A5007833252- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Acute Myeloid Leukemia Research
- Genetics, Bioinformatics, and Biomedical Research
- Protein Degradation and Inhibitors
- Scientific Computing and Data Management
- Physiological and biochemical adaptations
- Single-cell and spatial transcriptomics
- Genomics and Rare Diseases
- Cell Image Analysis Techniques
- Genetics, Aging, and Longevity in Model Organisms
- Cancer Genomics and Diagnostics
- Research Data Management Practices
- bioluminescence and chemiluminescence research
- Molecular Biology Techniques and Applications
- Atherosclerosis and Cardiovascular Diseases
- Chronic Myeloid Leukemia Treatments
- Evolution and Paleontology Studies
- Congenital heart defects research
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Toxoplasma gondii Research Studies
- Genomics and Chromatin Dynamics
- Mitochondrial Function and Pathology
Cincinnati Children's Hospital Medical Center
2018-2025
University of Oregon
2004-2024
Oregon Health & Science University
2010-2019
University of Cincinnati
2009
University of Calgary
2007-2008
Centre National de la Recherche Scientifique
2007
Université Paris-Sud
2007
Abstract In biology and biomedicine, relating phenotypic outcomes with genetic variation environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants be in genes that haven’t been characterized, research organisms recapitulate human or veterinary affecting disease are unknown undocumented, many resources must queried to find potentially significant associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack community-wide, consensus-based, human- machine-interpretable language for describing phenotypes genomic environmental contexts is perhaps most pressing scientific bottleneck integration across many key fields in biology, including genomics, systems development, medicine, evolution, ecology, systematics. Here we survey phenomics...
Abstract Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web-accessible resource that integrates diverse genomic and biological data from research on laboratory frogs laevis tropicalis. The goal of to accelerate discovery empower research, enhance impact data, facilitate dissemination these data. also enhances value through high-quality curation, integration, providing bioinformatics tools optimized for experiments, linking human other organisms. plays an...
The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides central location curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map positions, publications community resources facilitates use as a studying gene function, development, behavior disease. Access to ZFIN is provided via web-based query forms through bulk...
Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is principal centralized resource of genomic, development data community information research. Recent improvements include addition literature interaction tabs to gene catalog pages. New content has been added including a section on expression patterns that incorporates image from literature, large scale screens submissions. Gene are integrated into via an tab also searchable by multiple...
FLT3 mutations are prevalent in AML patients and confer poor prognosis. Crenolanib, a potent type I pan-FLT3 inhibitor, is effective against both internal tandem duplications resistance-conferring tyrosine kinase domain mutations. While crenolanib monotherapy has demonstrated clinical benefit heavily pretreated relapsed/refractory patients, responses transient relapse eventually occurs. Here, to investigate the mechanisms of resistance, we perform whole exome sequencing patient samples...
Xenbase (www.xenbase.org) is a model organism database integrating diverse array of biological and genomic data on the frogs, Xenopus laevis (Silurana) tropicalis. Data collected from other databases, high-throughput screens scientific literature integrated into number modules covering subjects such as community, literature, gene analysis. Gene pages are automatically assembled piped Entrez Gene, Gurdon Institute, JGI, Metazome, MGI, OMIM, PubMed, Unigene, Zfin, commercial suppliers others....
Xenbase (http://www.xenbase.org) is a model organism database that provides genomic, molecular, cellular and developmental biology content to biomedical researchers working with the frog, Xenopus data workers using other organisms. As an amphibian serves as useful evolutionary bridge between invertebrates more complex vertebrates such birds mammals. collated from variety of external sources automated semi-automated pipelines then processed via combination manual annotation. A link-matching...
Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, pivotal clinical use cases such as disease diagnostics treatment development. For over a century, vast quantities phenotype have been collected in many different contexts covering variety organisms. The emerging field phenomics focuses on integrating interpreting these to inform hypotheses. A major impediment is the wide range distinct disconnected approaches recording observable...
The skeleton is of fundamental importance in research comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by questions that require computational access to reasoning across the diverse skeletal phenotypes vertebrates, we developed a module anatomical concepts for system, Vertebrate Skeletal Anatomy Ontology (VSAO), accommodate unify existing terminologies species-specific (mouse, frog Xenopus, zebrafish) multispecies (teleost,...
Abstract Background The frogs Xenopus laevis and (Silurana) tropicalis are model systems that have produced a wealth of genetic, genomic, developmental information. Xenbase is organism database provides centralized access to this information, including gene function data from high-throughput screens the scientific literature. A controlled, structured vocabulary for anatomy development essential organizing these data. Results We constructed anatomical ontology represents lineage tissues...
The African clawed frogs Xenopus laevis and tropicalis are prominent animal model organisms. research contributes to the understanding of genetic, developmental molecular mechanisms underlying human disease. Anatomy Ontology (XAO) reflects anatomy embryological development Xenopus. XAO provides consistent terminology that can be applied anatomical feature descriptions along with a set relationships indicate how each entity is related others in embryo, tadpole, or adult frog. integral...
Development of biocuration processes and guidelines for new data types or projects is a challenging task. Each project finds its way toward defining annotation standards ensuring consistency with varying degrees planning different tools to support and/or report on consistency. Further, this process may be type specific even within the context single project. This article describes our experiences eagle-i, 2-year pilot develop federated network repositories in which unpublished, unshared...
Ocular toxoplasmosis is the commonest clinical manifestation of infection with obligate intracellular parasite, Toxoplasma gondii. Active ocular characterized by replication T. gondii tachyzoites in retina, reactive inflammation. The multifunctional retinal pigment epithelium a key target cell population for Since global gene expression profile germane to understanding molecular involvements epithelial cells toxoplasmosis, we performed RNA-Sequencing (RNA-Seq) human following tachyzoites....
Abstract Background Ontologies of precisely defined, controlled vocabularies are essential to curate the results biological experiments such that data machine searchable, can be computationally analyzed, and interoperable across biomedical research continuum. There is also an increasing need for methods interrelate phenotypic easily accurately from in animal models with human development disease. Results Here we present Xenopus phenotype ontology (XPO) annotate , one major vertebrate model...
Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much knowledge these organisms has not previously been codified in a machine-readable way using modern web standards.The Ontology is intended standardized coding system for sponge anatomical features...