Patrick Dunn
A5024859023- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Glioma Diagnosis and Treatment
- interferon and immune responses
- vaccines and immunoinformatics approaches
- Immune Cell Function and Interaction
- Systemic Lupus Erythematosus Research
- Biomedical Text Mining and Ontologies
- Immunotherapy and Immune Responses
- Ferroptosis and cancer prognosis
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- T-cell and B-cell Immunology
- Virus-based gene therapy research
- Genomics and Phylogenetic Studies
- Cancer, Hypoxia, and Metabolism
- Molecular Biology Techniques and Applications
- Renal Diseases and Glomerulopathies
- Immunodeficiency and Autoimmune Disorders
- Cancer Genomics and Diagnostics
- RNA Interference and Gene Delivery
- Immune cells in cancer
- Gut microbiota and health
- Advanced Electron Microscopy Techniques and Applications
- Brain Metastases and Treatment
National Institute of Allergy and Infectious Diseases
2022-2025
National Institutes of Health
2022-2025
Northrop Grumman (United States)
2010-2025
University of Michigan
2018-2023
University of Pittsburgh
2023
Yale University
2013-2020
Michigan Medicine
2020
U-M Rogel Cancer Center
2020
Health Solutions (Sweden)
2019
University of Pennsylvania
1991-2000
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion human genome was generated by whole-genome shotgun sequencing method. The 14.8-billion bp DNA over 9 months from 27,271,853 high-quality reads (5.11-fold coverage genome) both ends plasmid clones made five individuals. Two assembly strategies—a and a regional chromosome assembly—were used, each combining data Celera publicly funded effort. public were shredded into 550-bp segments to create 2.9-fold those regions...
The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for investigation many developmental cellular processes common to higher eukaryotes, including humans. We have determined nucleotide sequence nearly all ∼120-megabase euchromatic portion genome using whole-genome shotgun sequencing strategy supported by extensive clone-based high-quality bacterial artificial chromosome physical map. Efforts are under way close remaining...
We report on the quality of a whole-genome assembly Drosophila melanogaster and nature computer algorithms that accomplished it. Three independent external data sources essentially agree with support assembly's sequence ordering contigs across euchromatic portion genome. In addition, there are isolated we believe represent nonrepetitive pockets within heterochromatin centromeres. Comparison previously sequenced 2.9- megabase region indicates sequencing accuracy segments is greater than 99....
Abstract Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses immunology data. Open-access datasets being applied in validation methods used original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, ImmPort data repository was created broader research community wide spectrum clinical basic associated findings. The ecosystem consists four components– Private Data, Shared Data...
Several studies have shown that the pre-vaccination immune state is associated with antibody response to vaccination. However, generalizability and mechanisms underlie this association remain poorly defined. Here, we sought identify a common signature could predict across 13 different vaccines. Analysis of blood transcriptional profiles revealed three distinct endotypes, characterized by differential expression genes pro-inflammatory response, cell proliferation, metabolism alterations....
Abstract Background: Advances in multiparameter flow cytometry (FCM) now allow for the independent detection of larger numbers fluorochromes on individual cells, generating data with increasingly higher dimensionality. The increased complexity these has made it difficult to identify cell populations from high‐dimensional FCM using traditional manual gating strategies based single‐color or two‐color displays. Methods: To address this challenge, we developed a novel program, FLOCK (FLOw...
Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study evolution, mechanisms of drug response and resistance, tailoring chemotherapeutic approaches for individual patients. The lack robust standards reporting on PDX has hampered the ability researchers find relevant associated data. Here we present minimal information standard (PDX-MI) generation, quality assurance, use models. PDX-MI defines describing clinical attributes a...
Intra-tumoral heterogeneity is a hallmark of glioblastoma that challenges treatment efficacy. However, the mechanisms set up tumor and cell migration remain poorly understood. Herein, we present comprehensive spatiotemporal study aligns distinctive intra-tumoral histopathological structures, oncostreams, with dynamic properties specific, actionable, spatial transcriptomic signature. Oncostreams are multicellular fascicles spindle-like aligned cells mesenchymal properties, detected using ex...
Abstract Rheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA repertoire sequencing on paired synovial tissue blood samples from 12 seropositive RA patients. We identify clonally expanded CD4 + cells, including CCL5+ cells peripheral helper (Tph) which show a prominent transcriptomic signature of recent activation effector function. CD8 higher oligoclonality than with the largest clones enriched in GZMK+ possibly...
Abstract Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation these yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution 30 samples, including 12 samples with transcriptional data multimodal experiments. We identify 24 classes and predict their associated transcription factors,...
While meta-analysis has demonstrated increased statistical power and more robust estimations in studies, the application of this commonly accepted methodology to cytometry data been challenging. Different studies often involve diverse sets markers. Moreover, detected values same marker are inconsistent between due different experimental designs cytometer configurations. As a result, cell subsets identified by existing auto-gating methods cannot be directly compared across studies. We...
Highlights•Subject-level immunology data from >10,000 healthy normal human subjects•Curated are available in raw or batch-corrected and normalized formats•Interactive visualizations downloads at 10kimmunomes.orgSummaryThere is increasing appreciation that the immune system plays critical roles not only traditional domains of infection inflammation but also many areas biology, including tumorigenesis, metabolism, even neurobiology. However, one major barriers for understanding immunological...
Abstract Background High-grade gliomas are aggressive and immunosuppressive brain tumors. Molecular mechanisms that regulate the inhibitory immune tumor microenvironment (TME) glioma progression remain poorly understood. Fyn tyrosine kinase is a downstream target of oncogenic receptor pathway overexpressed in human gliomas. Fyn’s role vivo growth remains unknown. We investigated whether regulates initiation, invasion. Methods evaluated using genetically engineered mouse models (GEMMs). also...
Summary Rheumatoid arthritis (RA) is a prototypical autoimmune disease that causes destructive tissue inflammation in joints and elsewhere. Clinical challenges RA include the empirical selection of drugs to treat patients, inadequate responders with incomplete remission, lack cure. We profiled full spectrum cells inflamed synovium from patients goal deconstructing cell states pathways characterizing pathogenic heterogeneity RA. Our multicenter consortium effort used multi-modal CITE-seq,...
Abstract Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding mechanisms by which vaccines protect. Systems immunology combines traditional with modern ‘omic profiling techniques computational modeling promote rapid transformative advances in vaccinology vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems approaches identify...
Delayed detection of LN associates with worse outcomes. There are conflicting recommendations regarding a threshold level proteinuria at which biopsy will likely yield actionable management. This study addressed the association urine protein:creatinine ratios (UPCR) clinical characteristics and investigated incidence proliferative membranous histology in patients UPCR between 0.5 1.A total 275 SLE (113 first biopsy, 162 repeat) were enrolled multicentre multi-ethnic/racial Accelerating...
Importance Value in health care is quality per unit cost (V = Q/C), and an emergency department–based intensive (ED-ICU) model has been associated with improved quality. To assess the value of this delivery model, it essential to determine incremental direct care. Objective association ED-ICU inflation-adjusted change mean care, net revenue, margin ED patient encounter. Design, Setting, Participants This retrospective economic analysis evaluated patients before after deployment Joyce Don...