A5004988948- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Semantic Web and Ontologies
- Insect symbiosis and bacterial influences
- Bacteriophages and microbial interactions
- Protist diversity and phylogeny
- Scientific Computing and Data Management
- Microbial infections and disease research
- Gene expression and cancer classification
- Data Quality and Management
- Insect behavior and control techniques
- Legume Nitrogen Fixing Symbiosis
- Single-cell and spatial transcriptomics
- Parasitic Diseases Research and Treatment
- Research Data Management Practices
- Genomics and Rare Diseases
- Mycobacterium research and diagnosis
- Microbial Community Ecology and Physiology
- Cancer Genomics and Diagnostics
- Respiratory viral infections research
- Wastewater Treatment and Nitrogen Removal
- Insect Utilization and Effects
- Bacterial Infections and Vaccines
- Carbohydrate Chemistry and Synthesis
University of Maryland, Baltimore
2012-2025
Stanford University
2023
University of Padua
2023
University College London
2023
SIB Swiss Institute of Bioinformatics
2023
Phoenix Bioinformatics
2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
University of Baltimore
2016
Human Genome Sciences (United States)
2013
Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding functions of genes and gene products. Here, we report advances consortium over past two years. new GO-CAM annotation framework was notably improved, formalized model with a computational schema to check validate rapidly increasing repository 2838 GO-CAMs. In addition, describe impacts several collaborations refine GO 10% increase in number annotations,...
The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). DO web browser has been designed for speed, efficiency robustness through the use graph database. Full-text contextual searching functionality using Lucene allows querying name, synonym, definition, DOID cross-reference (xrefs) with complex Boolean search strings. semantically integrates disease...
Abstract FDA proactively invests in tools to support innovation of emerging technologies, such as infectious disease next generation sequencing (ID-NGS). Here, we introduce FDA-ARGOS quality-controlled reference genomes a public database for diagnostic purposes and demonstrate its utility on the example two use cases. We provide quality control metrics genomic resource outline need genome gap filling domain. In first case, show more accurate microbial identification Enterococcus avium from...
Abstract The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository manually curated annotations intrinsically disordered proteins and regions from literature. We report here recent updates DisProt version 9, including a restyled web interface, refactored Ontology (IDPO), improvements in curation process significant content growth around 30%. Higher quality consistency provided by newly implemented reviewing training curators. increased...
The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence assertion methods. ECO are used in the process biocuration to capture supports biological assertions (e.g. gene product X has function Y as supported by Z). Capture this information allows tracking annotation provenance, establishment quality control measures query evidence. over 1500 is use many leading resources including Gene Ontology, UniProt several model organism databases. continually...
Abstract The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type evidence supports biomedical annotations assertions. Consistent information with ECO allows tracking annotation provenance, establishment quality control measures, evidence-based data mining. in use by dozens repositories resources both specific general areas focus. continually being expanded enhanced response user requests as well our aim adhere...
Enterobacter radicincitans sp. nov. DSM16656(T) represents a new species of the genus which is biological nitrogen-fixing endophytic bacterium with growth-promoting effects on variety crop and model plant species. The presence genes for nitrogen fixation, phosphorous mobilization, phytohormone production reflects this microbe's potential activity.
Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding cell types states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Network (BICCN) is applying these at unprecedented scale map in mammalian brain. In an effort increase data FAIRness (Findable, Accessible, Interoperable, Reusable), NIH has established repositories make generated by BICCN related BRAIN projects accessible...
Abstract A comprehensive, computable representation of the functional repertoire all macromolecules encoded within human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating structured body information about gene functions, which now includes experimental findings reported in more than 175,000 publications genes experimentally tractable model organisms 1,2 . Here, we describe results large,...
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The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes Health without requiring owners move, reformat, or rehost those data. This is centered on catalog integrates detailed descriptions biomedical individual Programs' Coordination Centers (DCCs) into uniform metadata model can then be indexed and searched centralized portal. Crosscut Metadata Model (C2M2) supports wide variety...
The Gemina system (http://gemina.igs.umaryland.edu) identifies, standardizes and integrates the outbreak metadata for breadth of NIAID category A-C viral bacterial pathogens, thereby providing an investigative surveillance tool describing Who [Host], What [Disease, Symptom], When [Date], Where [Location] How [Pathogen, Environmental Source, Reservoir, Transmission Method] each pathogen. database will provide a greater understanding interactions pathogens with their hosts infectious diseases...
Members of the Mycoplasma mycoides cluster' represent important livestock pathogens worldwide. subsp. is etiologic agent contagious bovine pleuropneumonia (CBPP), which still endemic in many parts Africa. We report genome sequences and annotation two frequently used challenge strains mycoides, Afadé B237. The information provided will enable downstream 'omics' applications such as proteomics, transcriptomics reverse vaccinology approaches. Despite absence pneumoniae like cyto-adhesion...
Members of the "Mycoplasma mycoides cluster" represent important livestock pathogens worldwide. We report genome sequence Mycoplasma feriruminatoris sp. nov., closest relative to and fastest-growing species described date.
Despite significant interest and past work to elucidate the phylogeny photochemistry of species Heliobacteriaceae, genomic analyses heliobacteria date have been limited just one published genome, that thermophilic Heliobacterium (Hbt.) modesticaldum str. Ice1T. Here we present an analysis complete genome a second heliobacterium, Heliorestis (Hrs.) convoluta HHT, alkaliphilic, mesophilic, morphologically distinct heliobacterium isolated from Egyptian soda lake. The Hrs. is single circular...
ABSTRACT Here, we report the complete genome sequence of Bifidobacterium pseudolongum strain UMB-MBP-01, isolated from feces C57BL/6J mice. This was identified in microbiome profiling studies and associated with improved transplant outcome a murine model cardiac heterotypic transplantation.
The 13,647-bp complete mitochondrial genome of Mansonella perstans was sequenced and is syntenic to the ozzardi . Phylogenetic analysis consistent with known phylogeny ONC5 group filarial nematodes.
ABSTRACT Infectious disease next generation sequencing (ID-NGS) diagnostics are on the cusp of revolutionizing clinical market. To facilitate this transition, FDA proactively invested in tools to support innovation emerging technologies. and collaborators established a publicly available database, dAtabase for Regulatory-Grade micrObial Sequences (FDA-ARGOS), as tool fill reference database gaps with quality-controlled genomes. This manuscript discusses quality control metrics proposed...
Here, we present the complete genome sequence of Wolbachia endosymbiont wAna, isolated from Drosophila ananassae and derived Oxford Nanopore Illumina sequencing. We anticipate that this will aid in comparative genomics assembly D. specifically regions containing extensive lateral gene transfer events.
Abstract The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables users to discover datasets from across the U.S. National Institutes Health without requiring owners move, reformat, or rehost those data. CFDE’s is centered on catalog ingests metadata individual Program’s Coordination Centers (DCCs) into uniform model can then be indexed and searched centralized portal. This Crosscut Metadata Model (C2M2) supports wide variety types terms used by...
Brugia pahangi is a zoonotic parasite that closely related to human-infecting filarial nematodes. Here, we report the nearly complete genome of pahangi, including assemblies four autosomes and an X chromosome, with only seven gaps. The Y chromosome still not completely assembled.
Erwinia dacicola is a dominant endosymbiont of the pestiferous olive fly. Its genome similar in size and GC content to those free-living species, including plant pathogen amylovora. The E. encodes metabolic capability supplement detoxify fly's diet larval adult stages.
Enterobacter sp. strain OLF colonizes laboratory-reared and wild individuals of the olive fruit fly Bactrocera oleae. The 5.07-kbp genome sequence encodes metabolic pathways that allow bacterium to partially supplement diet when its dominant endosymbiont, Erwinia dacicola, is absent.
Lymphatic filariasis is a devastating disease caused by filarial nematode roundworms, which contain obligate