Le Min Tan
A5031924545- Single-cell and spatial transcriptomics
- SARS-CoV-2 and COVID-19 Research
- T-cell and B-cell Immunology
- Cancer Genomics and Diagnostics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Immune Cell Function and Interaction
- Immune responses and vaccinations
- Immune cells in cancer
- Alzheimer's disease research and treatments
- COVID-19 Clinical Research Studies
- Long-Term Effects of COVID-19
- Cell Adhesion Molecules Research
- Mitochondrial Function and Pathology
- CRISPR and Genetic Engineering
- Neurological diseases and metabolism
- Liver Disease Diagnosis and Treatment
- RNA Research and Splicing
- Diet, Metabolism, and Disease
- Bioinformatics and Genomic Networks
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
Agency for Science, Technology and Research
2021-2025
Genome Institute of Singapore
2021-2025
The University of Texas MD Anderson Cancer Center
2022
Nanyang Technological University
2019
Abstract Single-cell omics technologies enable molecular characterization of diverse cell types and states, but how the resulting transcriptional epigenetic profiles depend on cell’s genetic background remains understudied. We describe Monopogen, a computational tool to detect single-nucleotide variants (SNVs) from single-cell sequencing data. Monopogen leverages linkage disequilibrium external reference panels identify germline SNVs detects putative somatic using allele cosegregating...
Summary Lack of diversity and proportionate representation in genomics datasets databases contributes to inequity healthcare outcomes globally 1,2 . The relationships human with biological biomedical phenotypes are pervasive 3 , yet remain understudied, particularly a single-cell context. Here we present the Asian Immune Diversity Atlas (AIDA), multi-national RNA-sequencing (scRNA-seq) healthy reference atlas immune cells. AIDA comprises 1,265,624 circulating cells from 619 donors 6...
The dynamics of SARS-CoV-2 infection in COVID-19 patients are highly variable, with a subset demonstrating prolonged virus shedding, which poses significant challenge for disease management and transmission control. In this study, the long-term were investigated using human well-differentiated nasal epithelial cell (NEC) model infection. NECs observed to release onto apical surface up 28 days postinfection (dpi), further corroborated by viral antigen staining. Single-cell transcriptome...
Several X-linked genes escape from X chromosome inactivation (XCI), while differences in across cell types and tissues are still poorly characterized. Here, we developed scLinaX for directly quantifying relative gene expression the inactivated with droplet-based single-cell RNA sequencing (scRNA-seq) data. The differentially expressed analyses large-scale blood scRNA-seq datasets consistently identified stronger lymphocytes than myeloid cells. An extension of to a 10x multiome dataset...
Due to the paucity of longitudinal molecular studies COVID-19, particularly those covering early stages infection (Days 1-8 symptom onset), our understanding host response over disease course is limited. We perform single cell RNA-seq on 286 blood samples from 108 age- and sex-matched COVID-19 patients, including 73 with samples. examine discrete subtypes continuous states longitudinally, we identify upregulation type I IFN-stimulated genes (ISGs) as predominant signature subsequent...
Alternative splicing contributes to complex traits, but whether this differs in trait-relevant cell types across diverse genetic ancestries is unclear. Here we describe cell-type-specific, sex-biased and ancestry-biased alternative ~1 M peripheral blood mononuclear cells from 474 healthy donors the Asian Immune Diversity Atlas. We identify widespread differential splicing, most of which cell-type-specific. 11,577 independent cis-splicing quantitative trait loci (sQTLs), 607 trans-sGenes 107...
Abstract One of the two X chromosomes females is silenced through chromosome inactivation (XCI) to compensate for difference in dosage between sexes. Among X-linked genes, several genes escape from XCI, which could contribute differential gene expression However, differences across cell types and tissues are still poorly characterized because no methods directly evaluate under a physiological condition at cell-cluster resolution with versatile technology. Here, we developed method, s ingle-...
Abstract Distinguishing how genetics impact cellular processes can improve our understanding of variable risk for diseases. Although single-cell omics have provided molecular characterization cell types and states on diverse tissue samples, their genetic ancestry effects traits are largely understudied. Here, we developed Monopogen, a computational tool enabling researchers to detect single nucleotide variants (SNVs) from variety transcriptomic epigenomic sequencing data. It leverages...
Abstract Distinguishing how genetics impact cellular processes can improve our understanding of variable risk for diseases. Although single-cell omics have provided molecular characterization cell types and states on diverse tissue samples, their genetic ancestry effects traits are largely understudied. Here, we developed Monopogen, a computational tool enabling researchers to detect single nucleotide variants (SNVs) from variety transcriptomic epigenomic sequencing data. It leverages...