Genomic variants-driven drug repurposing for tuberculosis by utilizing the established bioinformatic-based approachShort communication Published on 2022-12-012022-10-05 Journal: Biochemistry and Biophysics Reports [Category] 신약개발, [키워드] annotations applied approach bioinformatics biological process CCR5 CD44 cellular component contribute CXCR4 demonstrated deregulation disease disease-associated drug Drug discovery Drug repurposing drug target evaluated Evidence facilitate functional functional annotation Genes genomic genomic variant genomic variants GWAS HLA-B identify implementation in-silico indication involved KEGG Missense mutation molecular overlapped Pathogenesis Pathway analysis provided risk SELP suggested target Treatment Tuberculosis variant [DOI] 10.1016/j.bbrep.2022.101334 [Article Type] Short communication
Genetics of COVID-19 and myalgic encephalomyelitis/chronic fatigue syndrome: a systematic reviewArticle Published on 2022-11-012022-11-16 Journal: Annals of Clinical and Translational Neurology [Category] 변종, [키워드] ACE affected Analysis association chemokine cohort study components conditions COVID-19 cytokine signaling Enzymes evolutionary relationship expression fatigue functional annotation Genetic genetic component Genetic variant highlight HLA-A HLA-C HLA-DQA1 HLA-DRB1 immune dysfunction Inflammation investigated Mental Ontology Pathogenesis Pathway analysis Pathways performed physical Protein Proteins receptor signaling significantly similarity Symptoms syndrome systematic review T cell activation TYK2 [DOI] 10.1002/acn3.51631 PMC 바로가기
CASA: a comprehensive database resource for the COVID-19 Alternative Splicing AtlasArticle Published on 2022-10-202022-11-15 Journal: Journal of Translational Medicine [Category] 유전자 메커니즘, 치료기술, 치료제, [키워드] affected alteration Analysis Atla cell line conditions COVID-19 database dataset Diseases drug-target interaction event events facilitate functional annotation help host cell human cell identify immune response IMPROVE Infectious disease mechanism mechanisms Organoid performed platform profile Protein protein expression provided Quantitative data regulate Regulatory Research resource RNA RNA-seq dataset severity splicing tissues transcriptional virus [DOI] 10.1186/s12967-022-03699-8 PMC 바로가기
Bioinformatics analysis of potential common pathogenic mechanisms for COVID-19 infection and primary Sjogren’s syndromeCOVID-19 감염 및 원발성 쇼그렌 증후군에 대한 잠재적인 일반적인 병원성 메커니즘의 생물정보학 분석Article Published on 2022-07-262022-09-11 Journal: Frontiers in Immunology [Category] 유전자 메커니즘, [키워드] analysis Analysis CDCA2 cellular component cellular components CMPK2 COVID-19 COVID-19 infection cytoHubba database DEGs diagnostic Diagnostic markers differentially expressed differentially expressed gene Differentially expressed genes downloaded Evidence functional annotation Gene Expression Omnibus gene expression profile Gene expression profiles gene regulatory network General population Genes GEO HERC5 hub genes Ifi44 IFI44L IFIT1 IFIT2 IFIT3 marker mechanism metabolic pathway metabolic pathways molecular mechanism molecular mechanisms MX1 participated Pathogenesis pathogenic mechanism pathway Patient performed PPI Prevalence primary Sjogren’s syndrome. progression protein-protein interaction regulatory network reveal RRM2 selected significantly higher Sjögren’s syndrome subsequent analyses syndrome TOP2A transcription factor TYMS [DOI] 10.3389/fimmu.2022.938837 PMC 바로가기 [Article Type] Article
A network biology approach to identify crucial host targets for COVID-19Article Published on 2022-03-292023-07-02 Journal: Methods (San Diego, Calif.) [Category] COVID19(2023년), SARS, [키워드] 2019-nCoV, 2019 novel coronavirus AAV2, Adeno-associated virus AP-MS, Affinity purification-mass spectrometry ARDS, acute respiratory distress syndrome ARDS, adult respiratory distress syndrome BC, Betweenness centrality BP, Biological process CC, Cellular component CC, Closeness centrality CDK5RAP2, Cyclin dependent kinase 5 regulatory subunit associated protein 2 CNS, Central Nervous System COVID-19 COVID-19, coronavirus disease-2019 DC, Degree centrality Drug repurposing EC, eigenvector centrality functional annotation GO, Gene ontology HCMV, Human cytomegalovirus HCV, hepatitis C virus HIV-1, human immunodeficiency virus 1 IL-2, interleukin-2 MERS-CoV, Middle East respiratory syndrome coronavirus MF, Molecular function MgADP, Magnesium ADP MgATP, Magnesium ATP network biology Novel coronavirus PD-L1, Programmed death-ligand 1 PKA, protein kinase A PPIN, Protein-Protein interaction network PPIs, Protein-Protein interactions Rank aggregation RdRP SARS-CoV-2 SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 VSV, Vesicular stomatitis virus [DOI] 10.1016/j.ymeth.2022.03.016 PMC 바로가기 [Article Type] Article
Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomesAcademicSubjects/SCI00010 Published on 2022-02-222022-10-31 Journal: Nucleic Acids Research [Category] COVID-19, COVID19(2023년), MERS, SARS, [키워드] ADAR Alter Analysing Analysis antigenicity APOBEC B.1.617.1 B.1.617.2 collected consensus sequence contribute Course COVID-19 pandemic Critical Delta Factor fixed functional annotation Genome Genome sequencing GISAID Host hosts Immune escape India Intra-host variability iSNV iSNVs majority Mutation Next-generation sequencing observé Prevalence Protein RdRP recorded reported residue SARS-CoV-2 SARS-CoV-2 genome sequenced single nucleotide variation SNV spike Spread submitted Surveillance the SARS-CoV-2 genome Variability variants of concern Variation VoC [DOI] 10.1093/nar/gkab1297 PMC 바로가기 [Article Type] AcademicSubjects/SCI00010
HumanNet v3: an improved database of human gene networks for disease researchHumanNet v3: 질병 연구를 위한 인간 유전자 네트워크의 개선된 데이터베이스AcademicSubjects/SCI00010 Published on 2022-01-072022-09-10 Journal: Nucleic Acids Research [Category] 유전자 메커니즘, [키워드] accumulated Algorithms approach association citation complex database dataset demonstrated disease Diseases feasible functional functional annotation functional gene Genetic host gene host genes human diseases human gene human genes Interaction network outperform physical protein coding genes Protein–protein interaction provide Research significantly Support user with COVID-19 [DOI] 10.1093/nar/gkab1048 PMC 바로가기 [Article Type] AcademicSubjects/SCI00010
Core genes involved in the regulation of acute lung injury and their association with COVID-19 and tumor progression: A bioinformatics and experimental study급성 폐 손상의 조절 및 COVID-19 및 종양 진행과의 연관성에 관여하는 핵심 유전자 : 생물 정보학 및 실험 연구Research Article Published on 2021-11-222022-09-10 Journal: PLoS ONE [Category] MERS, 유전자 메커니즘, 진단, [키워드] acute lung injury administration analysed anti-inflammatory agents Anti-inflammatory therapy association Atla bioinformatics Bioinformatics analysis cancers caused CCL2 changes in core correlation COVID-19 patient COVID-19 patients datasets DEGs Dexamethasone differentially expressed gene Differentially expressed genes down-regulation element expression functional annotation gene expression pattern gene expression patterns identify Ifi44 infectious involved LPS lung lung damage Lung inflammation lung inflammatory response Lung injury lung tissue marker mechanism mice Mmp8 molecular molecular markers molecular mechanism molecular mechanisms murine murine model neoplasia NODAL non-infectious overlap pathology Patient Plaur progression protein-protein interaction Ptx3 reconstruction Regulation regulatory network respiratory reversed RSAD2 Rtp4 Saa1 SARS-CoV-2 SARS-COV-2 infection SERPINE1 SOCS3 survival susceptible systemic inflammation text mining therapeutic target therapeutic targets Timp1 up-regulated were assessed whole-genome microarray with COVID-19 [DOI] 10.1371/journal.pone.0260450 PMC 바로가기 [Article Type] Research Article
Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, IndiaMedicine Published on 2021-03-092022-10-31 Journal: Frontiers in Medicine [Category] COVID-19, [키워드] absence amino acid sequence analyses analysis Analysis clades clinical collected Comparative COVID-19 criteria downstream duration of illness Evidence functional annotation Genome genome coverage genome variation genomic genomic variation IgG Immunity India individual information mandatory molecular Mumbai Neutralizing Non-synonymous nucleotide Oropharyngeal Patient patients Post-infection Prolonged infection Region Reinfection reported RNA RT-PCR tests S1 RBD SARS-CoV-2 SARS-COV-2 infection sequence Sequencing Seroconversion serological serology specific mutation supported sVNT symptomatic synonymous the SARS-CoV-2 genome upstream viral isolate virus was performed WGS while Whole blood whole genome Whole genome sequencing [DOI] 10.3389/fmed.2021.631769 PMC 바로가기 [Article Type] Medicine
Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2Research Article Published on 2021-02-232022-10-29 Journal: mSystems [Category] COVID-19, [키워드] ACE2 acute respiratory syndrome affected affecting Amino acid Analysis angiotensin-converting enzyme 2 Antiviral binding caused clade co-occurrence Combination Comparative Comparative genomics Complete condition conditions contributing to coronavirus coronavirus disease country COVID-19 CpG D614G effective FIVE full-length genome functional annotation Genome Genomics geographical region highlighting host cell host proteins host-pathogen interaction hypoxia inhibiting Interaction membrane Mutation mutational studies MYO5A MYO5B MYO5C network network analysis novel nucleocapsid ORF8 pandemic pathogenicity pathway patients Phylogenomics Phylogeny polymorphism predicted Protein protein stability Proteins provided rate of infection receptor reduction in Region SARS-CoV-2 SARS-CoV-2 genome SARS-COV-2 infection SARS-CoV-2 virus screened Severity of infection single nucleotide SNP Spike protein strain Strains structural biology suggested the United State The United States thrombotic TMPRSS2 translation Transmissibility Transmission Treatment Variation Viral protein ZAP [DOI] 10.1128/mSystems.00030-21 PMC 바로가기 [Article Type] Research Article