A5085958503- Biomedical Text Mining and Ontologies
- Topic Modeling
- Natural Language Processing Techniques
- Bacteriophages and microbial interactions
- Microbial infections and disease research
- Poxvirus research and outbreaks
- Bioinformatics and Genomic Networks
- Bacillus and Francisella bacterial research
- Biomedical and Engineering Education
- Machine Learning in Healthcare
- Genomics and Phylogenetic Studies
- Aquaculture disease management and microbiota
- Genetics, Bioinformatics, and Biomedical Research
- Geriatric Care and Nursing Homes
- Hormonal Regulation and Hypertension
- Gene expression and cancer classification
- Herpesvirus Infections and Treatments
- Intensive Care Unit Cognitive Disorders
- Family and Patient Care in Intensive Care Units
- Pituitary Gland Disorders and Treatments
- Adrenal and Paraganglionic Tumors
- Virology and Viral Diseases
- Semantic Web and Ontologies
- Electronic Health Records Systems
- Blood groups and transfusion
University of Alabama at Birmingham
2014-2025
Naval Information Warfare Center Pacific
2008
Centers for Disease Control and Prevention
2006-2007
Northwestern University
2007
National Center for Emerging and Zoonotic Infectious Diseases
2006
Imperial College London
2006
Universität der Bundeswehr München
2006
Institut für Mikrobiologie der Bundeswehr
2006
National Center for Infectious Diseases
2006
University of Victoria
2002
The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally diseases.We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as directed acyclic graph (the Disease Ontology), filter interpret results MMTx. were validated against Homayouni gene collection using...
This study reports a comprehensive environmental scan of the generative AI (GenAI) infrastructure in national network for clinical and translational science across 36 institutions supported by CTSA Program led National Center Advancing Translational Sciences (NCATS) Institutes Health (NIH) at United States. Key findings indicate diverse range institutional strategies, with most organizations experimental phase GenAI deployment. The results underscore need more coordinated approach to...
Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years smallpox era indicate low sequence diversity, suggesting that there is probably little difference in isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; latter implicated putative proteins mediate viral virulence differences. Analysis linear DNA genome suggests its evolution involved direct descent...
There are over 6,000 different rare diseases estimated to impact 300 million people worldwide. As genetic testing becomes more common practice in the clinical setting, number of disease diagnoses will continue increase, resulting need for novel treatment options. Identifying treatments these disorders is challenging due a limited understanding mechanisms, small cohort sizes, interindividual symptom variability, and little commercial incentive develop new treatments. A promising avenue drug...
Several mycoplasma species have been shown to form biofilms that confer resistance antimicrobials and which may affect the host immune system, thus making treatment eradication of pathogens difficult. The present study shows formed by two strains human pathogen Mycoplasma pneumoniae differ quantitatively qualitatively. Compared with strain UAB PO1, M129 grows well but forms are less robust, towers smooth at margins. A polysaccharide containing N-acetylglucosamine is secreted into culture...
Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40 % community-acquired pneumonias. It also wide array extrapulmonary autoimmune phenomena. Phylogenetic studies the organism have been generally restricted specific genes or regions genome, because whole genome sequencing has completed only 4 strains. To better understand physiology pathogenicity this important human pathogen, we performed...
To help cancer registrars efficiently and accurately identify reportable cases.The Cancer Registry Control Panel (CRCP) was developed to detect mentions of cases using a pipeline built on the Unstructured Information Management Architecture - Asynchronous Scaleout (UIMA-AS) architecture containing National Library Medicine's UIMA MetaMap annotator as well variety rule-based annotators that primarily act filter out concepts referring nonreportable cancers. CRCP inspects pathology reports...
Electronic health record (EHR) data are a rich and invaluable source of real-world clinical information, enabling detailed insights into patient populations, treatment outcomes, healthcare practices. The availability large volumes EHR critical for advancing translational research developing innovative technologies such as artificial intelligence. Evolve to Next-Gen Accrual Clinical Trials (ENACT) network, established in 2015 with funding from the National Center Advancing Translational...
Despite recent methodology advancements in clinical natural language processing (NLP), the adoption of NLP models within translational research community remains hindered by process heterogeneity and human factor variations. Concurrently, these factors also dramatically increase difficulty developing multi-site settings, which is necessary for algorithm robustness generalizability. Here, we reported on our experience an solution Coronavirus Disease 2019 (COVID-19) signs symptom extraction...
Abstract Background Hospital‐associated disability (HAD) is a common complication during the course of acute care hospitalizations in older adults. Many admissions are for ambulatory sensitive conditions (ACSCs), considered potentially avoidable hospitalizations—conditions that might be treated outpatient settings to prevent hospitalization and HAD. We compared incidence HAD between adults hospitalized ACSCs versus those other diagnoses. Methods conducted retrospective cohort study inpatient...
Abstract Summary: Poxvirus Orthologous Clusters (POCs) is a JAVA client–server application which accesses an updated database containing all complete poxvirus genomes; it automatically groups orthologous genes into families based on BLASTP scores for assessment by human curator. POCs has user-friendly interface permitting complex SQL queries to retrieve interesting of DNA and protein sequences as well gene subsequent interrogation variety integrated tools: BLASTP, BLASTX, TBLASTN, Jalview...
Mycoplasma iowae is a well-established avian pathogen that can infect and damage many sites throughout the body. One potential mediator of cellular by mycoplasmas production H2O2 via glycerol catabolic pathway whose genes are widespread amongst mycoplasma species. Previous sequencing M. serovar I strain 695 revealed presence not only for through catabolism but also first documented gene catalase, which degrades H2O2. To test activity catalase in degrading H2O2, we studied accumulation both K...
Vaccinia virus (VACV)-DUKE was isolated from a lesion on 54 year old female who presented to doctor at the Duke University Medical Center. She diagnosed with progressive vaccinia and treated immune globulin. The availability of VACV-DUKE genome sequence permits first time genomic comparison VACV isolate associated smallpox vaccine complication culture-derived clonal isolates Dryvax vaccine.This study showed that is most similar VACV-ACAM2000 CLONE3, two clones stock confirming as an Dryvax....
We developed a set of seven resequencing GeneChips, based on the complete genome sequences 24 strains smallpox virus (variola virus), for rapid characterization this human-pathogenic virus. Each GeneChip was designed to analyze divergent segment approximately 30,000 bases genome. This study includes hybridization results 14 strains. Of hybridized, only 7 had sequence information included in design GeneChips; similar remaining not tiled as reference these GeneChips. By use variola...
Hymenobacter sp. IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica, produces extracellular polymeric substance (EPS) and manifests tolerance to cold, UV radiation (UVR), oxidative stress. We report the 5.26-Mb draft genome of strain which will help us understand its adaptation survival mechanisms Antarctic extreme ecosystems.
We used MetaMap and YTEX as a basis for the construc- tion of two separate systems to participate in 2013 ShARe/CLEF eHealth Task 1[9], recognition clinical concepts. No modifications were directly made these systems, but output concepts filtered using stop concepts, concept text UMLS semantic type. Con- cept boundaries also adjusted small collection rules increase precision on strict task. Overall had better per- formance than task, primarily due 20% perfor- mance improvement precision. In...