A5047705879- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Advanced Biosensing Techniques and Applications
- RNA and protein synthesis mechanisms
- Cancer Immunotherapy and Biomarkers
- Cell Image Analysis Techniques
- Bacterial Genetics and Biotechnology
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Enzyme Structure and Function
- Inflammatory mediators and NSAID effects
- Cytokine Signaling Pathways and Interactions
- T-cell and B-cell Immunology
- PI3K/AKT/mTOR signaling in cancer
- Innovative Microfluidic and Catalytic Techniques Innovation
- Fungal and yeast genetics research
- Cancer, Lipids, and Metabolism
- Cancer, Stress, Anesthesia, and Immune Response
- Adenosine and Purinergic Signaling
- Tryptophan and brain disorders
- CAR-T cell therapy research
- Cancer Mechanisms and Therapy
- Prostate Cancer Treatment and Research
- Immune Cell Function and Interaction
University of California, San Francisco
2020-2024
City College of San Francisco
2023
Arc Research Institute
2023
UCSF Helen Diller Family Comprehensive Cancer Center
2023
NYU Langone Health
2019-2020
Universidad Católica de Santa Fe
2020
University of Richmond
2017-2019
Stanford University
2017
Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas 100 million transcriptomic profiles measuring 1,100 small-molecule impact cells across 50 cancer lines. Our high-throughput Mosaic platform, composed highly diverse optimally balanced 'cell village', reduces batch effects enables parallel profiling thousands conditions at resolution an...
RNA structural switches are key regulators of gene expression in bacteria, but their characterization Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification functional switches. We applied SwitchSeeker to the human transcriptome identified 245 putative To validate our approach, characterized previously unknown switch 3' untranslated region RORC (RAR-related orphan receptor C) transcript. In vivo dimethyl...
BACKGROUND. The reshaping of the immune landscape by nivolumab (NIVO) and ipilimumab (IPI) its relation to patient outcomes is not well described.
ABSTRACT RNA structural switches are key regulators of gene expression in bacteria, yet their characterization Metazoa remains limited. Here we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification functional switches. We applied SwitchSeeker to the human transcriptome identified 245 putative To validate our approach, characterized previously unknown switch 3’UTR RORC transcript. In vivo DMS-MaPseq, coupled with cryogenic electron...
Abstract The development of DNA-barcoded antibodies to tag cell-surface molecules has enabled the use droplet-based single cell sequencing (dsc-seq) profile surface proteomes cells. Compared flow and mass cytometry, major limitation current dsc-seq-based workflows is high cost associated with profiling each cell, thus precluding its in applications where millions cells are required. Here, we introduce SCITO-seq, a new workflow that combines combinatorial indexing commercially available...
Abstract BACKGROUND The androgen receptor (AR) is the central therapeutic target in advanced prostate cancer (PCa). While treatments that directly AR are effective prolonging patient survival, aggressive cancers invariably find a way to evade these therapies. Frequently, evasion mechanisms reestablish expression and therefore AR-driven oncogenic pathways restored. Comprehensively understanding protein regulation machinery of identifying alternative targets crucial for treatment this disease....
Ded1p is an essential translation initiation factor that interacts with and modulated by eIF4F. also promotes the assembly disassembly of stress granules, which contain repressed mRNAs factors. As affects both mRNA storage initiation, regulation Ded1p's function may affect whether are stored or translated. To identify regulators in Saccharomyces cerevisiae, we screened for over‐expression suppressors severe growth defect conferred high levels Ded1p. We found HAT1, a lysine acetyltransferase...
The ability to simultaneously query both protein and mRNA expression on tens of thousands single cells has emerged only recently, with the development CITE-seq, REAP-seq, Ab-seq platforms. Each technology relies antibodies conjugated oligonucleotide tags, followed by capture antibody-stained for cell RNA-sequencing. technologies have important advantages over flow cytometry, chiefly in that they allow study a limitless number parameters, RNA sequencing, which cannot identify populations as...
Ded1, an RNA‐dependent ATPase, promotes translation initiation of many mRNAs in yeast. Ded1 is extremely important for the predicted to have substantial secondary structure (Sen et al., 2015). interacts directly with eIF4A and eIF4G this complex has increased helicase activity compared either or alone (Hilliker 2011; Gao 2016). Consistent role translation, DDX3, human homolog been shown be misregulated several cancers hijacked by HIV allow highly structured (Valiente‐Echeverria 2015; Xiang...
Abstract The ability to simultaneously query both protein and mRNA expression on tens of thousands single cells has emerged only recently, with the development CITE-seq, REAP-seq, Ab-seq platforms. Each technology relies antibodies conjugated oligonucleotide tags, followed by capture antibody-stained for cell RNA-sequencing. technologies have important advantages over flow cytometry, chiefly in that they allow study a limitless number parameters, RNA sequencing, which cannot identify...
Abstract Immunotherapies have revolutionized the treatment of many cancers, but most patients fail to respond. To investigate immune phenotypes associated with patient response, we assessed 68 unique peripheral blood markers using high-dimension flow cytometry. Samples from 41 metastatic melanoma treated αPD1 or αCTLA4 and 12 healthy donors (HD) were evaluated. avoid a loss higher order data, used novel computational approach, CytoBrute, analyze data through semi-comprehensive Boolean...
Abstract Cancer immunotherapy has emerged as one of the most potent therapeutic tools in treating melanoma and a variety other malignancies. Immunotherapy includes inhibition modulators T cell antitumor function, immune checkpoints, by using antibodies against them. In advanced patients, checkpoint inhibitors ipilimumab (IPI) nivolumab (NIVO) have had unprecedented efficacy. Although many patients respond well to this therapy, remain unresponsive. The mechanism underlying treatment failures...