N. Tessa Pierce‐Ward

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

An interactive dashboard for global reports of the Ralstonia solanacearum species complex

The paper develops an interactive dashboard to visualize and analyze genetic diversity data of the Ralstonia solanacearum species complex, aiding in disease control and regulation.

Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances

This paper analyzes FracMinHash, showing it can be corrected for bias and used to estimate mutation distances with confidence intervals.

Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

The paper benchmarks taxonomic classification and profiling methods for long-read metagenomic datasets, finding long-read methods outperform short-read ones in precision and recall.

Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search

The paper introduces branchwater, a tool for fast petabase-scale sequence search across public metagenomes using FracMinHash k-mer sketching.

Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn's disease

The paper identifies five bacterial strains associated with Crohn's disease using a novel method combining machine learning and assembly graphs for metagenomic analysis.

Protein k-mers enable assembly-free microbial metapangenomics

This paper introduces a method using protein k-mers to perform metapangenomics without assembly, identifying strain fluctuations in stool metagenomes during antibiotic treatment.

Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers

Greedy minimum set cover over FracMinHash k-mer sketches selects a small set of reference genomes explaining a metagenome, supporting species-level taxonomic profiling and choice of genomes for read mapping.

Single-cell transcriptomics for the 99.9% of species without reference genomes

This paper introduces Kmermaid and Orpheum to enable scRNA-seq analysis in species without reference genomes by detecting cell type-specific sequences without gene annotations.

Streamlining Data-Intensive Biology With Workflow Systems

The paper provides strategies for using workflow systems to streamline biological data analysis, emphasizing reproducibility and scalability in high-throughput sequencing projects.

Tximeta: reference sequence checksums for provenance identification in RNA-seq

Tximeta automatically identifies reference transcriptomes and gathers metadata for RNA-seq analysis using checksums, improving reproducibility and reducing errors.

Large-scale sequence comparisons with sourmash

The paper introduces sourmash, a software package that uses MinHash to create compressed sequence signatures for efficient large-scale sequence comparison and database searching.