Jacob D. Davis
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View article: Utilization of phase I studies for target validation of first-in-class drugs
Utilization of phase I studies for target validation of first-in-class drugs Open
This review discusses the growing importance of target validation within phase I (P1) trials as a new trend in drug development, especially in establishing proof of concept (POC) for first-in-class drugs. The paper describes two approaches…
View article: Racial inequities and rare CFTR variants: Impact on cystic fibrosis diagnosis and treatment
Racial inequities and rare CFTR variants: Impact on cystic fibrosis diagnosis and treatment Open
View article: Mathematical models of cystic fibrosis as a systemic disease
Mathematical models of cystic fibrosis as a systemic disease Open
Cystic fibrosis (CF) is widely known as a disease of the lung, even though it is in truth a systemic disease, whose symptoms typically manifest in gastrointestinal dysfunction first. CF ultimately impairs not only the pancreas and intestin…
View article: Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models
Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models Open
Networks are ubiquitous throughout biology, spanning the entire range from molecules to food webs and global environmental systems. Yet, despite substantial efforts by the scientific community, the inference of these networks from data sti…
View article: Methods of quantifying interactions among populations using Lotka-Volterra models
Methods of quantifying interactions among populations using Lotka-Volterra models Open
The Lotka-Volterra (LV) model was introduced in the early 20th Century to describe predator-prey systems. Since then, the model has been expanded to capture the dynamics of numerous types of interacting populations and to include the effec…
View article: A Passaged 3-species Synthetic Microbial Community
A Passaged 3-species Synthetic Microbial Community Open
We constructed de novo a community of three model bacterial species, Vibrio cholerae, Staphylococcus aureus, and Escherichia coli, which all constitutively produce a distinct fluorescent protein. This fluorescenc…
View article: A Passaged 3-species Synthetic Microbial Community
A Passaged 3-species Synthetic Microbial Community Open
We constructed de novo a community of three model bacterial species, Vibrio cholerae, Staphylococcus aureus, and Escherichia coli, which all constitutively produce a distinct fluorescent protein. This fluorescenc…
View article: Antibiotics Drive Expansion of Rare Pathogens in a Chronic Infection Microbiome Model
Antibiotics Drive Expansion of Rare Pathogens in a Chronic Infection Microbiome Model Open
We develop and clinically benchmark an experimental model of the cystic fibrosis (CF) lung infection microbiome to investigate the impacts of antibiotic exposures on chronic, polymicrobial infections. We show that a single experimental mod…
View article: Comparison Between Lotka-Volterra and Multivariate Autoregressive Models of Ecological Interaction Systems
Comparison Between Lotka-Volterra and Multivariate Autoregressive Models of Ecological Interaction Systems Open
Lotka-Volterra (LV) and Multivariate Autoregressive (MAR) models are computational frameworks with different mathematical structures that have both been proposed for the same purpose of extracting governing features of dynamic interactions…
View article: Inference and Validation of The Structure of Lotka-Volterra Models
Inference and Validation of The Structure of Lotka-Volterra Models Open
For close to a century, Lotka-Volterra (LV) models have been used to investigate interactions among populations of different species. For a few species, these investigations are straightforward. However, with the arrival of large and compl…
View article: Inference and Validation of the Structure of Lotka-Volterra Models
Inference and Validation of the Structure of Lotka-Volterra Models Open
For close to a century, Lotka-Volterra (LV) models have been used to investigate interactions among populations of different species. For a few species, these investigations are straightforward. However, with the arrival of large and compl…
View article: Antibiotics drive expansion of rare pathogens in a chronic infection microbiome model
Antibiotics drive expansion of rare pathogens in a chronic infection microbiome model Open
Chronic (long-lasting) infections are globally a major and rising cause of morbidity and mortality. Unlike typical acute infections, chronic infections are ecologically diverse, characterized by the presence of a polymicrobial mix of oppor…
View article: The System of Cystic Fibrosis
The System of Cystic Fibrosis Open
Cystic fibrosis (CF) is caused by mutations in the gene encoding CFTR, an epithelial ion channel protein, yet the disease is truly systemic—CF is characterized not only by impairment of the lungs, but also by impairment of the pancreas, li…
View article: Models for Personalized Medicine
Models for Personalized Medicine Open
The customization of medicine to specific individuals promises clear improvements in disease treatment, but also faces substantial challenges, many of which have their roots in the complexity of the human body. This complexity cannot be gr…
View article: Dynamical systems approaches to personalized medicine
Dynamical systems approaches to personalized medicine Open
View article: Metrics for regulated biochemical pathway systems
Metrics for regulated biochemical pathway systems Open
Motivation The assessment of graphs through crisp numerical metrics has long been a hallmark of biological network analysis. However, typical graph metrics ignore regulatory signals that are crucially important for optimal pathway operatio…
View article: Generating tools to study protein quality control using Saccharomyces cerevisiae
Generating tools to study protein quality control using Saccharomyces cerevisiae Open
Proteins can occasionally behave aberrantly within the cell and cause a variety of physiological issues. Multiple pathways exist that resolve this problem and allow the cell to continue normal protein production. Endoplasmic Reticulum (ER)…