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References from Applying the digital data and the bioinformatics tools in SARS-CoV-2 research. Local targets link to admitted publications; unresolved targets remain external evidence.
2019-nCoV (Wuhan virus), a novel Coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness
10.3855/jidc.12425 · 2020 · External reference
10.1002/jmv.25678
10.1002/jmv.25678 · External reference
The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health - The latest 2019 novel coronavirus outbreak in Wuhan, China
10.1016/j.ijid.2020.01.009 · 2020 · External reference
10.1038/s41586-020-2008-3
10.1038/s41586-020-2008-3 · External reference
10.1016/j.jid.2017.07.095
10.1016/j.jid.2017.07.095 · External reference
Current trend and development in bioinformatics research
10.1186/s12859-020-03874-y · 2020 · External reference
Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020
10.1186/s12859-020-03890-y · 2020 · External reference
10.1016/j.gheart.2017.01.005
10.1016/j.gheart.2017.01.005 · External reference
Taking bioinformatics to systems medicine
10.1007/978-1-4939-3283-2_2 · 2016 · External reference
10.1093/nar/gkz899
10.1093/nar/gkz899 · External reference
10.1101/2020.02.17.951335
10.1101/2020.02.17.951335 · External reference
10.1002/jmv.25731
10.1002/jmv.25731 · External reference
Viral metagenomics revealed sendai virus and coronavirus infection of malayan pangolins (Manis javanica)
2019 · External reference
10.1093/nsr/nwaa036
10.1093/nsr/nwaa036 · External reference
10.1080/22221751.2020.1719902
10.1080/22221751.2020.1719902 · External reference
10.1016/s0140-6736(20)30251-8
10.1016/s0140-6736(20)30251-8 · External reference
10.1007/s11427-021-1964-4
10.1007/s11427-021-1964-4 · External reference
10.1016/j.jmb.2020.11.024
10.1016/j.jmb.2020.11.024 · External reference
The establishment of reference sequence for SARS-CoV-2 and variation analysis
10.1002/jmv.25762 · 2020 · External reference
Genetic diversity and evolution of SARS-CoV-2
10.1016/j.meegid.2020.104260 · 2020 · External reference
GISAID: Global initiative on sharing all influenza data - from vision to reality
2017 · External reference
10.1016/j.cell.2020.06.034
10.1016/j.cell.2020.06.034 · External reference
The 2019 novel coronavirus resource
2020 · External reference
CNGBdb: China National GeneBank DataBase
2020 · External reference
10.1101/2020.06.08.139451
10.1101/2020.06.08.139451 · External reference
The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data
10.1093/nar/gkab889 · 2022 · External reference
10.1038/s41588-020-0700-8
10.1038/s41588-020-0700-8 · External reference
10.1093/nar/gkaa1070
10.1093/nar/gkaa1070 · External reference
10.1093/nar/gkac1072
10.1093/nar/gkac1072 · External reference
ViralZone: recent updates to the virus knowledge resource
10.1093/nar/gks1220 · 2013 · External reference
10.1093/nar/gkac1003
10.1093/nar/gkac1003 · External reference
10.1093/bioinformatics/bty407
10.1093/bioinformatics/bty407 · External reference
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing
10.1093/nar/gkab417 · 2021 · External reference
A database resource and online analysis tools for coronaviruses on a historical and global scale
2020 · External reference
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
10.1186/s12859-021-04294-2 · 2021 · External reference
ViralFlow: a versatile automated workflow for SARS-CoV-2 genome assembly, lineage assignment, mutations and intrahost variant detection
10.3390/v14020217 · 2022 · External reference
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts
10.1093/bioinformatics/btac176 · 2022 · External reference
10.1093/bioinformatics/btab015
10.1093/bioinformatics/btab015 · External reference
COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data
10.1186/s12859-022-04632-y · 2022 · External reference
10.1101/2021.01.16.425365
10.1101/2021.01.16.425365 · External reference
poreCov-an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing
10.3389/fgene.2021.711437 · 2021 · External reference
HAPHPIPE: haplotype reconstruction and phylodynamics for deep sequencing of intrahost viral populations
10.1093/molbev/msaa315 · 2021 · External reference
10.1101/852657
10.1101/852657 · External reference
10.1101/2020.05.01.071050
10.1101/2020.05.01.071050 · External reference
MicroGMT: a mutation tracker for SARS-CoV-2 and other microbial genome sequences
10.3389/fmicb.2020.01502 · 2020 · External reference
CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
10.1093/bioinformatics/btaa1047 · 2021 · External reference
SWAV: a web-based visualization browser for sliding window analysis
10.1038/s41598-019-57038-x · 2020 · External reference
Coronapp: A web application to annotate and monitor SARS-CoV-2 mutations
10.1002/jmv.26678 · 2021 · External reference
10.1016/j.csbj.2021.09.002 · Admitted local publication
VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants
10.1093/nar/gkab478 · 2021 · External reference
10.1093/bioinformatics/btab856
10.1093/bioinformatics/btab856 · External reference
Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants
10.1186/s12967-020-02675-4 · 2020 · External reference
10.1016/j.cell.2020.06.043
10.1016/j.cell.2020.06.043 · External reference
CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants
10.3390/v14030561 · 2022 · External reference
DeepIPs: comprehensive assessment and computational identification of phosphorylation sites of SARS-CoV-2 infection using a deep learning-based approach
10.1093/bib/bbab244 · 2021 · External reference
How big data and artificial intelligence can help better manage the COVID-19 pandemic
10.3390/ijerph17093176 · 2020 · External reference
A fully automatic deep learning system for COVID-19 diagnostic and prognostic analysis
10.1183/13993003.00775-2020 · 2020 · External reference
Artificial Intelligence (AI) applications for COVID-19 pandemic
10.1016/j.dsx.2020.04.012 · 2020 · External reference
10.1126/science.abc0473
10.1126/science.abc0473 · External reference
nCov2019: an R package for studying the COVID-19 coronavirus pandemic
10.7717/peerj.11421 · 2021 · External reference
10.1093/nar/gkab921
10.1093/nar/gkab921 · External reference
10.1101/2020.04.10.036343
10.1101/2020.04.10.036343 · External reference
CoV-GLUE: a web application for tracking SARS-CoV-2 genomic variation
2020 · External reference
CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants
10.1016/s1473-3099(21)00078-5 · 2021 · External reference
SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database
10.1093/nargab/lqad037 · 2023 · External reference
ViruSurf: an integrated database to investigate viral sequences
10.1093/nar/gkaa846 · 2021 · External reference
IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution
10.3389/fmed.2021.765249 · 2021 · External reference
PAUP*. phylogenetic analysis using parsimony (*and other methods), 4.0
2002 · External reference
Bioinformatics resources for SARS-CoV-2 discovery and surveillance
10.1093/bib/bbaa386 · 2021 · External reference
10.1016/j.cell.2020.06.043
10.1016/j.cell.2020.06.043 · External reference
Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
10.1038/s41598-020-79484-8 · 2020 · External reference
10.1093/molbev/msp077
10.1093/molbev/msp077 · External reference
FastTree 2--approximately maximum-likelihood trees for large alignments
10.1371/journal.pone.0009490 · 2010 · External reference
10.1093/molbev/msu300
10.1093/molbev/msu300 · External reference
BEAST: Bayesian evolutionary analysis by sampling trees
10.1186/1471-2148-7-214 · 2007 · External reference
Bayesian phylodynamic inference with complex models
10.1371/journal.pcbi.1006546 · 2018 · External reference
10.1093/sysbio/syy032
10.1093/sysbio/syy032 · External reference
10.1093/sysbio/syy007
10.1093/sysbio/syy007 · External reference
Assessing Immune Response to SARS-CoV-2 Infection
10.2147/itt.s264138 · 2020 · External reference
CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study
10.2196/22299 · 2020 · External reference
10.1101/2020.01.31.928796
10.1101/2020.01.31.928796 · External reference
Covidex: An ultrafast and accurate tool for SARS-CoV-2 subtyping
10.1016/j.meegid.2022.105261 · 2022 · External reference
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
10.1093/ve/veab064 · 2021 · External reference
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes
10.1093/ve/veab092 · 2021 · External reference
10.3390/v14061239
10.3390/v14061239 · External reference
Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2
10.1038/s41598-020-78703-6 · 2020 · External reference
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection
10.1093/bioinformatics/btaa695 · 2021 · External reference
10.1093/bioinformatics/btac030
10.1093/bioinformatics/btac030 · External reference
10.1016/j.envres.2021.111909
10.1016/j.envres.2021.111909 · External reference
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
10.1093/bioinformatics/btac401 · 2022 · External reference
10.1038/s41579-021-00630-8
10.1038/s41579-021-00630-8 · External reference
10.1093/nar/28.1.235
10.1093/nar/28.1.235 · External reference
10.1126/science.abd5223
10.1126/science.abd5223 · External reference
Structural analysis of SARS-CoV-2 ORF8 protein: pathogenic and therapeutic implications
10.3389/fgene.2021.693227 · 2021 · External reference
Identification of vaccine targets & design of vaccine against SARS-CoV-2 coronavirus using computational and deep learning-based approaches
10.7717/peerj.13380 · 2022 · External reference
10.1177/15353702211021348
10.1177/15353702211021348 · External reference
The NIH 3D print exchange: a public resource for bioscientific and biomedical 3d prints
10.1089/3dp.2014.1503 · 2014 · External reference
10.1002/pro.3959
10.1002/pro.3959 · External reference
10.1016/j.crmeth.2021.100014
10.1016/j.crmeth.2021.100014 · External reference
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence
10.1093/bioinformatics/btaa550 · 2020 · External reference
10.1093/nar/gkaa731
10.1093/nar/gkaa731 · External reference
10.1093/bib/bbaa404
10.1093/bib/bbaa404 · External reference
10.1093/nar/gkab977
10.1093/nar/gkab977 · External reference
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
10.1007/s10822-010-9352-6 · 2010 · External reference
10.3390/ijms222111627
10.3390/ijms222111627 · External reference
SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions
10.1093/bioinformatics/btab799 · 2022 · External reference
SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants
10.1093/bioinformatics/btac517 · 2022 · External reference
10.1093/nar/gku1121
10.1093/nar/gku1121 · External reference
10.1016/j.compbiomed.2020.104131
10.1016/j.compbiomed.2020.104131 · External reference
KEGG-based pathway visualization tool for complex omics data
10.3233/isb-00199 · 2005 · External reference
10.1093/nar/gkaa1024
10.1093/nar/gkaa1024 · External reference
10.1093/nar/gkab881
10.1093/nar/gkab881 · External reference
10.1021/acsomega.0c05701 · Admitted local publication
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies
10.1093/nar/gkaa1094 · 2021 · External reference
10.1101/2020.04.19.048991
10.1101/2020.04.19.048991 · External reference
CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers
10.1016/j.ygeno.2021.07.020 · 2021 · External reference
A2B-COVID: A Tool for Rapidly Evaluating potential SARS-CoV-2 transmission events
10.1093/molbev/msac025 · 2022 · External reference
CalmBelt: rapid SARS-CoV-2 genome characterization for outbreak tracking
10.3389/fmed.2021.790662 · 2021 · External reference
COVIDOUTCOME-estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome
10.1093/database/baab020 · 2021 · External reference
An online tool for predicting the prognosis of cancer patients with SARS-CoV-2 infection: a multi-center study
10.1007/s00432-020-03420-6 · 2021 · External reference
COVID-19 Pneumonia Diagnosis Using a Simple 2D Deep Learning Framework With a Single Chest CT Image: Model Development and Validation
10.2196/19569 · 2020 · External reference
Clinically Applicable AI System for Accurate Diagnosis, Quantitative Measurements, and Prognosis of COVID-19 Pneumonia Using Computed Tomography
10.1016/j.cell.2020.08.029 · 2020 · External reference
Early triage of critically ill COVID-19 patients using deep learning
10.1038/s41467-020-17280-8 · 2020 · External reference
AI aiding in diagnosing, tracking recovery of COVID-19 using deep learning on Chest CT scans
10.1007/s11042-020-10010-8 · 2020 · External reference
10.1016/j.compbiomed.2020.103792
10.1016/j.compbiomed.2020.103792 · External reference
10.2196/19515
10.2196/19515 · External reference
Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning
10.1038/s41551-020-00633-5 · 2020 · External reference
10.1093/nar/gkaa969
10.1093/nar/gkaa969 · External reference
10.1016/j.isci.2020.101297
10.1016/j.isci.2020.101297 · External reference
COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19
10.3389/fpubh.2023.1125917 · 2023 · External reference
iBioProVis: interactive visualization and analysis of compound bioactivity space
10.1093/bioinformatics/btaa496 · 2020 · External reference
10.1038/s42256-021-00335-w
10.1038/s42256-021-00335-w · External reference
Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds
10.1002/minf.202000028 · 2020 · External reference
10.1093/bioinformatics/btaa645
10.1093/bioinformatics/btaa645 · External reference
10.1093/nar/gkad414
10.1093/nar/gkad414 · External reference
10.1093/nar/gkx346
10.1093/nar/gkx346 · External reference
CRESSP: a comprehensive pipeline for prediction of immunopathogenic SARS-CoV-2 epitopes using structural properties of proteins
10.1093/bib/bbac056 · 2022 · External reference
10.1101/2022.02.05.479274
10.1101/2022.02.05.479274 · External reference
10.1038/s41467-020-17189-2
10.1038/s41467-020-17189-2 · External reference
A web-based platform on coronavirus disease-19 to maintain predicted diagnostic, drug, and vaccine candidates
10.1089/mab.2020.0035 · 2020 · External reference
10.1093/nar/gku938
10.1093/nar/gku938 · External reference
10.1016/j.chom.2020.03.002
10.1016/j.chom.2020.03.002 · External reference
ESC: a comprehensive resource for SARS-CoV-2 immune escape variants
10.1093/nar/gkab895 · 2022 · External reference
10.1093/bioinformatics/btaa739
10.1093/bioinformatics/btaa739 · External reference
10.1371/journal.pone.0261045
10.1371/journal.pone.0261045 · External reference
Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base
2021 · External reference
10.1038/s41596-020-0358-9
10.1038/s41596-020-0358-9 · External reference
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses
10.1093/database/baac017 · 2022 · External reference
10.1093/nar/gkab850
10.1093/nar/gkab850 · External reference
10.1093/nar/gkaa861
10.1093/nar/gkaa861 · External reference
D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19
10.1016/j.apsb.2020.04.006 · 2020 · External reference
10.1093/bib/bbaa155
10.1093/bib/bbaa155 · External reference
