Recognition of plausible therapeutic agents to combat COVID-19: An omics data based combined approach

Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics

(2020) David Gurwitz   DRUG DEVELOPMENT RESEARCH

Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China

(2020) Zunyou Wu et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The outbreak of COVID-19

(2020) Yi-Chi Wu et al.   Journal of the Chinese Medical Association

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

(2020) Nanshan Chen et al.   LANCET

Fear can be more harmful than the severe acute respiratory syndrome coronavirus 2 in controlling the corona virus disease 2019 epidemic

(2020) Shi-Yan Ren et al.   World Journal of Clinical Cases

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies

(2020) Jianjun Gao et al.   BioScience Trends

Remdesivir: A Review of Its Discovery and Development Leading to Emergency Use Authorization for Treatment of COVID-19

(2020) Richard T. Eastman et al.   ACS Central Science

The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro

(2020) Leon Caly et al.   ANTIVIRAL RESEARCH

Bat Coronaviruses in China

(2019) Yi Fan et al.   Viruses-Basel

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

(2019) Jiahua He et al.   NUCLEIC ACIDS RESEARCH

Novel Bat Alphacoronaviruses in Southern China Support Chinese Horseshoe Bats as an Important Reservoir for Potential Novel Coronaviruses

(2019) Lau et al.   Viruses-Basel

Human Coronavirus: Host-Pathogen Interaction

(2019) To Sing Fung et al.   Annual Review of Microbiology

Deep‐learning contact‐map guided protein structure prediction in CASP13

(2019) Wei Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved methods for predicting peptide binding affinity to MHC class II molecules

(2018) Kamilla Kjaergaard Jensen et al.   IMMUNOLOGY

CASTp 3.0: computed atlas of surface topography of proteins

(2018) Wei Tian et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Pathway based therapeutic targets identification and development of an interactive database CampyNIBase of Campylobacter jejuni RM1221 through non-redundant protein dataset

(2018) Mohammad Uzzal Hossain et al.   PLoS One

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

(2018) Steven Xijin Ge et al.   BMC BIOINFORMATICS

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

(2017) Martin Closter Jespersen et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

(2016) Lim Heo et al.   Scientific Reports

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

AllerTOP v.2—a server for in silico prediction of allergens

(2014) Ivan Dimitrov et al.   JOURNAL OF MOLECULAR MODELING

Designing of interferon-gamma inducing MHC class-II binders

(2013) Sandeep Kumar Dhanda et al.   Biology Direct

Antivirals in the 2009 pandemic - lessons and implications for future strategies

(2013) Deeva Berera et al.   Influenza and Other Respiratory Viruses

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

In Silico Approach for Predicting Toxicity of Peptides and Proteins

(2013) Sudheer Gupta et al.   PLoS One

Immunogenicity and Protection Efficacy of Monomeric and Trimeric Recombinant SARS Coronavirus Spike Protein Subunit Vaccine Candidates

(2013) Jie Li et al.   VIRAL IMMUNOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Comparative genomics allowed the identification of drug targets against human fungal pathogens

(2011) Ana Karina R Abadio et al.   BMC GENOMICS

Prediction of Specificity and Cross-Reactivity of Kinase Inhibitors

(2011) Nitish Kumar Mishra et al.   Letters in Drug Design & Discovery

High-throughput prediction of protein antigenicity using protein microarray data

(2010) Christophe N. Magnan et al.   BIOINFORMATICS

Endogenous toll-like receptor ligands and their biological significance

(2010) Li Yu et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

(2010) Daniel Seeliger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System

(2010) Nicolas Rapin et al.   PLoS One

INTERFEROME: the database of interferon regulated genes

(2008) Shamith A. Samarajiwa et al.   NUCLEIC ACIDS RESEARCH

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect

(2008) Kumiko Ui-Tei et al.   NUCLEIC ACIDS RESEARCH

ACToR — Aggregated Computational Toxicology Resource

(2008) Richard Judson et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY