Kelsey M. Beavers
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View article: A Model for Teaching Machine Learning, Deep Learning, and Research Computing to Domain Scientists on HPC Resources
A Model for Teaching Machine Learning, Deep Learning, and Research Computing to Domain Scientists on HPC Resources Open
View article: Leveraging machine learning to classify and characterize gene expression patterns in two coral diseases
Leveraging machine learning to classify and characterize gene expression patterns in two coral diseases Open
Anthropogenic climate change has had devastating effects on the Florida and Caribbean reef systems, in part due to increased disease outbreaks. Climate change exacerbates marine diseases by expanding pathogen ranges and heightening host su…
View article: Machine learning reveals distinct gene expression signatures across tissue states in stony coral tissue loss disease
Machine learning reveals distinct gene expression signatures across tissue states in stony coral tissue loss disease Open
Stony coral tissue loss disease (SCTLD) has rapidly degraded Caribbean reefs, compounding climate-related stressors and threatening ecosystem stability. Effective intervention requires understanding the mechanisms driving disease progressi…
View article: Characterizing gene expression profiles of various tissue states in stony coral tissue loss disease using a feature selection algorithm
Characterizing gene expression profiles of various tissue states in stony coral tissue loss disease using a feature selection algorithm Open
Stony coral tissue loss disease (SCTLD) remains a substantial threat to coral reef diversity already threatened by global climate change. Restoration efforts and effective treatment of SCTLD requires an in-depth understanding of its pathog…
View article: Trade-off between photosymbiosis and innate immunity influences cnidarian’s response to pathogenic bacteria
Trade-off between photosymbiosis and innate immunity influences cnidarian’s response to pathogenic bacteria Open
Mutualistic relationships with photosynthetic organisms are common in cnidarians, which form an intracellular symbiosis with dinoflagellates in the family Symbiodiniaceae. The establishment and maintenance of these symbionts are associated…
View article: Machine Learning Approaches for Classifying and Characterizing Coral Diseases
Machine Learning Approaches for Classifying and Characterizing Coral Diseases Open
Background: Anthropogenic climate change has had devastating effects on the Florida and Caribbean reef systems, primarily due to increased disease outbreaks. Climate change contributes to the rising frequency of marine diseases by expandin…
View article: Structural and Evolutionary Relationships of Melanin Cascade Proteins in Cnidarian Innate Immunity
Structural and Evolutionary Relationships of Melanin Cascade Proteins in Cnidarian Innate Immunity Open
Synopsis Melanin is an essential product that plays an important role in innate immunity in a variety of organisms across the animal kingdom. Melanin synthesis is performed by many organisms using the tyrosine metabolism pathway, a general…
View article: Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae
Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae Open
View article: Master Coral database used in USVI SCTLD Transmission Experiment Gene Expression Analysis
Master Coral database used in USVI SCTLD Transmission Experiment Gene Expression Analysis Open
The Master Coral Database fasta file is comprised of previously published genome-derived predicted gene models and transcriptomes spanning a wide diversity of coral families. Transcriptomes are from Davies et al., 2016 (doi: 10.3389/fmars.…
View article: Master Coral database used in USVI SCTLD Transmission Experiment Gene Expression Analysis
Master Coral database used in USVI SCTLD Transmission Experiment Gene Expression Analysis Open
The Master Coral Database fasta file is comprised of previously published genome-derived predicted gene models and transcriptomes spanning a wide diversity of coral families. Transcriptomes are from Davies et al., 2016 (doi: 10.3389/fmars.…
View article: Advances in coral immunity ‘omics in response to disease outbreaks
Advances in coral immunity ‘omics in response to disease outbreaks Open
Coral disease has progressively become one of the most pressing issues affecting coral reef survival. In the last 50 years, several reefs throughout the Caribbean have been severely impacted by increased frequency and intensity of disease …
View article: Disease resistance in coral is mediated by distinct adaptive and plastic gene expression profiles
Disease resistance in coral is mediated by distinct adaptive and plastic gene expression profiles Open
Infectious diseases are an increasing threat to coral reefs, resulting in altered community structure and hindering the functional contributions of disease-susceptible species. We exposed seven reef-building coral species from the Caribbea…
View article: Alphaflexivirus Genomes in Stony Coral Tissue Loss Disease-Affected, Disease-Exposed, and Disease-Unexposed Coral Colonies in the U.S. Virgin Islands
Alphaflexivirus Genomes in Stony Coral Tissue Loss Disease-Affected, Disease-Exposed, and Disease-Unexposed Coral Colonies in the U.S. Virgin Islands Open
Stony coral tissue loss disease (SCTLD) is decimating Caribbean corals. Here, through the metatranscriptomic assembly and annotation of two alphaflexivirus-like strains, we provide genomic evidence of filamentous viruses in SCTLD-affected,…