A5076179710- Immune Cell Function and Interaction
- Single-cell and spatial transcriptomics
- CAR-T cell therapy research
- T-cell and B-cell Immunology
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Immunotherapy and Immune Responses
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Cancer Cells and Metastasis
- Advanced biosensing and bioanalysis techniques
- SARS-CoV-2 and COVID-19 Research
- Cancer Immunotherapy and Biomarkers
- Chromosomal and Genetic Variations
- COVID-19 Clinical Research Studies
- SARS-CoV-2 detection and testing
- Wound Healing and Treatments
- Cancer-related molecular mechanisms research
- Protein Degradation and Inhibitors
- Immune cells in cancer
- vaccines and immunoinformatics approaches
- Muscle Physiology and Disorders
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
Stanford University
2018-2024
Whitehead Institute for Biomedical Research
2024
Dynamic Imaging (United Kingdom)
2020-2023
Creative Commons
2022
Parker Institute for Cancer Immunotherapy
2020
Howard Hughes Medical Institute
2020
National Cancer Institute
2019
National Institutes of Health
2019
Center for Cancer Research
2019
Stanford Cancer Institute
2018
Significance In the skin, tissue injury results in fibrosis form of a scar composed dense extracellular matrix deposited by fibroblasts. Therapies that promote regeneration rather than remain elusive because principles fibroblast programming and response to incompletely understood. Here, we present multimodal -omics platform for study cell populations complex tissue, which has allowed us characterize wound healing fibroblasts across both time space. We identify functionally distinct...
Simultaneous profiling of multiomic modalities within a single cell is grand challenge for single-cell biology. While there have been impressive technical innovations demonstrating feasibility-for example, generating paired measurements transcriptome (single-cell RNA sequencing [scRNA-seq]) and chromatin accessibility assay transposase-accessible using [scATAC-seq])-widespread application joint challenging due to its experimental complexity, noise, cost. Here, we introduce BABEL, deep...
Abstract Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance—random identity by descent—is poorly understood. Also unclear ecDNA somatic variation selection. Here integrating theoretical models random segregation, unbiased image analysis, CRISPR-based tagging with live-cell imaging CRISPR-C, we demonstrate that inheritance results in...
Abstract The human blood system is maintained through the differentiation and massive amplification of a limited number long-lived haematopoietic stem cells (HSCs) 1 . Perturbations to this process underlie diverse diseases, but clonal contributions haematopoiesis how changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems 2–5 , simultaneous detection cell states phylogenies natural barcodes humans remains challenging....
To the Editor: Case reports1Cannon J.G.D. Russell J.S. Kim J. Chang A.L.S. A case of metastatic basal cell carcinoma treated with continuous PD-1 inhibitor exposure even after subsequent initiation radiotherapy and surgery.JAAD Rep. 2018; 4: 248-250Abstract Full Text PDF PubMed Scopus (34) Google Scholar high tumor mutational burden2Jayaraman S.S. Rayhan D.J. Hazany S. Kolodney M.S. Mutational landscape carcinomas by whole-exome sequencing.J Invest Dermatol. 2014; 134: 213-220Abstract (146)...
Abstract Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify recurrent shedding. sequenced viruses two distinct episodes symptomatic separated by 140 days a single patient, to conclusively reinfection new strain harboring the spike variant D614G. With antibody B cell analytics, we show correlates adaptive immunity, including...
T cell dynamics reveal that immunotherapy responses may rely on peripheral cells
Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cell (ESC) pluripotency, differentiation, development. Polycomb repressive complex 2 (PRC2) can both read write H3K27me3, enabling progressive spreading H3K27me3 on linear genome. Long-range Polycomb-associated DNA contacts have also been described, but their regulation role remain...
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify recurrent shedding. sequenced viruses two distinct episodes symptomatic separated by 144 days a single patient, to conclusively reinfection different strain harboring the spike variant D614G. This case was one first cases reported 2020. With antibody, B cell T analytics, we show...
Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER decode interactions between T (TCR)-MHC peptides, antibody-antigen, pairs. A viral presentation strategy allows capture B any antigen. engineer genetic payloads antigen-specific or cells selectively modulate cellular behavior in mixed populations....
Abstract The T-cell receptor (TCR) allows T-cells to recognize and respond antigens presented by infected diseased cells. However, due TCRs’ staggering diversity the complex binding dynamics underlying TCR antigen recognition, it is challenging predict which a given may bind to. Here, we present TCR-BERT, deep learning model that applies self-supervised transfer this problem. TCR-BERT leverages unlabeled sequences learn general, versatile representation of sequences, enabling numerous...
The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role recruit chromatin silencing machinery these parasitic loci. Spen loss activates subset of endogenous (ERV) elements in mouse embryonic stem cells, with gain accessibility, active histone modifications, and ERV RNA transcription. directly RNAs structural similarity the A-repeat Xist, region...
Abstract Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens thousands single cells per sample (scATAC-seq). We obtain analyze profiles over 200,000 two primary human systems. In blood, scATAC-seq allows marker-free identification cell type-specific cis - trans -regulatory elements, disease-associated enhancer activity,...