A5070153270- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Fungal and yeast genetics research
- Data Analysis with R
- Microtubule and mitosis dynamics
- RNA modifications and cancer
- Gene expression and cancer classification
- Genetics, Aging, and Longevity in Model Organisms
- Chromatin Remodeling and Cancer
- T-cell and B-cell Immunology
- Telomeres, Telomerase, and Senescence
- Bacterial Genetics and Biotechnology
- Protein Degradation and Inhibitors
- Plant Virus Research Studies
- Immune cells in cancer
- Pluripotent Stem Cells Research
- Animal Genetics and Reproduction
- CAR-T cell therapy research
- Microplastics and Plastic Pollution
- DNA Repair Mechanisms
- Metabolomics and Mass Spectrometry Studies
- Developmental Biology and Gene Regulation
Stanford University
2013-2018
Harvey Mudd College
2009-2017
University of Cambridge
2013
Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to regulation gene expression. Using assay transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern DNA fragment lengths and positions around in Saccharomyces cerevisiae, use this distinctive two-dimensional nucleosomal "fingerprint" as basis for new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can...
Characterizing epigenetic heterogeneity at the cellular level is a critical problem in modern genomics era. Assays such as single cell ATAC-seq (scATAC-seq) offer an opportunity to interrogate through patterns of variability open chromatin. However, these assays exhibit technical that complicates clear classification and type identification heterogeneous populations. We present scABC, R package for unsupervised clustering single-cell data, classify scATAC-seq data discover regions chromatin...
The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli level functional differs depending on the stress. effect these differing concentrations global transcriptional remains unclear. We investigated concentration transcriptome during stationary phase rich media. found that 23% genes E. genome are regulated by RpoS, and we identified RpoS-transcribed promoters. observed three distinct classes response to regulon: whose expression changes linearly...
Abstract Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction DNA transposition, the levels multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry positions in arrayed microwells, then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies epigenomic heterogeneity individual cells. reveals...
Adaptive survival requires the coordination of nutrient availability with expenditure cellular resources. For example, in nutrient-limited environments, 50% all S. cerevisiae genes synchronize and exhibit periodic bursts expression respiration cell division yeast metabolic cycle (YMC). Despite importance proliferative synchrony, majority YMC regulators are currently unknown. Here, we demonstrate that INO80 chromatin-remodeling complex is required to coordinate gene expression. Specifically,...
During embryonic development, a complex organism is formed from single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which following the expression activity transcription factors (TFs). This study sought to compare TF during development in diverse group metazoan animals: representatives vertebrates (Danio rerio, Xenopus tropicalis), chordate (Ciona intestinalis) invertebrate phyla such as insects (Drosophila melanogaster, Anopheles...
Abstract Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic has hidden by ensemble averaging. We generated chromatin accessibility across 8 populations cell types. Using bulk profiles to scaffold our data analysis, we constructed an landscape...
Abstract Single cell ATAC-seq (scATAC) yields sparse data that makes application of conventional computational approaches for analysis challenging or impossible. We developed chromVAR, an R package analyzing chromatin accessibility by estimating the gain loss within sets peaks sharing same motif annotation while controlling known technical biases. chromVAR enables accurate clustering scATAC-seq profiles and characterization known, de novo identification novel, sequence motifs associated with...
Abstract Characterizing epigenetic heterogeneity at the cellular level is a critical problem in modern genomics era. Assays such as single cell ATAC-seq (scATAC-seq) offer an opportunity to interrogate through patterns of variability open chromatin. However, these assays exhibit technical that complicates clear classification and type identification heterogeneous populations. We present scABC, R package for unsupervised clustering data, classify scATAC-seq data discover regions chromatin...
Abstract Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction DNA transposition, the levels multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry positions in arrayed microwells, then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies epigenomic heterogeneity individual cells. reveals...
Abstract Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to regulation gene expression. We observe a highly structured pattern DNA fragment lengths and positions generated by assay transposase accessible chromatin (ATAC-seq) around in S. cerevisiae , use this distinctive two-dimensional nucleosomal “fingerprint” as basis for new nucleosome-positioning algorithm called NucleoATAC. show that NucleoATAC can...
Telomeres are regions of repeated DNA sequence that cap the ends eukaryotic chromosomes. They act as disposable safeguards to prevent loss important genetic information during replication due inability polymerase replicate linear The synthesis new telomeric repeats using an RNA molecule a template is catalyzed by enzyme telomerase. In embryonic stem cells, gene encoding catalytic protein subunit telomerase complex (telomere reverse transcriptase [TERT]) transcriptionally active and critical...
Abstract The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli. level functional differs depending on the stress. effect these differing concentrations global transcriptional remains unclear. We investigated concentration transcriptome during stationary phase rich media. show that 23% genes E. coli genome are regulated by level, and we identify RpoS-transcribed promoters. observe three distinct classes response to regulon: whose expression...
ABSTRACT Adaptive survival requires the coordination of nutrient availability with expenditure cellular resources. For example, in nutrient-limited environments, 50% all S . cerevisiae genes synchronize and exhibit periodic bursts expression respiration cell division Yeast Metabolic Cycle (YMC). Despite importance metabolic proliferative synchrony, majority YMC regulators are currently unknown. Here we demonstrate that INO80 chromatin-remodelling complex is required to coordinate gene...
The coordination of cellular function with the environment is essential for adaptation and survival. S. cerevisiae has a remarkable ability to sense diverse (i.e. nutrient‐rich or □limiting) environments reprogram their energy metabolism proliferative capacity accordingly. These adaptive responses are often achieved by rapid inducible changes in metabolic gene expression facilitated chromatin modification. Previously we identified INO80 remodeler as primary regulator pathways (Yao et al, MCB...