11-09       Impact factor: 16.971

3.  Pre-existing heterosubtypic immunity provides a barrier to airborne transmission of influenza viruses.

Authors:  Valerie Le Sage; Jennifer E Jones; Karen A Kormuth; William J Fitzsimmons; Eric Nturibi; Gabriella H Padovani; Claudia P Arevalo; Andrea J French; Annika J Avery; Richard Manivanh; Elizabeth E McGrady; Amar R Bhagwat; Adam S Lauring; Scott E Hensley; Seema S Lakdawala
Journal:  PLoS Pathog       Date:  2021-02-18       Impact factor: 6.823

4.  COVID-19 immune signatures reveal stable antiviral T cell function despite declining humoral responses.

Authors:  Agnes Bonifacius; Sabine Tischer-Zimmermann; Anna C Dragon; Daniel Gussarow; Alexander Vogel; Ulrike Krettek; Nina Gödecke; Mustafa Yilmaz; Anke R M Kraft; Marius M Hoeper; Isabell Pink; Julius J Schmidt; Yang Li; Tobias Welte; Britta Maecker-Kolhoff; Jörg Martens; Marc Moritz Berger; Corinna Lobenwein; Metodi V Stankov; Markus Cornberg; Sascha David; Georg M N Behrens; Oliver Witzke; Rainer Blasczyk; Britta Eiz-Vesper
Journal:  Immunity       Date:  2021-02-09       Impact factor: 31.745

5.  Correlates of protection against SARS-CoV-2 in rhesus macaques.

Authors:  Katherine McMahan; Jingyou Yu; Noe B Mercado; Carolin Loos; Lisa H Tostanoski; Abishek Chandrashekar; Jinyan Liu; Lauren Peter; Caroline Atyeo; Alex Zhu; Esther A Bondzie; Gabriel Dagotto; Makda S Gebre; Catherine Jacob-Dolan; Zhenfeng Li; Felix Nampanya; Shivani Patel; Laurent Pessaint; Alex Van Ry; Kelvin Blade; Jake Yalley-Ogunro; Mehtap Cabus; Renita Brown; Anthony Cook; Elyse Teow; Hanne Andersen; Mark G Lewis; Douglas A Lauffenburger; Galit Alter; Dan H Barouch
Journal:  Nature       Date:  2020-12-04       Impact factor: 49.962

6.  A Novel Coronavirus from Patients with Pneumonia in China, 2019.

Authors:  Na Zhu; Dingyu Zhang; Wenling Wang; Xingwang Li; Bo Yang; Jingdong Song; Xiang Zhao; Baoying Huang; Weifeng Shi; Roujian Lu; Peihua Niu; Faxian Zhan; Xuejun Ma; Dayan Wang; Wenbo Xu; Guizhen Wu; George F Gao; Wenjie Tan
Journal:  N Engl J Med       Date:  2020-01-24       Impact factor: 91.245

Review 7.  Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks.

Authors:  Hossam M Ashour; Walid F Elkhatib; Md Masudur Rahman; Hatem A Elshabrawy
Journal:  Pathogens       Date:  2020-03-04

8.  Heterogeneous antibodies against SARS-CoV-2 spike receptor binding domain and nucleocapsid with implications for COVID-19 immunity.

Authors:  Kathleen M McAndrews; Dara P Dowlatshahi; Jianli Dai; Lisa M Becker; Janine Hensel; Laura M Snowden; Jennifer M Leveille; Michael R Brunner; Kylie W Holden; Nikolas S Hopkins; Alexandria M Harris; Jerusha Kumpati; Michael A Whitt; J Jack Lee; Luis L Ostrosky-Zeichner; Ramesha Papanna; Valerie S LeBleu; James P Allison; Raghu Kalluri
Journal:  JCI Insight       Date:  2020-09-17

9.  BioBERT: a pre-trained biomedical language representation model for biomedical text mining.

Authors:  Jinhyuk Lee; Wonjin Yoon; Sungdong Kim; Donghyeon Kim; Sunkyu Kim; Chan Ho So; Jaewoo Kang
Journal:  Bioinformatics       Date:  2020-02-15       Impact factor: 6.937

10.  Antibody Response against SARS-CoV-2 and Seasonal Coronaviruses in Nonhospitalized COVID-19 Patients.

Authors:  Natalia Ruetalo; Ramona Businger; Karina Althaus; Simon Fink; Felix Ruoff; Michaela Pogoda; Angelika Iftner; Tina Ganzenmüller; Klaus Hamprecht; Bertram Flehmig; Tamam Bakchoul; Markus F Templin; Michael Schindler
Journal:  mSphere       Date:  2021-02-24       Impact factor: 4.389

  10 in total

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