A5011542875- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- CAR-T cell therapy research
- Cancer-related molecular mechanisms research
- Cancer Genomics and Diagnostics
- Hippo pathway signaling and YAP/TAZ
- Cancer Immunotherapy and Biomarkers
- Axon Guidance and Neuronal Signaling
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- 14-3-3 protein interactions
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Mycobacterium research and diagnosis
- Viral Infections and Immunology Research
- Protein Degradation and Inhibitors
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
Genome Institute of Singapore
2018-2025
Duke-NUS Medical School
2019-2023
Agency for Science, Technology and Research
2019-2020
National University of Singapore
2019
National Cancer Centre Singapore
2017
As the generation of complex single-cell RNA sequencing datasets becomes more commonplace it is responsibility researchers to provide access these data in a way that can be easily explored and shared. Whilst often case deposited for future bioinformatic analysis many studies do not release their easy explore by non-computational researchers.In order help address this we have developed ShinyCell, an R package converts into explorable shareable interactive interfaces. These interfaces...
Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identifies a subpopulation pre-metastatic cells, driven by actionable pathways including AXL AURK. Blocking these two proteins blunts tumor invasion patient-derived cultures. Furthermore, scRNAseq analyses tumor-infiltrating CD8 + T-lymphocytes show distinct...
Chemo-resistance is one of the major causes cancer-related deaths. Here we used single-cell transcriptomics to investigate divergent modes chemo-resistance in tumor cells. We observed that higher degree phenotypic intra-tumor heterogeneity (ITH) favors selection pre-existing drug-resistant cells, whereas phenotypically homogeneous cells engage covert epigenetic mechanisms trans-differentiate under drug-selection. This adaptation was driven by selection-induced gain H3K27ac marks on...
Fibrosis is a common pathology in many cardiac disorders and driven by the activation of resident fibroblasts. The global posttranscriptional mechanisms underlying fibroblast-to-myofibroblast conversion heart have not been explored.Genome-wide changes RNA transcription translation during human fibroblast were monitored with sequencing ribosome profiling. We then used RNA-binding protein-based analyses to identify translational regulators fibrogenic genes. integration occupancy levels 30...
Abstract Summary Emerging single-cell RNA-sequencing data technologies has made it possible to capture and assess the gene expression of individual cells. Based on similarity profiles, many tools have been developed generate an in silico ordering cells form pseudo-time trajectories. However, these do not provide a means find critical changes over pseudo-time. We present GeneSwitches, tool that takes any trajectory determines precise order functional-event time. GeneSwitches uses statistical...
Abstract Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single profiling with long read RNA-Seq promises to enable the discovery quantification of individual isoforms at single-cell level. However, highly multiplexed data such as a experiment only generates limited number reads for each cell, constituting major challenge transcript existing approaches that usually power samples low sequencing depth....
Abstract Motivation As the generation of complex single-cell RNA sequencing datasets becomes more commonplace it is responsibility researchers to provide access these data in a way that can be easily explored and shared. Whilst often case deposited for future bioinformatic analysis many studies do not release their easy explore by non-computational researchers. Results In order help address this we have developed ShinyCell, an R package converts into explorable shareable interactive...
Abstract The Eph family of receptor tyrosine kinases is crucial for assembly and maintenance healthy tissues. Dysfunction in signaling causally associated with cancer progression. In breast cells, dysregulated has been linked to alterations clustering abilities. Here, we implemented a single-cell assay scoring scheme systematically probe the spatial organization activated EphA receptors multiple carcinoma cells. We show that cells retain phenotype over several generations, degree reported...
Abstract Eph receptors, a family of receptor tyrosine kinases, play crutial role in the assembly and maintenance healthy tissues. Dysfunction signaling are causally correlatively associated with cancer progression. In breast cells, dysregulated has been largely linked to alterations clustering abilities. present study, we implemented single-cell assay scoring scheme systematically probe spatial organization activated EphA carcinoma cells different origin. Using this assay, found that...
An amendment to this paper has been published and can be accessed via a link at the top of paper.
An amendment to this paper has been published and can be accessed via a link at the top of paper.
Abstract Summary Emerging single-cell RNA-seq technologies has made it possible to capture and assess the gene expression of individual cells. Based on similarity profiles, many tools have been developed generate an in silico ordering cells form pseudo-time trajectories. However, these do not provide a means find critical changes over pseudo-time. We present GeneSwitches, tool that takes any trajectory determines precise order gene-expression functional-event time. GeneSwitches uses...
Abstract Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identified a sub-population pre-metastatic cells, driven by actionable pathways including AXL AURK. Blocking these two proteins blunted tumor invasion patient-derived cultures. Furthermore, scRNAseq analyses tumor-infiltrating CD8+ T-lymphocytes...