Lenore Pipes

This paper presents a statistical framework for correcting SARS-CoV-2 genomic sequences using phylogenetic priors, improving call rate and accuracy in challenging regions.

The paper introduces ratePlacer, a method for dating ancient environmental DNA by accounting for DNA damage, showing it outperforms existing methods but highlights challenges in age estimation.

The paper benchmarks enrichment methods for sequencing low-abundance Influenza A Virus in wastewater and identifies suitable approaches for surveillance.

The paper introduces a fast approximate likelihood method for phylogenetic assignment of DNA sequences, showing improved accuracy in taxonomic classification compared to existing methods.

The paper evaluates nine computational tools for identifying SARS-CoV-2 lineages in wastewater sequencing data using simulated samples, finding most tools reliably detect lineages above 5% frequency.

AncestralClust clusters divergent nucleotide sequences by reconstructing ancestral sequences and using a greedy algorithm, showing higher accuracy and more even cluster sizes than existing methods.

The paper introduces Anacapa, a toolkit for processing multilocus eDNA metabarcoding data, enabling comprehensive reference database creation and accurate taxonomic assignment.

The paper describes the CALeDNA program, a community science initiative that uses environmental DNA to monitor biodiversity in California, providing public access to biodiversity data and analysis tools.

The paper investigates factors affecting transcriptome assembly quality, finding that input RNA-Seq data quality and base-calling accuracy are more critical than coverage.