A5054354429- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- T-cell and B-cell Immunology
- Immune Cell Function and Interaction
- IoT-based Smart Home Systems
- Underwater Vehicles and Communication Systems
- Energy Harvesting in Wireless Networks
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Peptidase Inhibition and Analysis
- RNA and protein synthesis mechanisms
- interferon and immune responses
- Genomics and Phylogenetic Studies
- Radiomics and Machine Learning in Medical Imaging
- Bioinformatics and Genomic Networks
- Cardiac tumors and thrombi
- Advanced Proteomics Techniques and Applications
- Biosensors and Analytical Detection
- Autoimmune and Inflammatory Disorders Research
- Cell Image Analysis Techniques
- Gene Regulatory Network Analysis
- American Sports and Literature
University of Washington
2022-2025
Allen Institute for Immunology
2020-2024
University of Washington Medical Center
2024
Seattle University
2021
Covance (United States)
2017
Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, responses to signals, and human disease. Recent advances allowed paired capture protein abundance transcriptomic state, but a lack epigenetic information these assays has left missing link gene regulation. Using mixture cells peripheral blood as test case, we developed novel scATAC-seq workflow increases signal-to-noise allows measurement cell...
Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule single-nucleotide resolution. studies encompass the direct identification of native cytosine methylation well exogenously placed N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using sequencing, coprocessing architectures, is limited by computational demands lack supporting tools. Here, we introduce fibertools, state-of-the-art...
Abstract Longitudinal bulk and single-cell omics data is increasingly generated for biological clinical research but challenging to analyze due its many intrinsic types of variations. We present PALMO ( https://github.com/aifimmunology/PALMO ), a platform that contains five analytical modules examine longitudinal multi-omics from multiple perspectives, including decomposition sources variations within the data, collection stable or variable features across timepoints participants,...
Abstract Most human cells contain two non-identical genomes, and differences in their regulation underlie development disease. We demonstrate that Fiber-seq Inferred Regulatory Elements (FIREs) enable the accurate quantification of chromatin accessibility across 6 Gbp diploid genome with single-molecule single-nucleotide precision. find can harbor >1,000 regulatory elements haplotype-selective (HSCA) show these preferentially localize to genomic loci containing most genetic diversity,...
Abstract Age-associated changes in the T cell compartment are well described. However, limitations of current single-modal or bimodal single-cell assays, including flow cytometry, RNA-seq (RNA sequencing) and CITE-seq (cellular indexing transcriptomes epitopes by sequencing), have restricted our ability to deconvolve more complex cellular molecular changes. Here, we profile >300,000 single cells from healthy children (aged 11–13 years) older adults 55–65 using trimodal assay TEA-seq...
The generation and maintenance of protective immunity is a dynamic interplay between host environment that impacted by age. Understanding fundamental changes in the healthy immune system occur over lifespan critical developing interventions for age-related susceptibility to infections diseases. Here, we use multi-omic profiling (scRNA-seq, proteomics, flow cytometry) examined human peripheral 300 adults, with 96 young older adults followed two years yearly vaccination. resulting resource...
Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms disease. The importance these platforms in clinical translational studies led us investigate the impact delayed processing on numbers state mononuclear cells (PBMC) plasma proteome. Similar previous studies, we show minimal effects general phenotype PBMC up 18 hours. In contrast, profound changes single-cell transcriptome composition proteome become evident as early...
Abstract Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule single-nucleotide resolution. studies encompass the direct identification of native cytosine methylation well exogenously placed N 6 -methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using sequencing, co-processing architectures, is limited by computational demands lack supporting tools. Here, we introduce fibertools ,...
Accurately quantifying the functional consequences of non-coding mosaic variants requires pairing DNA sequence with both accessible and closed chromatin architectures along individual molecules—a that cannot be achieved using traditional fragmentation-based assays. We demonstrate targeted single-molecule fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic epigenomic profiling across >100 kilobase loci ~10-fold enrichment over untargeted sequencing....
Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibers. However, our tools for deeply profiling how co-occupy fibers, especially at single-cell level, remain limited. We present Deaminase-Assisted single-molecule Fiber sequencing (DAF-seq), which leverages a non-specific double-stranded DNA deaminase toxin A (SsDddA) to efficiently stencil protein occupancy molecules via selective deamination accessible cytidines, are preserved C-to-T...
Abstract Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to diverse mechanisms by which genetic variants cause disease. To address this, we developed synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, enables accurate single-nucleotide, insertion-deletion, structural variant calling diploid de novo genome assembly, permits simultaneous elucidation haplotype-resolved CpG methylation, chromatin accessibility,...
Deep immune profiling is essential for understanding the human system in health and disease. Successful biological interpretation of this data requires consistent laboratory processing with minimal batch-to-batch variation. Here, we detail a robust pipeline peripheral blood mononuclear cells by both high-dimensional flow cytometry single-cell RNA-seq. These protocols reduce batch effects, generate reproducible data, increase throughput. For complete details on use execution protocol, please...
Abstract Background Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages flexibility of sample collection scale, there are additional complications the data deconvolution steps required assign each cell their originating samples. Results To meet computational needs for efficient deconvolution, we developed tools BarCounter BarMixer that compute barcode counts deconvolute mixed into...
Abstract Some autoimmune diseases, including rheumatoid arthritis (RA), are preceded by a critical subclinical phase of disease activity. Proactive clinical management is hampered lack biological understanding this ‘at-risk’ state and the changes underlying development. In cross-sectional longitudinal multi-omics study peripheral immunity in autoantibody-positive at-risk for RA period, we identified systemic inflammation, proinflammatory-skewed B cells, expanded Tfh17-like epigenetic bias...
Accurately quantifying the functional consequences of noncoding mosaic variants requires pairing DNA sequences with both accessible and closed chromatin architectures along individual molecules-a that cannot be achieved using traditional fragmentation-based assays. We demonstrate targeted single-molecule fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic, epigenomic profiling across >100 kb loci ∼10-fold enrichment over untargeted sequencing. Targeted...
Abstract Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, responses to extracellular signals, and human disease states. scATAC-seq has particularly challenging due large size genome processing artefacts resulting from DNA damage are an inherent source background signal. Downstream analysis integration with other single-cell assays is complicated by lack clear phenotypic information linking...
Resolving whether and how rare noncoding genetic variants cause Mendelian conditions remains challenging owing to the diverse mechanisms by which they disease. Here we demonstrate utility of single-molecule chromatin fiber sequencing (Fiber-seq) for resolving mechanistic basis condition autosomal dominant resistance thyrotropin (RTSH), had previously been linked within a short tandem repeat (STR) variant on chromosome 15.
Abstract Disclosure: H. Grasberger: None. A. Dumitrescu: X. Liao: E. Swanson: R.E. Weiss: P. Srichomkwun: T. Pappa: J. Chen: Yoshimura: Hoffmann: M. Franca: K. Onigata: S. Costagliola: Ranchalis: M.R. Vollger: A.B. Stergachis: J.X. Chong: M.J. Bamshad: G. Smits: Vassart: Refetoff: We previously identified a novel form of dominantly inherited resistance to TSH (RTSH), without or receptor mutations, that was linked locus on chromosome 15q (Grasberger et al., Hum. Genet. 2005). At birth,...
Abstract: The naive T cell compartment undergoes multiple changes across age that associate with altered susceptibility to infection and autoimmunity. In addition the acquisition of naive-like memory subsets, mouse studies describe substantial molecular reprogramming in adults compared adolescents. However, these alterations are not well delineated human aging. Using a new trimodal single technology (TEA-seq), we discovered composition transcriptional epigenetic programming children (11-13...
Summary Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms disease. The importance these platforms in clinical translational studies led us investigate the impact delayed processing on numbers state mononuclear cells (PBMC) plasma proteome. Similar previous studies, we show minimal effects general phenotype PBMCs up 18 hours. In contrast, profound changes single-cell transcriptome composition proteome become evident...