Literature DB >> 33279954

A review of COVID-19 biomarkers and drug targets: resources and tools.

Francesca P Caruso1, Giovanni Scala1, Luigi Cerulo1, Michele Ceccarelli2.   

Abstract

The stratification of patients at risk of progression of COVID-19 and their molecular characterization is of extreme importance to optimize treatment and to identify therapeutic options. The bioinformatics community has responded to the outbreak emergency with a set of tools and resource to identify biomarkers and drug targets that we review here. Starting from a consolidated corpus of 27 570 papers, we adopt latent Dirichlet analysis to extract relevant topics and select those associated with computational methods for biomarker identification and drug repurposing. The selected topics span from machine learning and artificial intelligence for disease characterization to vaccine development and to therapeutic target identification. Although the way to go for the ultimate defeat of the pandemic is still long, the amount of knowledge, data and tools generated so far constitutes an unprecedented example of global cooperation to this threat.
© The Author(s) 2020. Published by Oxford University Press.

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Year:  2021        PMID: 33279954      PMCID: PMC7799271          DOI: 10.1093/bib/bbaa328

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  78 in total

1.  Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.

Authors:  Mingfeng Liao; Yang Liu; Jing Yuan; Yanling Wen; Gang Xu; Juanjuan Zhao; Lin Cheng; Jinxiu Li; Xin Wang; Fuxiang Wang; Lei Liu; Ido Amit; Shuye Zhang; Zheng Zhang
Journal:  Nat Med       Date:  2020-05-12       Impact factor: 53.440

2.  Deep Docking: A Deep Learning Platform for Augmentation of Structure Based Drug Discovery.

Authors:  Francesco Gentile; Vibudh Agrawal; Michael Hsing; Anh-Tien Ton; Fuqiang Ban; Ulf Norinder; Martin E Gleave; Artem Cherkasov
Journal:  ACS Cent Sci       Date:  2020-05-19       Impact factor: 14.553

Review 3.  T cell responses in patients with COVID-19.

Authors:  Zeyu Chen; E John Wherry
Journal:  Nat Rev Immunol       Date:  2020-07-29       Impact factor: 53.106

4.  Computational screening of antagonists against the SARS-CoV-2 (COVID-19) coronavirus by molecular docking.

Authors:  Ran Yu; Liang Chen; Rong Lan; Rong Shen; Peng Li
Journal:  Int J Antimicrob Agents       Date:  2020-05-08       Impact factor: 5.283

5.  Network-based in silico drug efficacy screening.

Authors:  Emre Guney; Jörg Menche; Marc Vidal; Albert-László Barábasi
Journal:  Nat Commun       Date:  2016-02-01       Impact factor: 14.919

6.  Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2.

Authors:  Yadi Zhou; Yuan Hou; Jiayu Shen; Yin Huang; William Martin; Feixiong Cheng
Journal:  Cell Discov       Date:  2020-03-16       Impact factor: 10.849

7.  Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study.

Authors:  Maryam Enayatkhani; Mehdi Hasaniazad; Sobhan Faezi; Hamed Gouklani; Parivash Davoodian; Nahid Ahmadi; Mohammad Ali Einakian; Afsaneh Karmostaji; Khadijeh Ahmadi
Journal:  J Biomol Struct Dyn       Date:  2020-05-02

8.  Clinically Applicable AI System for Accurate Diagnosis, Quantitative Measurements, and Prognosis of COVID-19 Pneumonia Using Computed Tomography.

Authors:  Kang Zhang; Xiaohong Liu; Jun Shen; Zhihuan Li; Ye Sang; Xingwang Wu; Yunfei Zha; Wenhua Liang; Chengdi Wang; Ke Wang; Linsen Ye; Ming Gao; Zhongguo Zhou; Liang Li; Jin Wang; Zehong Yang; Huimin Cai; Jie Xu; Lei Yang; Wenjia Cai; Wenqin Xu; Shaoxu Wu; Wei Zhang; Shanping Jiang; Lianghong Zheng; Xuan Zhang; Li Wang; Liu Lu; Jiaming Li; Haiping Yin; Winston Wang; Oulan Li; Charlotte Zhang; Liang Liang; Tao Wu; Ruiyun Deng; Kang Wei; Yong Zhou; Ting Chen; Johnson Yiu-Nam Lau; Manson Fok; Jianxing He; Tianxin Lin; Weimin Li; Guangyu Wang
Journal:  Cell       Date:  2020-05-04       Impact factor: 41.582

9.  Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients.

Authors:  Yong Xiong; Yuan Liu; Liu Cao; Dehe Wang; Ming Guo; Ao Jiang; Dong Guo; Wenjia Hu; Jiayi Yang; Zhidong Tang; Honglong Wu; Yongquan Lin; Meiyuan Zhang; Qi Zhang; Mang Shi; Yingle Liu; Yu Zhou; Ke Lan; Yu Chen
Journal:  Emerg Microbes Infect       Date:  2020-12       Impact factor: 7.163

10.  A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Authors:  David E Gordon; Gwendolyn M Jang; Mehdi Bouhaddou; Jiewei Xu; Kirsten Obernier; Kris M White; Matthew J O'Meara; Veronica V Rezelj; Jeffrey Z Guo; Danielle L Swaney; Tia A Tummino; Ruth Hüttenhain; Robyn M Kaake; Alicia L Richards; Beril Tutuncuoglu; Helene Foussard; Jyoti Batra; Kelsey Haas; Maya Modak; Minkyu Kim; Paige Haas; Benjamin J Polacco; Hannes Braberg; Jacqueline M Fabius; Manon Eckhardt; Margaret Soucheray; Melanie J Bennett; Merve Cakir; Michael J McGregor; Qiongyu Li; Bjoern Meyer; Ferdinand Roesch; Thomas Vallet; Alice Mac Kain; Lisa Miorin; Elena Moreno; Zun Zar Chi Naing; Yuan Zhou; Shiming Peng; Ying Shi; Ziyang Zhang; Wenqi Shen; Ilsa T Kirby; James E Melnyk; John S Chorba; Kevin Lou; Shizhong A Dai; Inigo Barrio-Hernandez; Danish Memon; Claudia Hernandez-Armenta; Jiankun Lyu; Christopher J P Mathy; Tina Perica; Kala Bharath Pilla; Sai J Ganesan; Daniel J Saltzberg; Ramachandran Rakesh; Xi Liu; Sara B Rosenthal; Lorenzo Calviello; Srivats Venkataramanan; Jose Liboy-Lugo; Yizhu Lin; Xi-Ping Huang; YongFeng Liu; Stephanie A Wankowicz; Markus Bohn; Maliheh Safari; Fatima S Ugur; Cassandra Koh; Nastaran Sadat Savar; Quang Dinh Tran; Djoshkun Shengjuler; Sabrina J Fletcher; Michael C O'Neal; Yiming Cai; Jason C J Chang; David J Broadhurst; Saker Klippsten; Phillip P Sharp; Nicole A Wenzell; Duygu Kuzuoglu-Ozturk; Hao-Yuan Wang; Raphael Trenker; Janet M Young; Devin A Cavero; Joseph Hiatt; Theodore L Roth; Ujjwal Rathore; Advait Subramanian; Julia Noack; Mathieu Hubert; Robert M Stroud; Alan D Frankel; Oren S Rosenberg; Kliment A Verba; David A Agard; Melanie Ott; Michael Emerman; Natalia Jura; Mark von Zastrow; Eric Verdin; Alan Ashworth; Olivier Schwartz; Christophe d'Enfert; Shaeri Mukherjee; Matt Jacobson; Harmit S Malik; Danica G Fujimori; Trey Ideker; Charles S Craik; Stephen N Floor; James S Fraser; John D Gross; Andrej Sali; Bryan L Roth; Davide Ruggero; Jack Taunton; Tanja Kortemme; Pedro Beltrao; Marco Vignuzzi; Adolfo García-Sastre; Kevan M Shokat; Brian K Shoichet; Nevan J Krogan
Journal:  Nature       Date:  2020-04-30       Impact factor: 69.504

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  4 in total

1.  Longwise Cluster Analysis for the Prediction of COVID-19 Severity within 72 h of Admission: COVID-DATA-SAVE-LIFES Cohort.

Authors:  Rodrigo San-Cristobal; Roberto Martín-Hernández; Omar Ramos-Lopez; Diego Martinez-Urbistondo; Víctor Micó; Gonzalo Colmenarejo; Paula Villares Fernandez; Lidia Daimiel; Jose Alfredo Martínez
Journal:  J Clin Med       Date:  2022-06-10       Impact factor: 4.964

Review 2.  The Role of Interleukin-8 in Lung Inflammation and Injury: Implications for the Management of COVID-19 and Hyperinflammatory Acute Respiratory Distress Syndrome.

Authors:  Maria Candida Cesta; Mara Zippoli; Carolina Marsiglia; Elizabeth Marie Gavioli; Flavio Mantelli; Marcello Allegretti; Robert A Balk
Journal:  Front Pharmacol       Date:  2022-01-12       Impact factor: 5.810

Review 3.  Significance of Cardiac Troponins as an Identification Tool in COVID-19 Patients Using Biosensors: An Update.

Authors:  Yousef Rasmi; Osama F Mosa; Shahriar Alipour; Nadia Heidari; Farzaneh Javanmard; Ali Golchin; Shiva Gholizadeh-Ghaleh Aziz
Journal:  Front Mol Biosci       Date:  2022-02-24

4.  COVID-19 pandemic and artificial intelligence possibilities: A healthcare perspective.

Authors:  R M Gupta; Mahima Lall
Journal:  Med J Armed Forces India       Date:  2021-07-26
  4 in total

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