A5086158264- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Research Data Management Practices
- Data-Driven Disease Surveillance
- Species Distribution and Climate Change
- Gene expression and cancer classification
- Microbial Natural Products and Biosynthesis
- Viral Infections and Immunology Research
- SARS-CoV-2 and COVID-19 Research
- RNA regulation and disease
- COVID-19 diagnosis using AI
- Enzyme Production and Characterization
- SARS-CoV-2 detection and testing
- Semantic Web and Ontologies
- Genomics and Rare Diseases
- Ubiquitin and proteasome pathways
- Social Media in Health Education
- Service-Learning and Community Engagement
- Viral Infections and Outbreaks Research
- Wikis in Education and Collaboration
- Marine Sponges and Natural Products
- Peptidase Inhibition and Analysis
Scripps Research Institute
2015-2024
Scripps (United States)
2021-2023
Scripps Institution of Oceanography
2021-2023
San Diego State University
2011-2014
University of California, San Diego
2008-2012
Institute of Molecular and Cell Biology
2012
BioGPS (http://biogps.org) is a centralized gene-annotation portal that enables researchers to access distributed gene annotation resources. This article focuses on the updates since our last paper (2013 database issue). The unique features of BioGPS, compared those other portals, are its community extensibility and user customizability. Users contribute gene-specific resources accessible from ('plugins'), which helps ensure resource collection always up-to-date it will continue expanding...
Coxsackievirus B3 (CVB3), a member of the picornavirus family and enterovirus genus, causes viral myocarditis, aseptic meningitis, pancreatitis in humans. We genetically engineered unique molecular marker, "fluorescent timer" protein, within our infectious CVB3 clone isolated high-titer recombinant stock (Timer-CVB3) following transfection HeLa cells. "Fluorescent protein undergoes slow conversion fluorescence from green to red over time, Timer-CVB3 can be utilized track virus infection...
Efficient tools for data management and integration are essential many aspects of high-throughput biology. In particular, annotations genes human genetic variants commonly used but highly fragmented across resources. Here, we describe MyGene.info MyVariant.info, high-performance web services querying gene variant annotation information. These currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model organizing biological MyVariant.info...
A series of chlorinated bisindole pyrroles, lynamicins A−E (1−5), was discovered from a novel marine actinomycete, NPS12745, which isolated sediment collected off the coast San Diego, California. Close to full length 16S rRNA sequence analysis indicated that NPS12745 is strain recently described actinomycete with proposed genus name Marinispora. The antimicrobial spectrum these compounds evaluated against panel 11 pathogens, demonstrated substances possess broad-spectrum activity both...
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, adheres to FAIR principles findability, accessibility, interoperability reusability. Here we describe breadth depth biomedical contained within Wikidata, discuss open-source tools have built add information synchronize it with source databases. We also demonstrate several use cases for including...
Abstract The emergence of SARS-CoV-2 variants concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response this need, global scientific community, through unprecedented effort, sequenced and shared over 10 million genomes GISAID, as May 2022. This extraordinarily high sampling rate provides a unique opportunity track evolution virus in real-time. Here, we present outbreak.info , platform that currently tracks 40 combinations PANGO...
AIR data sharing is integral to spur research reproducibility, promote reuse, and accelerate research.However, the first step in using these assets -discovering that they exist -is compounded by problems incentives, standardization, coordination of efforts.In 2023, National Institutes Health (NIH) implemented their updated Data Sharing Policy, which mandates timely all NIH-funded data.However, for policy shift culture, improve several changes must happen.In a companion piece 1 , we present...
To combat the ongoing COVID-19 pandemic, scientists have been conducting research at breakneck speeds, producing over 52,000 peer-reviewed articles within first year. address challenge in tracking vast amount of new located separate repositories, we developed outbreak.info Research Library, a standardized, searchable interface and SARS-CoV-2 resources. Unifying metadata from sixteen assembled collection 350,000 publications, clinical trials, datasets, protocols, other resources as October...
To meet the increased need of making biomedical resources more accessible and reusable, Web Application Programming Interfaces (APIs) or web services have become a common way to disseminate knowledge sources. The BioThings APIs are collection high-performance, scalable, annotation as service that automate integration biological annotations from disparate data This currently includes MyGene.info, MyVariant.info MyChem.info for integrating on genes, variants chemical compounds, respectively....
Abstract Biomedical datasets are increasing in size, stored many repositories, and face challenges FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices promote transparency, encourage reproducibility, accelerate research advances through data reuse. To improve our computational tools, evaluated metadata standards across established biomedical repositories. The vast...
Coxsackievirus B3 (CVB3) has previously been shown to utilize autophagy in an advantageous manner during the course of infection host cell. However, few studies have determined whether stem cells induce a similar fashion, and virus-induced occurs following cells. Therefore, we compared induction CVB3 neural progenitor (NPSCs), which recently be highly susceptible infection, HL-1 cells, transformed cardiomyocyte cell line. As demonstrated for other showed increase activity autophagic...
Abstract The emergence of SARS-CoV-2 variants concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response this need, global scientific community, through unprecedented effort, sequenced and shared over 11 million genomes GISAID, as May 2022. This extraordinarily high sampling rate provides a unique opportunity track evolution virus in real-time. Here, we present outbreak.info, platform that currently tracks 40 combinations PANGO...
Large-scale fermentation of the marine actinomycete Salinispora tropica for production salinosporamide A (NPI-0052; 1) clinical trials materials provided crude extracts containing minor secondary metabolites, including B (2) and a new congener, 3. Spectroscopic characterization revealed that 3 is identical to antiprotealide, molecular hybrid 20S proteasome inhibitors 1 omuralide (4) not previously described as natural product. Analysis from shake flask cultures three wild-type S. strains...
Enteroviruses, including coxsackieviruses, exhibit significant tropism for the central nervous system, and these viruses are commonly associated with viral meningitis encephalitis. Previously, we described ability of coxsackievirus B3 (CVB3) to infect proliferating neuronal progenitor cells located in neonatal subventricular zone persist adult murine system (CNS). Here, demonstrate that cultured neurospheres, which comprise neural stem their progeny at different stages development, were...
Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular APIs developed by different research teams have adopted Javascript Object Notation (JSON) as their primary data format. While usage of a common format offers significant advantages, that alone is not sufficient for rich integrative queries across APIs.Here, we implemented JSON Linking Data (JSON-LD) technology on the BioThings developed, MyGene.info , MyVariant.info and MyChem.info ....
Biomedical literature represents one of the largest and fastest growing collections unstructured biomedical knowledge. Finding critical information buried in can be challenging. To extract from free-flowing text, researchers need to: 1. identify entities text (named entity recognition), 2. apply a standardized vocabulary to these (normalization), 3. how are related another (relationship extraction). Researchers have primarily approached extraction tasks through manual expert curation...