Aaron E. Darling

The paper evaluates the Illumina Complete Long Read (ICLR) assay for metagenomic assembly, finding it produces higher contiguity and completeness compared to short-read and nanopore long-read methods.

The paper describes the isolation and characterization of five bacterial isolates from Fragaria x ananassa, identifying them as a new species of Xanthomonas, Xanthomonas rydalmerenesis, which is non-pathogenic.

Rhometa estimates population recombination rates from metagenomic read datasets using a composite likelihood approach, showing accuracy with 80 genomes and real experimental data.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Hackflex is a low-cost method for Illumina library prep that produces high-quality, uniform libraries at 14 times lower cost than standard Nextera Flex.

The paper introduces a reference-free quality control method for Hi-C sequencing data, demonstrating its accuracy on simulated and real datasets.

Strainberry uses long-read data to separate microbial strains in low-complexity metagenomes, achieving high accuracy and additional genomic material in real datasets.

This tutorial explains how to use the CAMI benchmarking toolkit to evaluate metagenomics software performance using standardized datasets and metrics.

STRONG identifies strains de novo from metagenome samples using coassembly, binning, and a Bayesian algorithm to resolve haplotypes and abundances.

This study compares variational inference and MCMC methods for phylogenetic inference using Stan, finding variational methods faster but less accurate.

The paper compares manual and automated taxonomic assignment methods for bacterial genomes from the canine oral cavity, finding GTDB to be less subjective and labor-intensive.

The paper analyzes whole-genome sequences of 16 ExPEC ST73 isolates from a single hospital to identify circulating clonal groups and their mobile genetic elements.

The paper introduces bin3C, an unsupervised method using Hi-C data to resolve MAGs from a single time-point, validated against simulated data and compared to ProxiMeta.

CAMISIM simulates microbial communities and metagenomes with truth standards, enabling benchmarking of metagenomic analysis tools.

This study analyzes the genomic features of 141 commensal E. coli from healthy pigs, identifying antimicrobial resistance genes, class 1 integrons, and IS26 elements associated with zoonotic potential.

This paper develops and evaluates online Bayesian phylogenetic inference methods using sequential Monte Carlo with guided proposals, showing reduced computation time compared to MCMC-based methods without significant accuracy loss.

Sim3C simulates HiC and Meta3C sequencing data by modeling genomic spatial structures and errors, aiding in algorithm testing and experimental design.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.

The paper evaluates ddRADseq for reduced representation metagenome sequencing, finding it feasible with small taxonomic bias compared to DNA extraction bias.