Susan M. Bello
A5084390524- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Semantic Web and Ontologies
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Research Data Management Practices
- Toxic Organic Pollutants Impact
- Genomics and Chromatin Dynamics
- Molecular Biology Techniques and Applications
- Animal Genetics and Reproduction
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- Nutrition, Genetics, and Disease
- RNA Research and Splicing
- Environmental Toxicology and Ecotoxicology
- Pharmaceutical and Antibiotic Environmental Impacts
- Single-cell and spatial transcriptomics
- Gender Roles and Identity Studies
- Genetic and phenotypic traits in livestock
- Cardiac tumors and thrombi
- Genetic Mapping and Diversity in Plants and Animals
- Fish Ecology and Management Studies
- Reproductive System and Pregnancy
- Bone fractures and treatments
Jackson Laboratory
2016-2025
University of Wisconsin–Madison
2001-2004
Woods Hole Oceanographic Institution
2001-2002
Instituto Nacional del Tórax
1982-1983
The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for laboratory mouse. MGD authoritative source biological reference data sets related to mouse genes, gene functions, phenotypes, models of human disease. primary outlet official gene, allele strain nomenclature based on guidelines set by International Committee Standardized Nomenclature Mice. In this report we describe significant enhancements MGD, including two new...
The Human Phenotype Ontology (HPO)—a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases—is used by thousands researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions clinical computable disease definitions have made HPO de facto standard for deep phenotyping in field rare disease. HPO's interoperability other ontologies has enabled it to be improve diagnostic accuracy incorporating model organism...
The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for laboratory mouse, a widely used animal comparative studies of genetic and genomic basis human health disease. MGD authoritative source biological reference data related to mouse genes, gene functions, phenotypes models primary official gene, allele, strain nomenclature based on guidelines set by International Committee Standardized Nomenclature Mice. MGD's biocuration scientists...
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...
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,...
Abstract The Alliance of Genome Resources (Alliance) is a consortium the major model organism databases and Gene Ontology that guided by vision facilitating exploration related genes in human well-studied organisms providing highly integrated comprehensive platform enables researchers to leverage extensive body genetic genomic studies these organisms. Initiated 2016, building central portal (www.alliancegenome.org) for access data primary along with gene ontology data. All types represented...
Abstract The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference supporting genomic analyses through semantic similarity machine learning algorithms. HPO has widespread applications in clinical diagnostics translational research, including diagnostics, gene-disease discovery, cohort analytics. In recent years, groups around world have developed translations from English...
The Alliance of Genome Resources (the Alliance) is a combined effort 7 knowledgebase projects: Saccharomyces Database, WormBase, FlyBase, Mouse the Zebrafish Information Network, Rat and Gene Ontology Resource. seeks to provide several benefits: better service various communities served by these projects; harmonized view data for all biomedical researchers, bioinformaticians, clinicians, students; more sustainable infrastructure. has cross-organism useful comparative views gene function,...
Abstract Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic genomic aspects human biology disease using the laboratory mouse as model system. The Database (MGD) Gene Expression (GXD) are core MGI databases that share data system architecture. serves central community resource integrated about genome features, variation, expression, gene function, phenotype, models acquired...
The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western experiments wild-type mutant mice. GXD's gene expression information integrated with the other Mouse Genome Informatics interconnected databases, placing these larger biological biomedical context. Since...
Abstract Despite progress in the development of standards for describing and exchanging scientific information, lack easy-to-use mapping between different representations same or similar objects databases poses a major impediment to data integration interoperability. Mappings often metadata needed be correctly interpreted applied. For example, are two terms equivalent merely related? Are they narrow broad matches? Or associated some other way? Such relationships mapped not documented, which...
New Bedford Harbor (NBH), MA, is a federal Superfund site that heavily contaminated with polychlorinated biphenyls (PCBs) and other halogenated aromatic hydrocarbons (HAHs), including some potent aryl hydrocarbon receptor (AhR) agonists. A population of Atlantic killifish (Fundulus heteroclitus) continues to inhabit this site, despite accumulating extraordinarily high concentrations PCBs (272 μg/g dry weight). To determine if NBH have developed resistance HAHs act through the AhR, we...
Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting integrating relevant model organism and/or data often apply disparate terminologies (vocabularies ontologies), making larger scale comparisons inferences challenging at best. A single ontology that connects annotated using diverse terminologies, in which terminology relationships applicable animal models continuously maintained, is needed. The Mouse Genome...
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...
Abstract Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation wild-type or other reference. However, these do not include the phenotypic trait attribute categories required for annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings any population-focussed measurable data. The integration and biological information with an ever increasing body chemical, environmental data greatly...
Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge an accurate computable form. However, their construction maintenance demand substantial resources necessitate collaboration between domain experts, curators, ontology experts. We present Dynamic Retrieval Augmented Generation using AI (DRAGON-AI), generation method employing Large Language Models (LLMs) (RAG). DRAGON-AI can...
A role for the aryl hydrocarbon receptor (AHR) pathway in vascular maturation has been implicated by studies Ahr-null mice. In this study hypothesis that activation of AHR signaling 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) alters common cardinal vein (CCV) development zebrafish embryo was investigated. The CCV is a paired vessel grows across yolk, connecting to heart. It extensively remodeled and regresses as heart migrates dorsally within pericardium. TCDD significantly reduced growth...
The use of ontologies to standardize biological data and facilitate comparisons among datasets has steadily grown as the complexity amount available have increased. Despite numerous available, one area currently lacking a robust ontology is description vertebrate traits. A trait defined any measurable or observable characteristic pertaining an organism its substructures. While there are several describe entities processes in phenotypes, diseases, clinical measurements, not been developed for...
A core part of the Mouse Genome Informatics (MGI) resource is collection mouse mutations and annotation phenotypes diseases displayed by mice carrying these mutations. These data are integrated with rest in MGI exported to numerous other resources. The use phenotype drive translational research into human disease has expanded rapidly improvements sequencing technology. implemented many allele annotation, search, display facilitate access through multiple avenues. For example, description...
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...