TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversityTopHap: 다양성이 제한된 대규모 게놈 컬렉션의 공통 일배체형에서 주요 계통 발생 구조의 신속한 추론Article Published on 2022-05-132022-09-11 Journal: Bioinformatics [Category] COVID19(2023년), SARS, 변종, [키워드] acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 analyses approach bioinformatics bootstrap build building co-occurrence common variants coronavirus datasets determine develop evaluated evolutionary relationship evolutionary relationships Features fraction Genome genomes genomic global effort Haplotype haplotypes IMPROVE interfere massive Mutation pandemic Phylogenetic phylogenetic inference Phylogenetic relationship Phylogenetic tree phylogenetically Phylogeny produced provided reconstructed SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 genomes SARS-CoV-2 phylogeny sequence sequences Sequencing sequencing error sequencing errors severe acute respiratory syndrome Coronavirus signal signal-to-noise ratio strain Strains Structure the SARS-CoV-2 traditional methods variant variants variants of concern [DOI] 10.1093/bioinformatics/btac186 PMC 바로가기 [Article Type] Article
Assessment of SARS-CoV-2 Genome Sequencing: Quality Criteria and Low-Frequency VariantsSARS-CoV-2 게놈 시퀀싱 평가: 품질 기준 및 저주파 변이Virology Published on 2021-07-282022-09-10 Journal: Journal of Clinical Microbiology [Category] SARS, 변종, [키워드] accreditation Amplicon assessment Bioinformatics analysis can be used Contamination criteria criterion Critical cross cutoff value distribution evaluate fixed Genome Genome sequencing identify Interpretation investigated Laboratory Lineage Metrics Mutation PCR amplification Prevalence Prevent proportion Quality quality assessment Quality control reported robust sample selection SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 genomes SARS-CoV-2 sequencing SARS-CoV2 genome SARS-CoV2 genomes selected sequence sequenced Sequencing sequencing error sequencing errors submission Surveillance thresholds variant variants variants of concern Viral Viral RNA [DOI] 10.1128/JCM.00944-21 PMC 바로가기 [Article Type] Virology
A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3′ Untranslated Region (UTR) Is Evolving and Generating Increased Viral DiversityMicrobiology Published on 2021-06-212022-10-31 Journal: Frontiers in Microbiology [Category] COVID-19, [키워드] 3cpsdummy′UTR accumulating Analysis analyzed annotation arising assist B.1.1.7 Bioinformatic conserved dataset Diversity downstream format Frequency Genetic testing Genome genomes greater Host immune response inactivation Increased interfere K68 less novel nucleotide diversity (π) orf3a gene ORF8 ORF8 gene performed Polymorphisms processed Region regions researcher SARS-CoV-2 SARS-CoV-2 genome sequencing SARS-CoV-2 lineage SARS-CoV-2 sequencing SARS-CoV-2 variants SARS-CoV-2 viral sequence sequencing errors Spread stop codon Tajima’s D-statistic United Kingdom UTR variant Variation VCF viral evolution virulence [DOI] 10.3389/fmicb.2021.665041 PMC 바로가기 [Article Type] Microbiology
Essential interpretations of bioinformatics in COVID-19 pandemicReview article Published on 2021-02-012022-10-05 Journal: Meta Gene [Category] 신약개발, 유전자 메커니즘, [키워드] analyzed applied bioinformatics candidate computer-aided drug design COVID-19 COVID-19 pandemic COVID-19 research drug candidate drug design Essential Genetic Genetic variations Genome wide association study Genome-wide association studies global pandemic implementation in silico in viral information Interpretation methodology next generation sequencing Next-generation sequencing pathogen produced public health Research SARS-CoV-2 SARS-CoV-2 viral Scientific community sequenced sequencing errors the SARS-CoV-2 genome unique Vaccine development [DOI] 10.1016/j.mgene.2020.100844 [Article Type] Review article
Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence주요 대립 유전자 참조 서열을 사용한 가족 4중주에서의 단계적 전체 게놈 유전적 위험Research Article Published on 2011-09-152022-09-06 Journal: PLoS Genetics [Category] Communicable Disease, [키워드] Accuracy allele Analysis approach Author base pairs base pairs) Blood blood clot characterization coding compound heterozygosity contribute contributing to demonstrated develop disease disease risk disease-associated estimation facilitate family Gene genetic determinant genetic determinants genetic information genetic profile genetic risk genetic risk factor genetic risk factors Genetic variation Genome genomes Genotype Haplotype Human human leukocyte antigen identify Interpretation leukocyte loci lowest lung Major median medications methodology nuclear nuclear family occur pharmacological predisposition Pulmonary embolism quantification Quartet Recombination reference reference sequence risk Risk assessment risk for disease sequence Sequencing sequencing error sequencing errors therapy Thrombophilia variant whole-genome sequencing [DOI] 10.1371/journal.pgen.1002280 PMC 바로가기 [Article Type] Research Article