Benjamin J. Callahan

TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization

TrIdent automates transductomics analysis by identifying DNA mobilized by virus-like particles, showing high agreement with manual classifications and revealing enriched bacterial families in murine gut transductomes.

Gut Microbiome Alterations in Canine Idiopathic Epilepsy: A Pairwise Case-Control Study

This study compares gut microbiomes of dogs with idiopathic epilepsy and healthy controls, finding a significant shift in microbial composition associated with epilepsy.

Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome

The paper analyzes the murine gut transductome before and after perturbations to identify bacterial families and mobile genetic elements involved in horizontal gene transfer.

Generating, curating, and evaluating trnL reference sequence databases: Benchmarking OBITools3/ecoPCR, RESCRIPt, and MetaCurator

The paper evaluates three trnL reference sequence databases generated using different curation tools and assesses their classification performance across trnL regions.

Assessing contamination in DNA extraction kits commonly used for microbiome research

The paper evaluates contamination in commonly used DNA extraction kits for microbiome research and provides guidance for low biomass measurements.

Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella

This study identifies pseudo-pac site sequences in Salmonella genomes that enable P22 phage to initiate generalized transduction, using bioinformatics analysis of sequencing data.

Implications of taxonomic bias for microbial differential-abundance analysis

The paper examines how taxonomic bias affects differential-abundance analysis in microbiome studies and proposes methods to mitigate its effects.

Consistent and correctable bias in metagenomic sequencing measurements

The paper identifies and corrects systematic bias in metagenomic sequencing by modeling how bias distorts measurements and validating it across different protocols and datasets.

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

This paper introduces a high-throughput amplicon sequencing method for full-length 16S rRNA gene analysis with single-nucleotide resolution and near-zero error rate.

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

decontam, an R package, classifies contaminant sequences in marker-gene and metagenomic data by their inverse frequency-DNA concentration relationship and higher prevalence in negative controls.