sequencing data – Page 9 – Communicable Diseases Research

SARS-CoV-2 variants reveal features critical for replication in primary human cells

SARS-CoV-2 변이체는 1차 인간 세포에서 복제에 중요한 기능을 나타냅니다

Research Article

Published on 2021-03-242022-08-13
Journal: PLoS Biology [Category] SARS, 유전자 메커니즘,

Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19

코로나19에 적용한 scMLnet을 사용하여 단일 세포 RNA 시퀀싱 데이터에서 유전자 발현의 미세 환경 조절 추론

Article

Published on 2021-03-222022-09-11
Journal: Briefings in Bioinformatics [Category] 유전자 메커니즘,

[키워드] ACE2 ACE2 expression activated addition anti-cytokine therapies anti-cytokine therapy applied approach Cell cellular cellular microenvironment correlated COVID-19 COVID-19 infection COVID-19 patient COVID-19 severity cytokine Cytokines dataset EGF expression of SARS-CoV-2 Extracellular facilitate functional Gene Expression gene regulatory network human lung cell human lung cells IFN-γ Infection Inflammatory cytokine Inflammatory cytokines Intercellular communication mechanism methodology microenvironment multilayer network predicted provided receptor ACE2 Regulation reported SARS-CoV-2 SARS-COV-2 infection SARS-CoV-2 receptor scMLnet scRNA-seq sequencing data Signaling signaling pathway significantly Single-cell RNA sequencing single-cell RNA-seq Single-cell RNA-sequencing targeted therapy TNF-α
[DOI] 10.1093/bib/bbaa327 PMC 바로가기 [Article Type] Article

Functional profiling of COVID-19 respiratory tract microbiomes

Article

Published on 2021-03-192022-10-29
Journal: Scientific Reports [Category] COVID-19, SARS,

[키워드] alteration Analysis biological processe Bronchoalveolar lavage fluid carbohydrate cohorts community-acquired pneumonia Computational biology and bioinformatics connection COVID-19 COVID-19 cases COVID-19 infection decrease Degradation eight function functional global pandemic Gut healthy controls Host include increase in interact Interaction lipid metabolism Lower respiratory tract lung metabolic pathways metabolism metabolite metagenomics microbial Microbiome new coronavirus SARS-CoV-2 overlap pathway Pathways patients previous study profile protein domain Research respiratory tract respiratory viral infections responsible resulting SARS-COV-2 infection sequence sequencing data understanding viral invasion virus
[DOI] 10.1038/s41598-021-85750-0 PMC 바로가기 [Article Type] Article

Intestinal Receptor of SARS-CoV-2 in Inflamed IBD Tissue Seems Downregulated by HNF4A in Ileum and Upregulated by Interferon Regulating Factors in Colon

염증이 있는 IBD 조직에서 SARS-CoV-2의 장 수용체는 회장에서 HNF4A에 의해 하향 조절되고 결장에서 인터페론 조절 인자에 의해 상향 조절되는 것으로 보입니다

Article

Published on 2021-03-052022-09-11
Journal: Journal of Crohn's & colitis [Category] SARS, 유전자 메커니즘,

[키워드] ACE2 ACE2 expression Alter analysed Analysis anti-TNF biopsy bowel Co-expression analysis collected Colon colonic Control COVID-19 Crohn's disease Cytokines Differential gene expression disease dysregulation entry mechanisms epithelial Factor HNF4A IBD IBD susceptibility gene ileal ileum Immunosuppressed inflamed CD ileum Inflammation Inflammatory Inflammatory bowel disease inflammatory bowel diseases inflammatory stimuli interferon intestinal intestinal inflammation intestine investigated Microarray Microarrays mucosal Necrosis network Organoid organoids Patient patients pro-inflammatory cytokine pro-inflammatory cytokines processed Prognosis regulated Regulating Regulation responders restored risk factor RNA sequencing SARS-CoV-2 SARS-COV-2 infection Sequencing sequencing data shown significantly Single Cell single-cell therapy tissue TMPRSS2 transcriptomics ulcerative colitis upregulated upstream
[DOI] 10.1093/ecco-jcc/jjaa185 PMC 바로가기 [Article Type] Article

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

COVID-19 퇴치를 위한 컴퓨팅 전략: SARS-CoV-2 및 코로나바이러스 연구를 가속화하는 유용한 도구

Review

Published on 2021-03-042022-09-10
Journal: Briefings in Bioinformatics [Category] SARS, 치료기술, 치료제,

VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples

Article

Published on 2021-01-282022-10-28
Journal: Patterns [Category] COVID-19,

[키워드] Abstract acute respiratory syndrome Analysis approach Cluster co-occurrence condition consensus sequences Contact tracing coronavirus COVID-19 COVID-19 pandemic data-driven dataset diffusion epidemiological Evolution Evolution of SARS-CoV-2 explain Frequency genomic Genomic surveillance highlight homoplasies homoplastic variants identify IMPROVE Infection infection chain Intra-host diversity intra-host genomic diversity involved joint limitation limitations mutations outperform pathogen phylogenetic inference Phylogenomics Phylogeny platform Positive selection predict profiles quantification raw sequencing data Research reveal RNA sequencing robust SARS-CoV-2 SARS-CoV-2 consensus sequence SARS-CoV-2 evolution selected sequencing data spike gene Surveillance variant viral evolution viral genomes viral sample Viral variants
[DOI] 10.1016/j.patter.2021.100212 PMC 바로가기 [Article Type] Article

Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys

단일 세포 RNA 시퀀싱은 아프리카 녹색 원숭이의 폐에서 SARS-CoV-2 감염 역학을 보여줍니다

Research Article

Published on 2021-01-272022-09-10
Journal: Science Translational Medicine [Category] 유전자 메커니즘, 치료기술, 치료제,

[키워드] acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 African green monkey African green monkeys Alveolar macrophages Analysis animal model animal models animals best Cell cellular debris clearance contribute coronavirus coronavirus disease Coronavirus disease 2019 Course COVID-19 dataset degrade determine Factor genomic RNA green monkeys Host Host immune response host response host responses identify immune cell population immune cell populations immune responses in vivo inactivated Indicator infected cell infected cells Infection infiltrating Inflammatory response information inoculated knowledge lung Lungs Lymph node Macrophage macrophages mediastinal lymph nodes Mild mild to moderate moderate monocyte Monocyte-derived macrophages occur Pathogenesis phagocytosis pneumocyte Pneumocytes provide recruited replicate Replication respiratory respiratory tract responsible reveal RNA RNA sequencing SARS-CoV-2 SARS-COV-2 infection Sequencing sequencing data severe acute respiratory syndrome Coronavirus Single-cell RNA sequencing switching therapeutic targets valuable resource Viral viral genome viral replication virus virus replication while
[DOI] 10.1126/scitranslmed.abe8146 PMC 바로가기 [Article Type] Research Article

Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

Article

Published on 2021-01-212022-10-29
Journal: Scientific Reports [Category] Coronavirus,

[키워드] Analysis bacterial invasion Bioinformatics analysis Cell Cell Biology Cellular signalling networks Computational biology and bioinformatics Control correlated correlation Correlation analysis Cytoscape DE miRNA DE miRNAs DESeq differential expression differentially expressed epidemic diarrhea Epigenetic epithelial cells expression expression pattern Gene regulatory networks group groups High-throughput screening Host immune response Immunity in vitro induce Infection Interaction involved mechanism Mechanisms of disease microRNA miRanda miRNA miRNA expression mRNA mRNAs Next-generation sequencing NF-κB signaling NGS Pathogenesis pathway PEDV performed polymerase chain predicted profile qRT-PCR Quantitative R package Randomly reverse transcription selected sequencing data Strains variant viral pathogenicity virulent virus
[DOI] 10.1038/s41598-021-81189-5 PMC 바로가기 [Article Type] Article

Carbapenemase-producing Enterobacterales causing secondary infections during the COVID-19 crisis at a New York City hospital

뉴욕시 병원에서 COVID-19 위기 동안 2차 감염을 유발하는 Carbapenemase 생성 Enterobacterales

Article

Published on 2021-01-192022-09-11
Journal: Journal of Antimicrobial Chemotherapy [Category] 유전자 메커니즘, 치료기술, 치료제,

[키워드] Antibiotic resistance antibiotic resistance gene Bacterial infections Clinical characteristics collected COVID-19 crisis COVID-19 patients CPE Culture declined Enterobacter cloacae complex genotyping global pandemic hospital Illumina Increased increased risk isolate isolates Klebsiella pneumoniae KPC Lineage MDR mechanism mitigate MOST Most patient Most patients Nanopore nanopore sequencing New York City pathogen Pathogens Patient patients patients with COVID-19 Phylogenetic analysis pneumoniae positive Prevalence respiratory SARS-CoV-2 secondary bacterial infection Secondary bacterial infections Secondary infection secondary infections Sequencing sequencing data Surveillance Treatment treatment approach treatment failure wake WGS while with COVID-19
[DOI] 10.1093/jac/dkaa466 PMC 바로가기 [Article Type] Article

Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19

Research

Published on 2020-12-242022-10-05
Journal: Nature biotechnology [Category] SARS, 유전자 메커니즘, 치료법,