Publications by authors named "Helena Winata"
Reference genomes are foundational to modern genomics. Our growing understanding of genome structure leads to continual improvements in reference genomes and new genome "builds" with incompatible coordinate systems. We quantified the impact of genome build on germline and somatic variant calling by analyzing tumour-normal whole-genome pairs against the two most widely used human genome builds.
View Article and Find Full Text PDFArticle Synopsis
- - Sarcomas are rare tumors with over 100 subtypes, making it challenging to find effective therapies; there's a need for personalized treatment approaches to enhance patient outcomes.
- - Patient-derived tumor organoids (PDTOs) were used to study drug resistance and sensitivity in sarcoma, analyzing 194 specimens from 126 patients across 24 subtypes.
- - The research developed a high-throughput screening method that provided results quickly and showed that drug sensitivity linked to tumor characteristics; 59% of samples matched with at least one effective FDA-approved treatment.
Article Synopsis
- Advances in DNA sequencing technology have made it faster and more affordable, leading to improved data availability and the need for complex algorithms and workflows.
- Metapipeline-DNA is a customizable and flexible analysis pipeline that handles various processing tasks like read alignment, variant calling, and quality control, making it easier to analyze DNA sequencing data.
- This open-source tool is available under the GPLv2 license and can be accessed for free at https://github.com/uclahs-cds/metapipeline-DNA.
Restoring functional β cell mass is a potential therapy for those with diabetes. However, the pathways regulating β cell mass are not fully understood. Previously, we demonstrated that Sox4 is required for β cell proliferation during prediabetes.
View Article and Find Full Text PDFAims/hypothesis: Pancreatic islets depend on cytosolic calcium (Ca) to trigger the secretion of glucoregulatory hormones and trigger transcriptional regulation of genes important for islet response to stimuli. To date, there has not been an attempt to profile Ca-regulated gene expression in all islet cell types. Our aim was to construct a large single-cell transcriptomic dataset from human islets exposed to conditions that would acutely induce or inhibit intracellular Ca signalling, while preserving biological heterogeneity.
View Article and Find Full Text PDFAims/hypothesis: While pancreatic beta cells have been shown to originate from endocrine progenitors in ductal regions, it remains unclear precisely where beta cells emerge from and which transcripts define newborn beta cells. We therefore investigated characteristics of newborn beta cells extracted by a time-resolved reporter system.
Methods: We established a mouse model, 'Ins1-GFP; Timer', which provides spatial information during beta cell neogenesis with high temporal resolution.