Richard H. Scheuermann
A5034262562- Single-cell and spatial transcriptomics
- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Cell Image Analysis Techniques
- vaccines and immunoinformatics approaches
- T-cell and B-cell Immunology
- Immune Cell Function and Interaction
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Immunotherapy and Immune Responses
- Neuroinflammation and Neurodegeneration Mechanisms
- Influenza Virus Research Studies
- RNA Research and Splicing
- Cytomegalovirus and herpesvirus research
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Phylogenetic Studies
- Semantic Web and Ontologies
- RNA and protein synthesis mechanisms
- Viral gastroenteritis research and epidemiology
- Viral Infections and Immunology Research
- Respiratory viral infections research
- Herpesvirus Infections and Treatments
- Viral-associated cancers and disorders
- Gene Regulatory Network Analysis
- Extracellular vesicles in disease
J. Craig Venter Institute
2016-2025
National Institutes of Health
2014-2025
United States National Library of Medicine
2024-2025
University of California, San Diego
2015-2024
La Jolla Institute for Immunology
2016-2024
Global Virus Network
2019-2023
Arizona State University
2023
Delft University of Technology
2020
InSituTec (United States)
2020
Fred Hutch Cancer Center
2014-2016
The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data analysis tools for multiple virus families, supported by the National Institute Allergy Infectious Diseases (NIAID) Bioinformatics Centers (BRC) program. ViPR contains information human pathogenic viruses belonging to Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae,...
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...
The emergence of SARS-CoV-2 variants with evidence antibody escape highlight the importance addressing whether total CD4
Abstract The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing growing body genome sequence other omics-related data. In this report, we describe merger PAThosystems Integration (PATRIC), Influenza Research Database (IRD) Virus Pathogen Analysis (ViPR) BRCs form Bacterial Viral (BV-BRC) https://www.bv-brc.org/. combined BV-BRC leverages functionality bacterial viral resources provide...
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...
In this analysis, the authors directly compared performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information practical utility about as applied different sets and challenges. Traditional methods for (FCM) rely on subjective gating. Recently, several groups have developed computational identifying cell populations in multidimensional FCM data. Flow Cytometry: Critical Assessment Population Identification Methods (FlowCAP) challenges were...
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...
Abstract A fundamental tenet of scientific research is that published results are open to independent validation and refutation. Minimum data standards aid providers, users, publishers by providing a specification what required unambiguously interpret experimental findings. Here, we present the Information about Flow Cytometry Experiment (MIFlowCyt) standard, stating minimum information report flow cytometry (FCM) experiments. We brought together cross‐disciplinary international...
The mutation rate of Escherichia coli increases approximately 100-fold after treatment with replication-inhibiting agents such as UV light. This enhanced requires the action UmuD and UmuC proteins, which are induced part SOS response to DNA damage. To initiate a biochemical characterization role these we have developed plasmid system that gives efficient expression umuD umuC genes. genes were placed under control regulated phage lambda PL promoter synthetic ribosome-binding site, distance...
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...
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
A major concern about the ongoing swine-origin H1N1 influenza virus (S-OIV) outbreak is that may be so different from seasonal little immune protection exists in human population. In this study, we examined molecular basis for pre-existing immunity against S-OIV, namely recognition of viral epitopes by T cells or B cells/antibodies have been previously primed circulating strains. Using data Immune Epitope Database, found only 31% (8/26) B-cell present recently strains are conserved with 17%...
Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza and surveillance. Other Respiratory Viruses 6(6), 404–416. Background The recent emergence of the 2009 pandemic A/H1N1 virus has highlighted value free open access to genome sequence data with information about other important characteristics. Design Research Database (IRD, http://www.fludb.org ) is a free, open, publicly‐accessible funded by U.S. National...
Abstract Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, is essential for successful cross-study cross-center comparison data. Experts developed five standardized, eight-color panels identification major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents 96-well plates. We present the results a coordinated analysis samples across nine laboratories using these...
A fundamental goal in the biological sciences is definition of groups organisms based on evolutionary history and naming those groups. For influenza viruses (IAVs) swine, understanding hemagglutinin (HA) genetic lineage a circulating strain aids vaccine antigen selection allows for inferences about efficacy. Previous reporting H1 virus HA swine relied colloquial names, frequently with incriminating stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome...