Todd J. Treangen

The paper develops a microfluidic Capture-Enrichment pipeline to identify potential pre-emergent pathogens in urban wastewater, revealing clinically relevant threats and emerging phenotypes.

Seqwin identifies microbial signature sequences by analyzing large genome collections, outperforming existing methods in efficiency and quality.

Kente detects horizontal gene transfer in microbiomes using a pangenome graph-based approach, achieving higher precision and reducing false positives in simulated and real human gut metagenomes.

The paper introduces Min-Frame Transformation (MFT) to improve viral genome alignment by enhancing MUM-based seeding, resulting in longer and more contiguous matches with better alignment coverage and SNP recall.

The paper introduces a new microbiome diversity measure based on graph sheaf Laplacian spectral energy, showing improved discrimination between healthy and IBD gut microbiomes.

bronko detects viral genome variation quickly and without alignment, outperforming existing tools in speed and accuracy for large datasets.

The paper introduces CLASSIC, a platform that maps sequence-to-function relationships in synthetic biology by combining long- and short-read sequencing to analyze gene circuits.

This study evaluates virome protocols to optimize recovery of human fecal viral genomes while minimizing contamination.

The paper evaluates sequence screening tools using a NIST dataset to assess their consistency in identifying sequences of concern.

Strainify estimates strain-level abundances from low-coverage short-read metagenomic data, outperforming existing methods in simulated and real datasets.

tMHG-Finder uses Mash guide trees and consensus representative sequences to find maximal homologous groups in bacterial genomes with linear scaling, reaching F-score 0.932 on simulated data.

The paper establishes a near-tight lower bound on the density of forward sampling schemes and shows existing schemes are closer to optimal than previously thought.

Olivar automates variant-aware primer design for tiled amplicon sequencing of pathogens, improving mapping rates and coverage compared to existing methods.

MethPhaser improves haplotype phasing by using methylation signals from Oxford Nanopore data, increasing phase length N50 by 3-fold with minimal error increase.

This paper introduces Lemur and Magnet, lightweight tools for accurate taxonomic profiling of long-read metagenomic datasets, showing they run efficiently on laptops.

This study shows that antibiotic treatment reduces neuroinflammation and neurodegeneration after TBI in mice by altering the gut microbiome.

Parsnp 2.0 improves scalability and control for multiple genome alignment of microbial datasets, reducing memory and runtime while maintaining accuracy.

This paper introduces rhea, a reference-free method for detecting structural variants in microbiomes using long-read coassembly graphs, showing improved performance over existing methods in simulated and real metagenomic data.

This study shows that probiotic treatment reduces TBI severity and behavioral deficits in male mice but not female mice.

The paper introduces minmers, a generalization of minimizers that provide unbiased local Jaccard similarity estimates, improving the accuracy and speed of sequence comparison tools like MashMap.

SeqScreen-Nano rapidly characterizes novel pathogens using ONT sequencing in resource-limited settings by identifying ORFs and classifying them functionally and taxonomically.

SeqScreen uses ensemble learning to accurately label pathogenic sequences with functional annotations, achieving high recall and precision for microbial pathogenesis.

This study identifies mobile genetic elements driving β-lactamase gene amplification in non-CP-CRE bloodstream infections through genomic analysis.

This study shows that fecal microbiota from Alzheimer's mice worsens brain injury outcomes in healthy mice.

Variabel identifies low frequency intra-host variants from Oxford Nanopore sequencing data, outperforming existing tools for this task.

Bakdrive identifies minimum sets of bacterial driver species in microbial communities using metagenomic data and control theory, showing potential to restore gut microbiomes in disease states.

Vulcan improves long-read mapping and structural variant calling by using dual-mode alignment, enhancing accuracy for Oxford Nanopore Technology reads.

The paper identifies intra-host single nucleotide variants (iSNVs) in influenza samples to track transmission links, finding that technical and systematic errors affect iSNV calling and that self-reference reduces noise.

Squeegee identifies microbial contaminants in low biomass microbiomes using de novo analysis, showing high precision in simulated and real datasets.

Emu provides species-level microbial community profiling using full-length 16S rRNA reads with improved accuracy over existing methods.