A5074980786- Single-cell and spatial transcriptomics
- Congenital heart defects research
- Cell Image Analysis Techniques
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Pluripotent Stem Cells Research
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Genetics and Neurodevelopmental Disorders
- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- Biomedical and Engineering Education
- Cardiac Structural Anomalies and Repair
- Histone Deacetylase Inhibitors Research
- CAR-T cell therapy research
- Protein Degradation and Inhibitors
- Congenital Heart Disease Studies
- Cardiac Fibrosis and Remodeling
- Hormonal Regulation and Hypertension
- Cardiomyopathy and Myosin Studies
- Renal and related cancers
The University of Queensland
2019-2025
Abstract Pluripotent stem cells provide a scalable approach to analyse molecular regulation of cell differentiation across developmental lineages. Here, we engineer barcoded induced pluripotent generate an atlas multilineage from pluripotency, encompassing eight-day time course with modulation WNT, BMP, and VEGF signalling pathways. Annotation in vitro types reference vivo development reveals diverse mesendoderm lineage including lateral plate paraxial mesoderm, neural crest, primitive gut....
Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential biological interpretation of processes. Here, we present TRIAGE-Cluster which uses genome-wide epigenetic diverse bio-samples to identify genes demarcating diversity in scRNA-seq data. By integrating patterns repressive chromatin deposited across types with weighted density estimation, determines type clusters a 2D UMAP space. We then TRIAGE-ParseR, machine learning method evaluates...
Abstract Aims The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). human lncRNA CARMEN, which is known to dictate specification toward cardiomyocyte (CM) smooth muscle (SMC) fates, generates a diversity of alternatively spliced isoforms. Methods results CARMEN locus can be manipulated direct primary cells...
SUMMARY Determining genes orchestrating cell differentiation in development and disease remains a fundamental goal of biology. This study establishes genome-wide metric based on the gene-repressive tri-methylation histone 3 lysine 27 (H3K27me3) across hundreds diverse types to identify genetic regulators differentiation. We introduce computational method, TRIAGE, that uses discordance between tendency expression drivers identity. apply TRIAGE millions single-cell transcriptomes, omics...
SUMMARY Pluripotent stem cells provide a scalable approach to analyse molecular regulation of cell differentiation across multiple developmental lineage trajectories. In this study, we engineered barcoded iPSCs generate an atlas multilineage from pluripotency, encompassing time-course WNT-induced perturbed using modulators WNT, BMP, and VEGF signalling. Computational mapping in vitro types vivo lineages revealed diversity iPSC-derived comprising mesendoderm including lateral plate paraxial...
Regulatory genes are critical determinants of cellular responses in development and disease, but standard RNA sequencing (RNA-seq) analysis workflows, such as differential expression analysis, have significant limitations revealing the regulatory basis cell identity function. To address this challenge, we present TRIAGE R package, a toolkit specifically designed to analyze elements both bulk single-cell RNA-seq datasets. The package is built upon methods, which leverage consortium-level...
Histone deacetylases (HDACs) are a class of enzymes that control chromatin state and influence cell fate. We evaluated the accessibility transcriptome dynamics zinc-containing HDACs during differentiation in vitro coupled with chemical perturbation to identify role mesendoderm fate specification. Single-cell RNA sequencing analyses HDAC expression human pluripotent stem (hPSC) mouse gastrulation vivo reveal unique association HDAC1 -3 gene programs exit from pluripotency. Functional small...
SUMMARY This study establishes the homeodomain only protein, HOPX, as a determinant controlling molecular switch between cardiomyocyte progenitor and maturation gene programs. Time-course single-cell expression with genome-wide footprinting reveal that HOPX interacts controls core cardiac networks by regulating activity of mutually exclusive developmental Upstream hypertrophy proliferation pathways compete to regulate transcription. Mitogenic signals override hypertrophic growth suppress...
A conversation with Lisa Suennen, part 1 Suennen is a co-founder and Managing Member of Psilos Group, healthcare venture capital growth equity investment firm over $577 million under management. Ms. has headed Psilos' West Coast office since the firm's founding in 1998 focuses on medical device, information technology services sectors. She serves as Director Board several portfolio companies, including AngioScore (chairman), PatientSafe Solutions, OmniGuide Ver-aLight (chairman).
Abstract Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential biological interpretation of processes. Here we present TRIAGE-Cluster which uses genome-wide epigenetic diverse bio-samples to identify genes demarcating diversity in scRNA-seq data. integrates patterns repressive chromatin deposited across types with weighted density estimation determine type clusters a 2D UMAP space. We then TRIAGE-ParseR, machine learning method that...
The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). CARMEN locus, which is known to dictate specification towards cardiomyocyte (CM) smooth muscle (SMC) fates, generates a diversity of alternatively spliced lncRNAs. Here, we identify one these isoforms, CARMEN-201, be crucial for SMC commitment....