Todd J Treangen

Latest

• 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
• 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
• 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