Samantha Kuan
A5048660446- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Cancer-related gene regulation
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Pluripotent Stem Cells Research
- Histone Deacetylase Inhibitors Research
- Advanced biosensing and bioanalysis techniques
- Chromosomal and Genetic Variations
- Animal Genetics and Reproduction
- Antimicrobial Resistance in Staphylococcus
- Plant Molecular Biology Research
- Intelligent Tutoring Systems and Adaptive Learning
- Protein Degradation and Inhibitors
- Virus-based gene therapy research
- Chromatin Remodeling and Cancer
- Gene Regulatory Network Analysis
- CAR-T cell therapy research
- Nuclear Receptors and Signaling
- Text Readability and Simplification
- Insect symbiosis and bacterial influences
University of California, San Diego
2010-2023
Ludwig Cancer Research
2013-2022
Ludwig Cancer Research
2014
The laboratory mouse shares the majority of its protein-coding genes with humans, making it premier model organism in biomedical research, yet two mammals differ significant ways. To gain greater insights into both shared and species-specific transcriptional cellular regulatory programs mouse, Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications replication domains throughout genome diverse cell tissue types. By...
While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation tumor suppressors, as well changes in chromatin modifications caused by mutations the chromatin-modifying machinery. However, extent cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution low-passage breast cell line and primary human mammary epithelial cells. We find...
As part of the Epigenome Roadmap project, this study uses a chromosome-spanning haplotype reconstruction strategy to construct haplotype-resolved epigenomic maps for diverse set human tissues; reveal extensive allelic biases in chromatin state and transcription, which vary across individuals due genetic backgrounds. Bing Ren colleagues use tissues. The tissues between individuals. They authors investigate cis-regulatory relationships genes their control sequences tissue-restricted activities...
Abstract The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical subcortical structures 1 . Recent surveys of mouse human brains with single-cell transcriptomics 2–6 high-throughput imaging technologies 7,8 have uncovered hundreds neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for unique identity function each type remain unknown. Here...
Abstract Recent advances in single-cell technologies have led to the discovery of thousands brain cell types; however, our understanding gene regulatory programs these types is far from complete 1–4 . Here we report a comprehensive atlas candidate cis -regulatory DNA elements (cCREs) adult mouse brain, generated by analysing chromatin accessibility 2.3 million individual cells 117 anatomical dissections. The includes approximately 1 cCREs and their across 1,482 distinct populations, adding...
Abstract Background To identify potential tumor suppressor genes, genome-wide data from exome and transcriptome sequencing were combined to search for genes with loss of heterozygosity allele-specific expression. The analysis was conducted on the breast cancer cell line HCC1954, a lymphoblast same individual, HCC1954BL. Results By comparing sequences two lines, we identified events at 403 in HCC1954 one gene combination sequence also revealed 86 50 allele specific expression HCC1954BL, which...
ABSTRACT The mammalian cerebrum performs high level sensory, motor control and cognitive functions through highly specialized cortical networks subcortical nuclei. Recent surveys of mouse human brains with single cell transcriptomics 1–3 high-throughput imaging technologies 4,5 have uncovered hundreds neuronal types a variety non-neuronal distributed in different brain regions, but the cell-type-specific transcriptional regulatory programs responsible for unique identity function each type...
Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with present in non-tumor genomes. A comparison the two would be crucial to better characterize genetic driving tumorigenesis. We sequenced genomes a lymphoblastoid (HCC1954BL) and breast (HCC1954) cell line derived from same patient compared both. The genome presents comparable number similar spectrum nucleotide substitutions that found genome. However, significant difference...
ABSTRACT Genome-wide analysis of chromatin accessibility in primary tissues has uncovered millions candidate regulatory sequences the human and mouse genomes 1–4 . However, heterogeneity biological samples used previous studies prevented a precise understanding dynamic landscape specific cell types. Here, we show that transposase-accessible-chromatin single nuclei isolated from frozen tissue can resolve cellular delineate transcriptional constituent Our strategy is based on combinatorial...
Multimodal foundation models, such as Gemini and ChatGPT, have revolutionized human-machine interactions by seamlessly integrating various forms of data. Developing a universal spoken language model that comprehends wide range natural instructions is critical for bridging communication gaps facilitating more intuitive interactions. However, the absence comprehensive evaluation benchmark poses significant challenge. We present Dynamic-SUPERB Phase-2, an open evolving instruction-based speech...
Abstract Cytosine methylation (5mC) is a well-established epigenetic mechanism essential for genomic imprinting, silencing of retrotransposons, and lineage-specific expression developmental genes. This mark extensively remodeled during mammalian development through the action several DNA methyltransferases (DNMT) Ten-Eleven-Translocation (TET) family protein dioxygenases. TET proteins function in de-methylation by catalyzing oxidation 5mC to 5-hydroxymethylcytosine (5hmC) other oxidized...