Publications by authors named "L E Waldron"
Prokaryote evolution is driven in large part by the incessant arms race with viruses. Genomic investments in antivirus defense can be coarsely classified into two categories, immune systems that abrogate virus reproduction resulting in clearance, and altruistic programmed cell death (PCD) systems. Prokaryotic defense systems are enormously diverse, as revealed by an avalanche of recent discoveries, but the basic ecological determinants of defense strategy remain poorly understood.
View Article and Find Full Text PDFAdvancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows.
View Article and Find Full Text PDFSummary: LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal-Wallis test, Wilcoxon Rank-Sum test, and Linear Discriminant Analysis. R/Bioconductor provides a large collection of tools for metagenomic data analysis but has lacked an implementation of this widely used algorithm, hindering benchmarking against other tools and incorporation into R workflows. We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility.
View Article and Find Full Text PDFArticle Synopsis
- The study analyzes the oral microbiome of over 7,000 salivary samples from families with children diagnosed with autism spectrum disorders (ASD) to identify differences compared to neurotypical siblings.
- Researchers found 108 species that differentiate ASD subjects from neurotypical counterparts, with specific connections to cognitive impairment measured by IQ.
- The findings suggest potential links between the oral microbiome and neurodevelopmental factors related to ASD, while noting that lifestyle differences might also play a role.
Motivation: Software is vital for the advancement of biology and medicine. Impact evaluations of scientific software have primarily emphasized traditional citation metrics of associated papers, despite these metrics inadequately capturing the dynamic picture of impact and despite challenges with improper citation.
Results: To understand how software developers evaluate their tools, we conducted a survey of participants in the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI).