A5090030592- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Gut microbiota and health
- Wikis in Education and Collaboration
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Natural Language Processing Techniques
- Distributed and Parallel Computing Systems
- Machine Learning in Bioinformatics
- Scientific Computing and Data Management
- Alzheimer's disease research and treatments
- Metabolomics and Mass Spectrometry Studies
- Genetics, Bioinformatics, and Biomedical Research
University of Colorado Denver
2023-2025
University of Colorado Anschutz Medical Campus
2023-2025
Abstract Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, methods exist construct them automatically. However, tackling biomedical problems flexibility way knowledge is modeled. Moreover, existing KG construction provide robust tooling cost...
The integration of many disparate forms data is essential for understanding the microbial world and its interaction with environment human health. Doing so particularly challenging in context microbe-host microbe-microbe interactions that contribute to health or environmental outcomes. There are often thousands relevant species, millions among those microbes their host. Some experimental observations only distinguish coarser taxonomic resolutions such as family phylum-level. Integrated...
Knowledge graphs have been a useful tool for many biomedical applications because of their effective representation biological concepts. Plentiful evidence exists linking the gut microbiome to disease in correlative context, but uncovering mechanistic explanation those associations remains challenge. Here we demonstrate potential knowledge hypothesize plausible accounts host-microbe interactions disease. We constructed graph linked microbes, genes and metabolites called MGMLink, and, using...
Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, methods exist construct them automatically. However, tackling biomedical problems flexibility way knowledge is modeled. Moreover, existing KG construction provide robust tooling cost fixed or...
Knowledge graphs have found broad biomedical applications, providing useful representations of complex knowledge. Although plentiful evidence exists linking the gut microbiome to disease, mechanistic understanding those relationships remains generally elusive. Here we demonstrate potential knowledge hypothesize plausible accounts host-microbe interactions in disease. To do so, constructed a graph linked microbes, genes and metabolites called MGMLink. Using semantically constrained shortest...
Molecular "cartoons," such as pathway diagrams, provide a visual summary of biomedical research results and hypotheses. Their ubiquitous appearance within the literature indicates their universal application in mechanistic communication. A recent survey diagrams identified 64,643 figures published between 1995 2019 with 1,112,551 mentions 13,464 unique human genes participating wide variety biological processes. Researchers generally create these using generic diagram editing software that...
Knowledge graphs have found broad biomedical applications, providing useful representations of complex knowledge. Although plentiful evidence exists linking the gut microbiome to disease, mechanistic understanding those relationships remains generally elusive. A structured analysis existing resources is necessary characterize and methodologies needed facilitate inference.Here we demonstrate potential knowledge hypothesize plausible accounts host-microbe interactions in disease define need...