This page contains papers from the Pipes Lab.

2024

A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets

Pipes & Nielsen. 2024. eLife.

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

Sutcliffe et al. 2024. Microbial Genomics.

2022

Estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples

Lenore Pipes, Chen, Afanaseva, and Nielsen. 2024. Cell Reports Methods.

2021

AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees

Pipes and Nielsen 2021. Bioinformatics.

Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny

Pipes et al. 2021. Molecular Biology and Evolution.

The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity

Meyer et al. 2021. California Agriculture.

Synonymous mutations and the molecular evolution of SARS-Cov-2 origins

Wang, Pipes, and Nielsen. 2021. Virus Evolution.

2019

Anacapa Toolkit: An environmental DNA toolkit for processing multilocus metabarcode datasets

Curd et al. 2019. Methods in Ecology and Evolution.