Scott T. Kelley
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View article: OR02-08 Necessity of the Gut Microbiome for Aspects of Metabolic Dysregulation in a Polycystic Ovary Syndrome Mouse Model
OR02-08 Necessity of the Gut Microbiome for Aspects of Metabolic Dysregulation in a Polycystic Ovary Syndrome Mouse Model Open
Disclosure: J. Brown: None. K. Twigg: None. S. Dhanala: None. L. Le: None. P. Jayaram: None. K. Nanavati: None. S. Kelley: None. V.G. Thackray: None. Background: Polycystic ovary syndrome (PCOS) is an endocrine disorder that affects 10-15%…
View article: Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis
Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis Open
Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengt…
View article: Influence of menstrual cycle and oral contraception on taxonomic composition and gas production in the gut microbiome
Influence of menstrual cycle and oral contraception on taxonomic composition and gas production in the gut microbiome Open
Introduction. Oral contraceptives (OCs) are widely used for birth control and offer benefits such as menstrual cycle regulation and reduced menstrual pain. However, they have also been associated with an increased risk of cancer and reduce…
View article: To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question
To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question Open
Untargeted metabolomics often produce large datasets with missing values. These missing values are derived from biological or technical factors and can undermine statistical analyses and lead to biased biological interpretations. Imputatio…
View article: PyBootNet: a python package for bootstrapping and network construction
PyBootNet: a python package for bootstrapping and network construction Open
Background Network analysis has emerged as a tool for investigating interactions among species in a community, interactions among genes or proteins within cells, or interactions across different types of data ( e.g. , genes and metabolites…
View article: To impute or not to impute in untargeted metabolomics - that is the compositional question
To impute or not to impute in untargeted metabolomics - that is the compositional question Open
Untargeted metabolomics often produce large datasets with missing values, arising from biological or technical factors, which can undermine statistical analyses and lead to biased biological interpretations. Imputation methods, such as k-N…
View article: PyBootNet: A Python Package for Bootstrapping and Network Construction
PyBootNet: A Python Package for Bootstrapping and Network Construction Open
PyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics amon…
View article: Point-of-Care Ultrasound Track in an Academic Family Medicine Department
Point-of-Care Ultrasound Track in an Academic Family Medicine Department Open
Introduction: Point-of-care ultrasound (POCUS) is increasingly being employed in family medicine. Residency tracks can be an effective way to increase mastery in a specific subdiscipline for interested residents, but no studies exist on th…
View article: AncFlow: An Ancestral Sequence Reconstruction Approach for Determining Novel Protein Structural
AncFlow: An Ancestral Sequence Reconstruction Approach for Determining Novel Protein Structural Open
The rapid growth of sequence data from high-throughput sequencing technologies has unveiled a vast number of previously unknown proteins, presenting a significant challenge in their functional characterization. Ancestral sequence reconstru…
View article: Genetic hypogonadal (Gnrh1<sup>hpg</sup>) mouse model uncovers influence of reproductive axis on maturation of the gut microbiome during puberty
Genetic hypogonadal (Gnrh1<sup>hpg</sup>) mouse model uncovers influence of reproductive axis on maturation of the gut microbiome during puberty Open
The gut microbiome plays a key role in human health and gut dysbiosis is linked to many sex-specific diseases including autoimmune, metabolic, and neurological disorders. Activation of the hypothalamic-pituitary-gonadal (HPG) axis during p…
View article: AutoPhy: Automated phylogenetic identification of novel protein subfamilies
AutoPhy: Automated phylogenetic identification of novel protein subfamilies Open
Phylogenetic analysis of protein sequences provides a powerful means of identifying novel protein functions and subfamilies, and for identifying and resolving annotation errors. However, automation of functional clustering based on phyloge…
View article: Data-driven mathematical and visualization approaches for removing rare features for Compositional Data Analysis (CoDA)
Data-driven mathematical and visualization approaches for removing rare features for Compositional Data Analysis (CoDA) Open
Sparse feature tables, in which many features are present in very few samples, are common in big biological data (e.g. metagenomics). Ignoring issues of zero-laden datasets can result in biased statistical estimates and decreased power in …
View article: Metagenomic analysis of microbial communities and antibiotic resistant genes in the Tijuana river, and potential sources
Metagenomic analysis of microbial communities and antibiotic resistant genes in the Tijuana river, and potential sources Open
The Tijuana River is a transborder river that flows northwest across the border from Baja California in Mexico into Southern California before discharging into the Pacific Ocean. The river is frequently contaminated with raw sewage due to …
View article: Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities
Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities Open
View article: Metabolic dysregulation and gut dysbiosis linked to hyperandrogenism in female mice
Metabolic dysregulation and gut dysbiosis linked to hyperandrogenism in female mice Open
Introduction Polycystic ovary syndrome (PCOS) is a common endocrine pathology in women. In addition to infertility, women with PCOS have metabolic dysregulation which predisposes them to Type 2 diabetes, cardiovascular disease and non‐alco…
View article: Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils
Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils Open
Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Dist…
View article: Hypogonadal (Gnrh1<sup>hpg</sup>) mice reveal niche-specific influence of reproductive axis and sex on intestinal microbial communities
Hypogonadal (Gnrh1<sup>hpg</sup>) mice reveal niche-specific influence of reproductive axis and sex on intestinal microbial communities Open
The gut microbiome has been linked to many diseases with sex bias including autoimmune, metabolic, neurological, and reproductive disorders. Numerous studies report sex differences in fecal microbial communities, but how this differentiati…
View article: Data-Driven Mathematical Approach for Removing Rare Features in Zero-Inflated Datasets
Data-Driven Mathematical Approach for Removing Rare Features in Zero-Inflated Datasets Open
Sparse feature tables, in which many features are present in very few samples, are common in big biological data (e.g., metagenomics, transcriptomics). Ignoring the problem of zero-inflation can result in biased statistical estimates and d…
View article: Escaping the heat: Climate change and visitation to the Lake Tahoe basin
Escaping the heat: Climate change and visitation to the Lake Tahoe basin Open
The Lake Tahoe Basin of California and Nevada is a popular destination for visitors. As temperatures rise globally, visitation to this climatic refuge is likely to grow. Increased visitation contributes to increases in vehicle miles of tra…
View article: Metagenome-Assembled Genomes from Murine Fecal Microbiomes Dominated by Uncharacterized Bacteria
Metagenome-Assembled Genomes from Murine Fecal Microbiomes Dominated by Uncharacterized Bacteria Open
The laboratory mouse gut microbiome has been extensively studied, but our understanding of its diversity remains incomplete. We report the assembly of 51 draft metagenome-assembled genomes (MAGs) from murine fecal samples dominated by unch…
View article: Point of Care Ultrasound Track at One Year in an Academic Family Medicine Department
Point of Care Ultrasound Track at One Year in an Academic Family Medicine Department Open
Point of care ultrasound (POCUS) is the bedside acquisition and interpretation of sonograms and is rapidly expanding in ambulatory primary care. Our department built a POCUS curriculum through obtaining an ultrasound fellowship-trained phy…
View article: Metagenomic Analysis of Microbial Communities in the Tijuana River, Antibiotic Resistant Genes, and Potential Sources
Metagenomic Analysis of Microbial Communities in the Tijuana River, Antibiotic Resistant Genes, and Potential Sources Open
View article: Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed
Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed Open
The Tijuana River watershed is binational, flowing from Tijuana, Mexico into San Diego and Imperial Beach, USA. Aging sewage and stormwater infrastructure in Tijuana has not kept pace with population growth, causing overflows into this wat…
View article: Sex, puberty, and the gut microbiome
Sex, puberty, and the gut microbiome Open
In brief Sex differences in the gut microbiome may impact multiple aspects of human health and disease. In this study, we review the evidence for microbial sex differences in puberty and adulthood and discuss potential mechanisms driving d…
View article: Socially Distanced Teaching: Faculty Feedback on Teaching During Telemedicine
Socially Distanced Teaching: Faculty Feedback on Teaching During Telemedicine Open
View article: AutoPhy: Automated phylogenetic identification of novel protein subfamilies
AutoPhy: Automated phylogenetic identification of novel protein subfamilies Open
Phylogenetic analysis of protein sequences provides a powerful means of identifying novel protein functions and subfamilies, and for identifying and resolving annotation errors. However, automation of functional clustering based on phyloge…
View article: Automated high confidence compound identification of electron ionization mass spectra for nontargeted analysis
Automated high confidence compound identification of electron ionization mass spectra for nontargeted analysis Open
Nontargeted analysis based on mass spectrometry is a rising practice in environmental monitoring for identifying contaminants of emerging concern. Nontargeted analysis performed using comprehensive two-dimensional gas chromatography couple…
View article: Gut Metabolites Are More Predictive of Disease and Cohoused States than Gut Bacterial Features in a Polycystic Ovary Syndrome-Like Mouse Model
Gut Metabolites Are More Predictive of Disease and Cohoused States than Gut Bacterial Features in a Polycystic Ovary Syndrome-Like Mouse Model Open
Using a combination of untargeted metabolomics and metagenomics, we performed a comparative longitudinal analysis of the feces collected in a cohousing study with a PCOS-like mouse model. Our results showed that gut metabolite composition …
View article: Compositional Data Analysis of Periodontal Disease Microbial Communities
Compositional Data Analysis of Periodontal Disease Microbial Communities Open
Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Culture-independent methods, such as next-generation sequencing (NGS) of bacteria 16S amplicon and shotgun metagenomic lib…
View article: Altered microbiomes in thirdhand smoke-exposed children and their home environments
Altered microbiomes in thirdhand smoke-exposed children and their home environments Open