Modifications of Lipid Pathways Restrict SARS-CoV-2 Propagation in Human Induced Pluripotent Stem Cell-derived 3D Airway Organoids.

[1]  Hongzhou Lu,et al.  Antiviral Efficacy and Safety of Molnupiravir Against Omicron Variant Infection: A Randomized Controlled Clinical Trial , 2022, Frontiers in Pharmacology.

[2]  P. Pandolfi,et al.  Two Different Therapeutic Approaches for SARS-CoV-2 in hiPSCs-Derived Lung Organoids , 2022, Cells.

[3]  Yuanlin Guan,et al.  Abnormal global alternative RNA splicing in COVID-19 patients , 2022, PLoS genetics.

[4]  Q. Ye,et al.  The emergence and epidemic characteristics of the highly mutated SARS‐CoV‐2 Omicron variant , 2022, Journal of medical virology.

[5]  I. Douglas,et al.  Metabolic Syndrome and Acute Respiratory Distress Syndrome in Hospitalized Patients With COVID-19 , 2021, JAMA network open.

[6]  J. Lammertyn,et al.  Potent neutralizing anti-SARS-CoV-2 human antibodies cure infection with SARS-CoV-2 variants in hamster model , 2021, bioRxiv.

[7]  Helen Y Wang,et al.  Pharmacological inhibition of fatty acid synthesis blocks SARS-CoV-2 replication , 2021, Nature Metabolism.

[8]  G. FitzGerald,et al.  The roles of lipids in SARS-CoV-2 viral replication and the host immune response , 2021, Journal of Lipid Research.

[9]  B. Clotet,et al.  SARS-CoV-2 Infection Modulates ACE2 Function and Subsequent Inflammatory Responses in Swabs and Plasma of COVID-19 Patients , 2021, Viruses.

[10]  Walter Gottlieb Land,et al.  Role of DAMPs in respiratory virus-induced acute respiratory distress syndrome—with a preliminary reference to SARS-CoV-2 pneumonia , 2021, Genes & Immunity.

[11]  Sayeeda Rahman,et al.  Epidemiology, pathogenesis, clinical presentations, diagnosis and treatment of COVID-19: a review of current evidence , 2021, Expert review of clinical pharmacology.

[12]  A. Orekhov,et al.  Involvement of Oxidative Stress and the Innate Immune System in SARS-CoV-2 Infection , 2021, Diseases.

[13]  Salah Ayoub,et al.  Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy , 2021, iScience.

[14]  S. Chiou,et al.  Expression of Endogenous Angiotensin-Converting Enzyme 2 in Human Induced Pluripotent Stem Cell-Derived Retinal Organoids , 2021, International journal of molecular sciences.

[15]  Mehdi Mohammadi Ashani,et al.  Potential role of glycoprotein 340 in milder SARS-CoV-2 infection in children , 2021, Expert review of anti-infective therapy.

[16]  D. Tegunov,et al.  Mechanism of SARS-CoV-2 polymerase stalling by remdesivir , 2021, Nature communications.

[17]  Qi Cui,et al.  ApoE-Isoform-Dependent SARS-CoV-2 Neurotropism and Cellular Response , 2021, Cell Stem Cell.

[18]  Bipasha Bose,et al.  Induced Pluripotent Stem Cell Derived Human Lung Organoids to Map and Treat the SARS-CoV2 Infections In Vitro. , 2021, Advances in experimental medicine and biology.

[19]  Adesh Baral,et al.  Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins , 2021, Bioinformatics and biology insights.

[20]  Anushya Muruganujan,et al.  The Gene Ontology resource: enriching a GOld mine , 2020, Nucleic Acids Res..

[21]  Mauro J. Muraro,et al.  An organoid‐derived bronchioalveolar model for SARS‐CoV‐2 infection of human alveolar type II‐like cells , 2020, The EMBO journal.

[22]  D. Bruzzese,et al.  The benefit of statins in SARS-CoV-2 patients: further metabolic and prospective clinical studies are needed , 2020, Endocrine.

[23]  Steven Lin,et al.  Humanized COVID‐19 decoy antibody effectively blocks viral entry and prevents SARS‐CoV‐2 infection , 2020, EMBO molecular medicine.

[24]  Minoru Kanehisa,et al.  KEGG: integrating viruses and cellular organisms , 2020, Nucleic Acids Res..

[25]  Jared L. Johnson,et al.  Identification of SARS-CoV-2 Inhibitors using Lung and Colonic Organoids , 2020, Nature.

[26]  D. Lye,et al.  Statin use is associated with lower disease severity in COVID-19 infection , 2020, Scientific Reports.

[27]  G. Atwal,et al.  REGN-COV2 antibodies prevent and treat SARS-CoV-2 infection in rhesus macaques and hamsters , 2020, Science.

[28]  A. Vacca,et al.  Neutrophil Extracellular Traps (NETs) and Damage-Associated Molecular Patterns (DAMPs): Two Potential Targets for COVID-19 Treatment , 2020, Mediators of inflammation.

[29]  M. Yanez-Bello,et al.  Atorvastatin associated with decreased hazard for death in COVID-19 patients admitted to an ICU: a retrospective cohort study , 2020, Critical Care.

[30]  Tokiko Watanabe,et al.  Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development , 2020, Proceedings of the National Academy of Sciences.

[31]  L. Dodd,et al.  Remdesivir for the Treatment of Covid-19 — Final Report , 2020, The New England journal of medicine.

[32]  S. Yeh,et al.  The role of phylogenetic analysis in clarifying the infection source of a COVID-19 patient , 2020, Journal of Infection.

[33]  Zebao He,et al.  Proteomic and Metabolomic Characterization of COVID-19 Patient Sera , 2020, Cell.

[34]  Hyeshik Chang,et al.  The Architecture of SARS-CoV-2 Transcriptome , 2020, Cell.

[35]  Andrea Marzi,et al.  Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses , 2020, Nature Microbiology.

[36]  Young-Jun Park,et al.  Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein , 2020, Cell.

[37]  G. Gao,et al.  A Novel Coronavirus from Patients with Pneumonia in China, 2019 , 2020, The New England journal of medicine.

[38]  Minoru Kanehisa,et al.  Toward understanding the origin and evolution of cellular organisms , 2019, Protein science : a publication of the Protein Society.

[39]  Michael Shi,et al.  Morphological and Molecular Defects in Human Three-Dimensional Retinal Organoid Model of X-Linked Juvenile Retinoschisis , 2019, Stem cell reports.

[40]  Hsin-Yang Li,et al.  Ash2l interacts with Oct4-stemness circuitry to promote super-enhancer-driven pluripotency network , 2019, Nucleic acids research.

[41]  Irving L. Weissman,et al.  A molecular cell atlas of the human lung from single cell RNA sequencing , 2019, Nature.

[42]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[43]  Dhiraj Kumar,et al.  RNA Splicing: A New Paradigm in Host-Pathogen Interactions. , 2019, Journal of molecular biology.

[44]  R. D. del Ángel,et al.  The Role of Host Cholesterol During Flavivirus Infection , 2018, Front. Cell. Infect. Microbiol..

[45]  Albin Sandelin,et al.  IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences , 2018, bioRxiv.

[46]  Diego Garrido-Martín,et al.  ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization , 2018, PLoS Comput. Biol..

[47]  D. Kotton,et al.  Derivation of Epithelial-Only Airway Organoids from Human Pluripotent Stem Cells. , 2018, Current protocols in stem cell biology.

[48]  Katja Schenke-Layland,et al.  Self-Organized Cerebral Organoids with Human-Specific Features Predict Effective Drugs to Combat Zika Virus Infection. , 2017, Cell reports.

[49]  Alyssa J. Miller,et al.  In Vitro Models to Study Human Lung Development, Disease and Homeostasis. , 2017, Physiology.

[50]  Xiang Zhang,et al.  Acetylated α-Tubulin Regulated by N-Acetyl-Seryl-Aspartyl-Lysyl-Proline(Ac-SDKP) Exerts the Anti-fibrotic Effect in Rat Lung Fibrosis Induced by Silica , 2016, Scientific Reports.

[51]  Jeffrey T Leek,et al.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown , 2016, Nature Protocols.

[52]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

[53]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[54]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[55]  M. Douglas,et al.  Virus induced inflammation and cancer development. , 2014, Cancer letters.

[56]  Weijun Luo,et al.  Pathview: an R/Bioconductor package for pathway-based data integration and visualization , 2013, Bioinform..

[57]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[58]  Timothy M. D. Ebbels,et al.  Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA , 2011 .

[59]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[60]  N. Karlsson,et al.  Deleted in Malignant Brain Tumors-1 Protein (DMBT1): A Pattern Recognition Receptor with Multiple Binding Sites , 2010, International journal of molecular sciences.

[61]  Chun-Houh Chen,et al.  GAP: A graphical environment for matrix visualization and cluster analysis , 2010, Comput. Stat. Data Anal..

[62]  Matthew D. Young,et al.  Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.

[63]  H. Clevers,et al.  Single Lgr5 stem cells build crypt–villus structures in vitro without a mesenchymal niche , 2009, Nature.

[64]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[65]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[66]  N. Enomoto,et al.  Targeting lipid metabolism in the treatment of hepatitis C virus infection. , 2008, The Journal of infectious diseases.

[67]  T. Ichisaka,et al.  Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors , 2007, Cell.

[68]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[69]  R. Compans,et al.  Antiviral effects of apolipoprotein A-I and its synthetic amphipathic peptide analogs. , 1990, Virology.

[70]  Kelsy C. Cotto,et al.  RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splicing variants in cancer , 2020 .

[71]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[72]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[73]  A. Lusis,et al.  PATIENT-ORIENTED AND EPIDEMIOLOGICAL RESEARCH Association of serum HDL-cholesterol and apolipoprotein A1 levels with risk of severe SARS-CoV-2 infection , 2022 .