A5039491087- Biomedical Text Mining and Ontologies
- vaccines and immunoinformatics approaches
- Vector-borne infectious diseases
- Bioinformatics and Genomic Networks
- Microbial infections and disease research
- Semantic Web and Ontologies
- Genomics and Phylogenetic Studies
- Mosquito-borne diseases and control
- Malaria Research and Control
- Insect symbiosis and bacterial influences
- Genomics and Rare Diseases
- Insect-Plant Interactions and Control
- Hymenoptera taxonomy and phylogeny
- Scientific Computing and Data Management
- Healthcare cost, quality, practices
- Vector-Borne Animal Diseases
- Neurobiology and Insect Physiology Research
- Topic Modeling
- Research Data Management Practices
- Aquatic Invertebrate Ecology and Behavior
- Sentiment Analysis and Opinion Mining
- Viral Infections and Vectors
- Potato Plant Research
- Patient Satisfaction in Healthcare
- Legume Nitrogen Fixing Symbiosis
Opinion (Norway)
2024
University of Maryland, Baltimore
2013-2023
Animal and Plant Health Inspection Service
2023
University System of Maryland
2019
East Stroudsburg University
2017
University of Baltimore
2016
UC Davis Comprehensive Cancer Center
2013
University of California, Riverside
2005-2011
Massachusetts Institute of Technology
2010
University of Stirling
2010
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 Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. DO disease classification includes specific formal semantic rules to express meaningful models and expanded from a single asserted include multiple-inferred mechanistic classifications, thus providing novel perspectives on related diseases. Expansion of terms, alternative anatomy, cell type genetic classifications workflow automation highlight updates for...
Chalcidoidea (Hymenoptera) is extremely diverse with an estimated 500 000 species. We present the first phylogenetic analysis of superfamily based on both morphological and molecular data. A web-based, systematics workbench mx was used to score 945 character states illustrated by 648 figures for 233 characters a total 66 645 observations 300 taxa. The matrix covers 22 chalcidoid families recognized herein includes 268 genera within 78 83 subfamilies. Morphological data were analysed alone in...
The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase website since DO's 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from DO have been annotated to over 1.5 million biomedical data elements citations, a 10× increase in past 5 years. DO, funded as NHGRI Genomic Resource, plays key role knowledge organization, representation,...
Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to proliferated during terrestrial colonization by insects (hexapods), association with other pancrustacean clades independent colonizations arthropod...
Chalcidoidea (Hymenoptera) are extremely diverse with more than 23,000 species described and over 500,000 estimated to exist. This is the first comprehensive phylogenetic analysis of superfamily based on a molecular 18S 28S ribosomal gene regions for 19 families, 72 subfamilies, 343 genera 649 species. The 56 outgroups comprised Ceraphronoidea most proctotrupomorph including Mymarommatidae. Data alignment impact ambiguous explored using secondary structure automated (MAFFT) alignments core...
A novel apicomplexan parasite was serendipitously discovered in horses at the United States – Mexico border. Phylogenetic analysis based on 18S rDNA showed erythrocyte-infective to be related to, but distinct from, Theileria spp. Africa, most similar taxa being from waterbuck and mountain zebra. The degree of sequence variability observed locus also suggests likely existence additional cryptic species. Among described species, genome this equid is that equi, a pathogen horses. estimated...
We analyze the secondary structure of two expansion segments (D2, D3) 28S ribosomal (rRNA)-encoding gene region from 527 chalcidoid wasp taxa (Hymenoptera: Chalcidoidea) representing 18 19 extant families. The sequences are compared in a multiple sequence alignment, with inferred primarily evidence compensatory base changes conserved helices rRNA molecules. This covariation analysis yielded 36 that composed pairs exhibiting positional covariation. Several additional regions also involved...
Next-generation patients are far from being peripheral to health-care. They central understanding the effectiveness and efficiency of services how they can be improved. Today a lot used reviewing local health on-line but this social information is just stored in natural language text it not machine-accessible machine-processable. To distil knowledge extremely unstructured we use Sentic Computing, new opinion mining sentiment analysis paradigm which exploits AI Semantic Web techniques better...
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...
Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed significantly higher durable homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation these results and understanding their relevance vaccine efficacy hampered by lack knowledge on genetic differences between...
With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, high-resolution method for assignment genera species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from lengths sequence identities core alignments along with phylogenetic analyses, evaluate or reevaluate genus- species-level diverse taxa, an emphasis on order Rickettsiales , where have been applied inconsistently. Our results...
Abstract In 2003, the Human Disease Ontology (DO, https://disease-ontology.org/) was established at Northwestern University. intervening 20 years, DO has expanded to become a highly-utilized disease knowledge resource. Serving as nomenclature and classification standard for human diseases, provides stable, etiology-based structure integrating mechanistic drivers of disease. Over past two decades grown from collection clinical vocabularies, into an expertly curated semantic resource over...
Approximately 30 years ago, it was discovered that free-living bacteria isolated from cold ocean depths could produce polyunsaturated fatty acids (PUFA) such as eicosapentaenoic acid (EPA) (20:5n-3) or docosahexaenoic (DHA) (22:6n-3), two PUFA essential for human health. Numerous laboratories have also EPA- and/or DHA-producing bacteria, many of them members the Shewanella genus, be intestinal tracts omega-3 acid-rich marine fish. If contribute to host fish in general if they assist some...
Significance Nontypeable Haemophilus influenzae (NTHi) exclusively colonize and infect humans play an important role in the course pathogenesis of chronic obstructive pulmonary disease (COPD). We conducted whole-genome sequencing 269 NTHi isolates from a 15-y prospective study COPD to assess vivo adaption NTHi. uses slipped-strand mispairing simple sequence repeats regulate critical virulence functions as primary mechanism adapt survival human airways. Analyses changes 12 candidate vaccine...
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...
Summary Identification of antigens targeted by a protective response is central quest in malaria vaccinology. Whole-genome sieve analysis (SA WG ) samples collected from placebo-controlled field trials Plasmodium falciparum (Pf) sporozoite (SPZ) vaccines may enable identification Pf pre-erythrocytic antigens. We applied SA to genomic data generated isolates during two measuring the efficacy, malaria-exposed African adults, PfSPZ vaccines. These randomized, double-blind, were conducted...
The evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject speculation and controversy. complete genome sequences the two most widespread parasites, P. falciparum vivax, monkey parasite knowlesi are now available, together with draft genomes chimpanzee reichenowi, three rodent yoelii yoelli, berghei chabaudi chabaudi, one avian parasite, gallinaceum.We present here an analysis 45 orthologous gene across eight species that resolves relationships major...
Saline migrants into freshwater habitats constitute among the most destructive invaders in aquatic ecosystems throughout globe. However, evolutionary and physiological mechanisms underlying such habitat transitions remain poorly understood. To explore of adaptation distinguish between adaptive (evolutionary) acclimatory (plastic) responses to salinity change, we examined genome-wide patterns gene expression ancestral saline derived populations Eurytemora affinis species complex, reared under...