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Analyzing single cell transcriptome data from severe COVID-19 patients
(2022)
SUMMARY:
We describe the protocol for identifying COVID-19 severity specific cell types and their regulatory marker genes using single-cell transcriptomics data. We construct COVID-19 comorbid disease-associated gene list ...
SARS-CoV-2 may hijack GPCR signaling pathways to dysregulate lung ion and fluid transport
(2021)
Abstract:
The tropism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, toward the host cells is determined, at least in ...
Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome
(2021)
Abstract:
The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases. For autism spectrum disorders (ASD) cases where pathogenic ...
Reply to Eisenhut
(2021)
Letter to the Editor:
The Pathophysiology of COVID-19 and SARS-CoV-2 Infection
oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR‑Cas9 edited cerebral organoids
(2023)
Abstract:
Cerebral organoids are comprised of diverse cell types found in the developing human brain, and can be leveraged in the identification of critical cell types perturbed by genetic risk variants in common, ...
Lack of ethnic diversity in single-cell transcriptomics hinders cell type detection and precision medicine inclusivity
(2023)
Abstract:
Perhaps one of the most revolutionary next generation sequencing technologies is single-cell (SC) transcriptomics, which was recognized by Nature in 2013 as the method of the year. SC-technologies delve deep ...
Cell‑specifc MAPT gene expression is preserved in neuronal and glial tau cytopathologies in progressive supranuclear palsy
(2023)
Abstract:
Microtubule-associated protein tau (MAPT) aggregates in neurons, astrocytes and oligodendrocytes in a number of neurodegenerative diseases, including progressive supranuclear palsy (PSP). Tau is a target of ...
Computational Analysis of Short Linear Motifs in the Spike Protein of SARS-CoV-2 Variants Provides Possible Clues into the Immune Hijack and Evasion Mechanisms of Omicron Variant
(2022-08)
Abstract:
Short linear motifs (SLiMs) are short linear sequences that can mediate protein–protein interaction. Mimicking eukaryotic SLiMs to compete with extra- or intracellular binding partners, or to sequester host ...
Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19
(2021)
Summary:
Understanding host cell heterogeneity is critical for unraveling disease mechanism. Utilizing large-scale single-cell transcriptomics, we analyzed multiple tissue specimens from patients with life-threatening ...
Single-cell reconstruction and mutation enrichment analysis identifies dysregulated cardiomyocyte and endothelial cells in congenital heart disease
(2023)
Abstract:
Congenital heart disease (CHD) is one of the most prevalent neonatal congenital anomalies. To catalog the putative candidate CHD risk genes, we collected 16,349 variants [single-nucleotide variants (SNVs) and ...