A5034599952- Single-cell and spatial transcriptomics
- Pluripotent Stem Cells Research
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Cancer Immunotherapy and Biomarkers
- Gene expression and cancer classification
- Radiomics and Machine Learning in Medical Imaging
- Cell Image Analysis Techniques
- Ferroptosis and cancer prognosis
- Immunotherapy and Immune Responses
- Cancer-related molecular mechanisms research
- Genetic and phenotypic traits in livestock
- Genomics and Chromatin Dynamics
- Immune cells in cancer
- SARS-CoV-2 and COVID-19 Research
- Genetic Associations and Epidemiology
- Congenital heart defects research
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Data Visualization and Analytics
- Extracellular vesicles in disease
- Viral Infectious Diseases and Gene Expression in Insects
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Insect Resistance and Genetics
The University of Queensland
2013-2025
Vietnam Posts and Telecommunications Group (Vietnam)
2025
Posts and Telecommunications Institute of Technology
2025
QIMR Berghofer Medical Research Institute
2023-2025
The University of Texas at Arlington
2023-2025
Hitachi (Japan)
2024
Washington University in St. Louis
2021-2024
Bạch Mai Hospital
2024
Ho Chi Minh City Medicine and Pharmacy University
2024
Queens University
2023
Abstract Single-cell RNA sequencing has enabled the characterization of highly specific cell types in many tissues, as well both primary and stem cell-derived lines. An important facet these studies is ability to identify transcriptional signatures that define a type or state. In theory, this information can be used classify an individual based on its profile. Here, we present scPred , new generalizable method able provide accurate classification single cells, using combination unbiased...
Spatial transcriptomics (ST) technologies generate multiple data types from biological samples, namely gene expression, physical distance between points, and/or tissue morphology. Here we developed three computational-statistical algorithms that integrate all to advance understanding of cellular processes. First, present a spatial graph-based method, pseudo-time-space (PSTS), model and uncover relationships transcriptional states cells across tissues undergoing dynamic change (e.g....
Abstract Purpose: The liver is the most frequent metastatic site for colorectal cancer. Its microenvironment modified to provide a niche that conducive cancer cell growth. This study focused on characterizing cellular changes in (mCRC) tumor (TME). Experimental Design: We analyzed series of microsatellite stable (MSS) mCRCs liver, paired normal tissue, and peripheral blood mononuclear cells using single-cell RNA sequencing (scRNA-seq). validated our findings multiplexed spatial imaging bulk...
Purpose Robust biomarkers that predict disease outcomes amongst COVID-19 patients are necessary for both patient triage and resource prioritisation. Numerous candidate have been proposed COVID-19. However, at present, there is no consensus on the best diagnostic approach to in infected patients. Moreover, it not clear whether such tools would apply other potentially pandemic pathogens therefore of use as stockpile future preparedness. Methods We conducted a multi-cohort observational study...
Abstract Of the many types of DNA damage, double-strand breaks (DSBs) are probably most deleterious. Mounting evidence points to an intricate relationship between DSBs and transcription. A cell system in which impact on transcription can be investigated at precisely mapped genomic is essential study this relationship. Here a human line, we map genome-wide high resolution induced by restriction enzyme, characterize their gene expression four independent approaches monitoring steady-state RNA...
Heterogeneity of cell states represented in pluripotent cultures has not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual cells function. Here, we present results from analysis data 18,787 WTC-CRISPRi human induced stem cells. We developed an unsupervised clustering method and, through this, identified four subpopulations distinguishable on basis their state, including a...
Abstract Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate molecular processes driving evolutionary change. Here we assess sheep domestication artificial selection by comparing genome sequence from 43 modern breeds ( Ovis aries ) their Asian mouflon ancestor O. orientalis identify sweeps. Next, provide a comparative functional annotation of genome, validated using experimental ChIP-Seq tissue. Using these annotations,...
Abstract The DNA damage response (DDR) is a set of cellular events that follows the generation damage. Recently, site-specific small non-coding RNAs, also termed RNAs (DDRNAs), have been shown to play role in DDR signalling and repair. Dysfunctional telomeres activate ageing, cancer an increasing number identified pathological conditions. Here we show that, mammals, telomere dysfunction induces transcription telomeric DDRNAs (tDDRNAs) their longer precursors from both strands. activation...
Abstract Background The discovery that somatic cells can be reprogrammed to induced pluripotent stem (iPSCs) has provided a foundation for in vitro human disease modelling, drug development and population genetics studies. Gene expression plays critical role complex risk therapeutic response. However, while the genetic background of cell lines been shown strongly influence gene expression, effect not evaluated at level individual which would provide significant resolution. By integrating...
Abstract With age, hematopoietic stem cells (HSC) undergo changes in function, including reduced regenerative potential and loss of quiescence, which is accompanied by a significant expansion the cell pool that can lead to haematological disorders. Elevated metabolic activity has been implicated driving HSC ageing phenotype. Here we show nicotinamide riboside (NR), form vitamin B3, restores youthful capacity modifying mitochondrial function multiple ways expression nuclear encoded pathway...
The prostate gland produces prostatic fluid, high in zinc and citrate essential for the maintenance of spermatozoa. Prostate cancer is a common condition with limited treatment efficacy castration-resistant metastatic disease, including immune checkpoint inhibitors. Using single-cell RNA-sequencing to perform an unbiased assessment cellular landscape human prostate, we identify subset tumor-enriched androgen receptor-negative luminal epithelial cells increased expression cancer-associated...
Abstract A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior pooling. We introduce scSplit utilizes genetic differences inferred from scRNA-seq data alone samples. also enables mapping clusters original Using simulated, merged, and multi-individual datasets, we show that prediction is highly concordant with demuxlet predictions consistent the known truth...
Large events and gatherings, particularly those taking place indoors, have been linked to multitransmission that accelerated the pandemic spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To provide real-time, geolocalized risk information, we developed an interactive online dashboard estimates at least one individual with SARS-CoV-2 is present in gatherings different sizes United States. The website combines documented case reports county level ascertainment bias...
Mucosal head and neck squamous cell carcinoma (HNSCC) are the seventh most common cancer, with approximately 50% of patients living beyond 5 years. Immune checkpoint inhibitors (ICIs) have shown promising results in recurrent or metastatic (R/M) disease, however, only a subset benefit from immunotherapy. Studies implicated tumor microenvironment (TME) HNSCC as major factor therapy response, highlighting need to better understand TME, particularly by spatially resolved means determine...
A mechanistic connection between aging and development is largely unexplored. Through profiling age-related chromatin transcriptional changes across 22 murine cell types, analyzed alongside previous mouse human organismal maturation datasets, we uncovered a transcription factor binding site (TFBS) signature common to both processes. Early-life candidate cis-regulatory elements (cCREs), progressively losing accessibility during aging, are enriched for cell-type identity TFBSs. Conversely,...
Preclinical data have confirmed that human pluripotent stem cell-derived cardiomyocytes (PSC-CMs) can remuscularize the injured or diseased heart, with several clinical trials now in planning recruitment stages. However, because ventricular arrhythmias represent a complication following engraftment of intramyocardially injected PSC-CMs, it is necessary to provide treatment strategies control prevent (EAs). Here, we show porcine model myocardial infarction and PSC-CM transplantation EAs are...
Large-scale human genotyping requires technologies with a minimal number of steps, high accuracy, and the ability to automate at reasonable cost. In this regard, we have developed rapid, cost-effective readout method for single nucleotide polymorphism (SNP) that combines an easily automatable single-tube allele-specific primer extension (ASPE) efficient throughput flow cytometric analysis performed on Luminex 100 cytometer. This robust technique employs ASPE reaction using PCR-derived target...