Brian D. Aevermann
A5055273184- Single-cell and spatial transcriptomics
- Neuroinflammation and Neurodegeneration Mechanisms
- Cell Image Analysis Techniques
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Extracellular vesicles in disease
- Cancer-related molecular mechanisms research
- vaccines and immunoinformatics approaches
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Immunotherapy and Immune Responses
- Influenza Virus Research Studies
- Cancer Genomics and Diagnostics
- Neuroscience and Neuropharmacology Research
- Heat shock proteins research
- Hepatitis B Virus Studies
- Neural dynamics and brain function
- Dermatological and COVID-19 studies
- Neurogenesis and neuroplasticity mechanisms
- SARS-CoV-2 and COVID-19 Research
- Immune Response and Inflammation
- Respiratory viral infections research
- Salivary Gland Disorders and Functions
- Molecular Biology Techniques and Applications
- MicroRNA in disease regulation
Chan Zuckerberg Initiative (United States)
2022-2024
J. Craig Venter Institute
2014-2023
San Diego State University
2008
Oregon Health & Science University
2007
Despite signs of infection—including taste loss, dry mouth and mucosal lesions such as ulcerations, enanthema macules—the involvement the oral cavity in coronavirus disease 2019 (COVID-19) is poorly understood. To address this, we generated analyzed two single-cell RNA sequencing datasets human minor salivary glands gingiva (9 samples, 13,824 cells), identifying 50 cell clusters. Using integrated normalization annotation, classified 34 unique subpopulations between gingiva. Severe acute...
Abstract The primary motor cortex (M1) is essential for voluntary fine-motor control and functionally conserved across mammals 1 . Here, using high-throughput transcriptomic epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys mice, we demonstrate a broadly cellular makeup this region, with similarities that mirror evolutionary distance are consistent between the transcriptome epigenome. core molecular identities neuronal non-neuronal cell types allow us to...
Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) affords some advantages over single-cell (scRNA-seq). snRNA-seq provides less biased cellular coverage, does not appear to suffer cell isolation-based transcriptional artifacts, and can be applied archived frozen specimens. We used well-matched scRNA-seq datasets from mouse visual cortex compare type detection. Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei...
The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research development vaccines, diagnostics therapeutics against by comprehensive collection influenza-related data integrated from various sources, growing suite analysis visualization tools mining hypothesis generation, personal workbench spaces...
Abstract Hundreds of millions single cells have been analyzed to date using high throughput transcriptomic methods, thanks technological advances driving the increasingly rapid generation single-cell data. This provides an exciting opportunity for unlocking new insights into health and disease, made possible by meta-analysis that span diverse datasets building on recent in large language models other machine learning approaches. Despite promise these emerging analytical tools analyzing...
Hundreds of millions single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the level cells. Meta-analyses that span diverse building on recent advances in large language models other machine-learning approaches pose new directions to model extract insight from single-cell data. Despite promise emerging analytical tools analyzing amounts...
The small heat shock proteins (sHSPs) are a diverse family of molecular chaperones. It is well established that these crucial components the plant response. They also have important roles in other stress responses and normal development. We conducted comparative sequence analysis sHSPs three complete angiosperms genomes: Arabidopsis thaliana, Populus trichocarpa, Oryza sativa. Our phylogenetic has identified four additional sHSP subfamilies thus increased number from 7 to 11. novel genes...
Abstract The primary motor cortex (M1) is essential for voluntary fine control and functionally conserved across mammals. Using high-throughput transcriptomic epigenomic profiling of over 450,000 single nuclei in human, marmoset monkey, mouse, we demonstrate a broadly cellular makeup this region, whose similarity mirrors evolutionary distance consistent between the transcriptome epigenome. core molecular identity neuronal non-neuronal types allowed generation cross-species consensus cell...
Abstract von Economo neurons (VENs) are bipolar, spindle-shaped restricted to layer 5 of human frontoinsula and anterior cingulate cortex that appear be selectively vulnerable neuropsychiatric neurodegenerative diseases, although little is known about other VEN cellular phenotypes. Single nucleus RNA-sequencing identifies a transcriptomically-defined cell cluster contained VENs, but also fork cells subset pyramidal neurons. Cross-species alignment this with well-annotated mouse...
Single-cell genomics is rapidly advancing our knowledge of the diversity cell phenotypes, including both types and states. Driven by single-cell/-nucleus RNA sequencing (scRNA-seq), comprehensive atlas projects characterizing a wide range organisms tissues are currently underway. As result, it critical that transcriptional phenotypes discovered defined disseminated in consistent concise manner. Molecular biomarkers have historically played an important role biological research, from defining...
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function cell types in brain. Classification neurons also essential manipulate controlled ways understand their variation vulnerability brain disorders. The BRAIN Initiative Cell Census Network (BICCN) an integrated network data-generating centers, archives, standards developers, with goal systematic multimodal type profiling characterization....
Cells are fundamental function units of multicellular organisms, with different cell types playing distinct physiological roles in the body. The recent advent single-cell transcriptional profiling using RNA sequencing is producing 'big data', enabling identification novel human at an unprecedented rate. In this review, we summarize work characterizing central nervous and immune systems single-nuclei sequencing, discuss implications that these discoveries having on representation reference...
A fundamental characteristic of multicellular organisms is the specialization functional cell types through process differentiation. These specialized not only characterize normal functioning different organs and tissues, they can also be used as cellular biomarkers a variety disease states therapeutic/vaccine responses. In order to serve reference for type representation, Cell Ontology has been developed provide standard nomenclature defined comparative analysis biomarker discovery....
ABSTRACT Despite signs of infection, the involvement oral cavity in COVID-19 is poorly understood. To address this, single-cell RNA sequencing data-sets were integrated from human minor salivary glands and gingiva to identify 11 epithelial, 7 mesenchymal, 15 immune cell clusters. Analysis SARS-CoV-2 viral entry factor expression showed enrichment epithelia including ducts acini suprabasal cells mucosae. autopsy tissues confirmed vivo infection mucosa. Saliva SARS-CoV-2-infected individuals...
Large-scale single-cell 'omics profiling is being used to define a complete catalogue of brain cell types, something that traditional methods struggle with due the diversity and complexity brain. But this poses problem: How do we organise such - providing standard way refer types discovered, linking their classification properties supporting data? Cell ontologies provide partial solution these problems, but no existing ontology schemas support definition by direct reference data, using...
The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and to investigate host-pathogen interactions at a systems level. This generated 47 transcriptomic proteomic datasets from 30 studies that in vivo vitro host responses viral infections. Human pathogens Orthomyxoviridae Coronaviridae families, especially pandemic H1N1 avian H5N1 influenza A viruses severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated....
With the advent of single cell/nucleus RNA sequencing (sc/snRNA-seq), field cell phenotyping is now a data-driven exercise providing statistical evidence to support type/state categorization. However, task classifying cells into specific, well-defined categories with empirical data provided by sc/snRNA-seq remains nontrivial due difficulty in determining specific differences between related types close transcriptional similarities, resulting challenges matching identified separate...
Abstract Elucidating the cellular architecture of human neocortex is central to understanding our cognitive abilities and susceptibility disease. Here we applied single nucleus RNA-sequencing perform a comprehensive analysis cell types in middle temporal gyrus cerebral cortex. We identify highly diverse set excitatory inhibitory neuronal that are mostly sparse, with being less layer-restricted than expected. Comparison similar mouse cortex dataset revealed surprisingly well-conserved enables...
The ability to trace every cell in some model organisms has led the fundamental understanding of development and cellular function. However, plants complexity number, organ size, developmental time makes this a challenge even diminutive plant Arabidopsis (Arabidopsis thaliana). Duckweed, basal nongrass aquatic monocots, provide an opportunity follow entire due their small reduced body plan, fast clonal growth habit. Here we present chromosome-resolved genome for highly invasive Lesser...
Abstract Reference cell atlases powered by single and spatial transcriptomics technologies are becoming available to study healthy diseased tissue at resolution. One important use of these data resources is compare types from new dataset with in the reference evaluate their phenotypic similarities differences, for example, identifying novel under disease conditions. For this purpose, rigorously-validated computational algorithms needed perform type matching tasks that can datasets different...