Todd J Treangen

Latest

Improved Annotation of Sequences of Concern to Better Understand Biorisk in Engineered Microbes
GraSSRep: Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly
Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA
MetaCompass: Reference-guided Assembly of Metagenomes
Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets
Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs
Sensitivity and consistency of long-and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater
The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern
KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome
MethPhaser: methylation-based haplotype phasing of human genomes
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens
The long game of tenure
Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis
De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee
Enabling earlier detection of recently emerged SARS-CoV-2 variants of concern in wastewater
Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in wild-type controls
KOMB: K-core based de novo characterization of copy number variation in microbiomes
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters
Multiple genome alignment in the telomere-to-telomere assembly era
QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets
Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis
Enhanced Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater
It takes guts to learn: machine learning techniques for disease detection from the gut microbiome
KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities
PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment
QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater
Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data
Squeegee: de-novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities
To petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics
Diversified RACE sampling on data streams applied to metagenomic sequence analysis
Diversified race sampling on data streams applied to metagenomic sequence analysis. bioRxiv
Faster pan-genome construction for efficient differentiation of naturally occurring and engineered plasmids with plaster
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Traumatic brain injury in mice induces acute bacterial dysbiosis within the fecal microbiome
You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details
MetaCompass: reference-guided assembly of metagenomes
Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes.
Diversity in a polymicrobial community revealed by analysis of viromes, endolysins and CRISPR spacers
Identification and genomic analysis of a novel group C Orthobunyavirus isolated from a mosquito captured near Iquitos, Peru
Limitations of current approaches for reference-free, graph-based variant detection
Mash: fast genome and metagenome distance estimation using MinHash
Automated ensemble assembly and validation of microbial genomes
Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
De novo likelihood-based measures for comparing metagenomic assemblies
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Deep sequencing of the oral microbiome reveals signatures of periodontal disease
GAGE: A critical evaluation of genome assemblies and assembly algorithms
Bambus 2: scaffolding metagenomes
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
Next generation sequence assembly with AMOS
Repetitive DNA and next-generation sequencing: computational challenges and solutions
Repeatoire: Detecting intragenomic repeat families within the context of intergenomic comparisons
Genesis, effects and fates of repeats in prokaryotic genomes
The impact of the neisserial DNA uptake sequences on genome evolution and stability
Analyzing patterns of microbial evolution using the mauve genome alignment system
Procrastination leads to efficient filtration for local multiple alignment