A5090430288- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- vaccines and immunoinformatics approaches
- Single-cell and spatial transcriptomics
- Marine and coastal plant biology
- Gene Regulatory Network Analysis
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
- Gene expression and cancer classification
- Marine Biology and Ecology Research
- Long-Term Effects of COVID-19
- Genomic variations and chromosomal abnormalities
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- COVID-19 and healthcare impacts
- COVID-19 and Mental Health
- Crustacean biology and ecology
- Animal Virus Infections Studies
- Genetic diversity and population structure
- Genomics and Rare Diseases
- COVID-19 epidemiological studies
- Immune responses and vaccinations
- Molecular Biology Techniques and Applications
- COVID-19 Impact on Reproduction
- Neuroinflammation and Neurodegeneration Mechanisms
Adaptive Biotechnologies (United States)
2020-2025
Brown University
2017-2021
Princeton University
2019-2021
Providence College
2020
T cells are involved in the early identification and clearance of viral infections also support development antibodies by B cells. This central role for makes them a desirable target assessing immune response to SARS-CoV-2 infection. Here, we combined two high-throughput profiling methods create quantitative picture T-cell SARS-CoV-2. First, at individual level, deeply characterized 3 acutely infected 58 recovered COVID-19 subjects experimentally mapping their CD8 through antigen stimulation...
Single-cell RNA-sequencing (scRNA-seq) enables high-throughput measurement of RNA expression in single cells. However, because technical limitations, scRNA-seq data often contain zero counts for many transcripts individual These counts, or dropout events, complicate the analysis using standard methods developed bulk RNA-seq data. Current typically overcome by combining information across cells a lower-dimensional space, leveraging observation that generally occupy small number states. We...
Abstract Motivation Structural variation, including large deletions, duplications, inversions, translocations and other rearrangements, is common in human cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification remains challenging because many breakpoints repetitive regions the genome thus are difficult with short reads. The recently linked-read technology 10X Genomics combines a novel...
BACKGROUNDMeasuring the immune response to SARS-CoV-2 enables assessment of past infection and protective immunity. induces humoral T cell responses, but these responses vary with disease severity individual characteristics.METHODSA receptor (TCR) immunosequencing assay was conducted using small-volume blood samples from 302 individuals recovered COVID-19. Correlations between magnitude neutralizing antibody (nAb) titers or indicators were evaluated. Sensitivity testing assessed compared...
The burden and duration of persistent symptoms after nonsevere coronavirus disease 2019 (COVID-19) remains uncertain. This study aimed to assess postinfection symptom trajectories in home-isolated COVID-19 cases compared with age- time- matched seronegative controls, investigate immunological correlates long COVID.
Lay Summary T-cell and antibody responses to severe acute respiratory syndrome coronavirus 2 vaccination in inflammatory bowel disease patients are poorly correlated. preserved by most biologic therapies, but augmented anti-tumor necrosis factor (anti-TNF) treatment. While anti-TNF therapy blunts the response, cellular immunity after is robust.
Abstract T-cell receptors (TCRs) interacting with peptides presented by human leukocyte antigens (HLAs) are the foundation of adaptive immune system but population-level analysis TCR-HLA interactions is lacking. Here we statistically associate ∼ 10 6 public TCRs to specific HLAs using TCR β repertoires sampled from 4,144 HLA-genotyped subjects. The unique HLA allotypes, not allelic groups, and paired α - heterodimer class II though exceptions observed. This specificity permits highly...
Abstract Tumors are highly heterogeneous, consisting of cell populations with both transcriptional and genetic diversity. These diverse spatially organized within a tumor, creating distinct tumor microenvironment. A new technology called spatial transcriptomics can measure patterns gene expression tissue by sequencing RNA transcripts from grid spots, each containing small number cells. In cells, these represent the combined contribution regulatory mechanisms, which alter rate at is...
T cells play a prominent role in orchestrating the immune response to viral diseases, but their clinical presentation and subsequent immunity SARS-CoV-2 infection remains poorly understood. As part of population-based survey municipality Vo', Italy, conducted after initial outbreak, we sampled cell receptor (TCR) repertoires population 2 months PCR followed up positive cases 9 15 later. At months, found that 97.0% (98 101) had elevated levels TCRs associated with SARS-CoV-2. frequency...
Elderly are an understudied, high-risk group vulnerable to severe COVID-19. We comprehensively analyzed the durability of humoral and cellular immune responses after BNT162b2 vaccination SARS-CoV-2 infection in elderly younger adults.
Abstract The Omicron SARS-CoV-2 variant contains 34 mutations in the spike gene likely impacting protective efficacy from vaccines. We evaluated potential impact of these on cellular immune response. Combining epitope mapping to vaccines that we have determined past experiments along with T cell receptor (TCR) repertoire sequencing thousands vaccinated or naturally infected individuals, estimate abrogation response Omicron. Although 20% CD4 + epitopes are potentially affected, loss immunity...
ABSTRACT Memory T cells are records of clonal expansion from prior immune exposures, such as infections, vaccines and chronic diseases like cancer. A subset the receptors these expanded in a typical repertoire highly public, i.e., present many individuals exposed to same exposure. For most part, exposures associated with public unknown. To identify T-cell receptor signatures we mined immunosequencing repertoires tens thousands donors define clusters co-occurring cells. We first built...
T cells are involved in the early identification and clearance of viral infections also support development antibodies by B cells. This central role for makes them a desirable target assessing immune response to SARS-CoV-2 infection. Here, we combined two high-throughput profiling methods create quantitative picture T-cell SARS-CoV-2. First, at individual level, deeply characterized 3 acutely infected 58 recovered COVID-19 subjects experimentally mapping their CD8 through antigen stimulation...
Abstract In viral diseases T cells exert a prominent role in orchestrating the adaptive immune response and yet comprehensive assessment of T-cell repertoire, compared contrasted with antibody response, after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is currently lacking. A prior population-scale study municipality Vo’, Italy, conducted initial SARS-CoV-2 outbreak uncovered high frequency asymptomatic infected individuals their transmission this town. Two months...
The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations highly heterogeneous environments. Adult barnacles may be exposed dissimilar levels thermal stress depending on where they settle in intertidal (i.e., closer upper or lower tidal boundary). For instance, near limit experience episodic summer temperatures above recorded heat coma levels. This differential at microhabitat level also dependent aspect sun exposure. In present study,...
Obesity is a known risk factor for severe respiratory tract infections. In this prospective study, we assessed the impact of being obese or overweight on longitudinal SARS-CoV-2 humoral and cellular responses up to 18 months after infection. 274 patients provided blood samples at regular time intervals including (BMI ≥30, n=32), 25-29.9, n=103) normal body weight 18.5-24.9, n=134) patients. We determined spike-specific IgG, IgA, IgM levels by ELISA neutralising antibody titres neutralisation...
T-cells specifically bind antigens to induce adaptive immune responses using highly specific molecular recognition, and a diverse T-cell repertoire with expansion of antigen-specific clones can indicate robust after infection or vaccination. For patients inflammatory bowel disease (IBD), spectrum chronic intestinal diseases usually requiring immunomodulatory treatment, the response has not been well characterized. Understanding patient factors that result in strong vaccination is critical...
Abstract Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question how adaptation to high variability is maintained in face strong juvenile dispersal and mortality. Here, we show that 4% genes genome balancing selection across entire range species. Many these harbor mutations 2 My evolution between Pacific Atlantic oceans. These are involved ion regulation, pain reception, heat tolerance, functions which...
A classic problem in computational biology is the identification of altered subnetworks: subnetworks an interaction network that contain genes/proteins are differentially expressed, highly mutated, or otherwise aberrant compared with other genes/proteins. Numerous methods have been developed to solve this under various assumptions, but statistical properties these often unknown. For example, some widely used reported output very large difficult interpret biologically. In work, we formulate...
Abstract Background Vaccination against SARS-CoV-2 is a highly effective strategy to protect infection, which predominantly mediated by vaccine-induced antibodies. Postvaccination antibodies are robustly produced those with inflammatory bowel disease (IBD) even on immune-modifying therapies but blunted anti-TNF therapy. In contrast, T-cell response primarily determines long-term efficacy progression,, less well understood. We aimed assess the post-vaccination and its relationship antibody...
Abstract Measuring the adaptive immune response to SARS-CoV-2 can enable assessment of past infection as well protective immunity and risk reinfection. While neutralizing antibody (nAb) titers are one measure protection, such assays challenging perform at a large scale longevity nAb is not fully understood. Here, we apply T-cell receptor (TCR) sequencing assay that be performed on small volume standard blood sample assess infection. Samples were collected from cohort 302 individuals...
Abstract Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification remains challenging because many breakpoints repetitive regions the genome thus are difficult with short reads. The recently linked-read technology 10X Genomics combines a novel barcoding...
Abstract Motivation Single-cell RNA-sequencing (scRNA-seq) enables high throughput measurement of RNA expression in individual cells. Due to technical limitations, scRNA-seq data often contain zero counts for many transcripts These counts, or dropout events , complicate the analysis using standard methods developed bulk RNA-seq data. Current typically overcome by combining information across cells, leveraging observation that cells generally occupy a small number states. Results We introduce...