Author: Aaron E. Darling

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Preprints

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

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Hackflex: low cost Illumina sequencing library construction for high sample counts

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Alignathon: A competitive assessment of whole genome alignment methods.

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CAMISIM: Simulating metagenomes and microbial communities

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Effective Online Bayesian Phylogenetics Via Sequential Monte Carlo With Guided Proposals

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bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs)

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Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

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Sim3C: Simulation Of HiC And Meta3C Proximity Ligation Sequencing Technologies

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A new massively-parallel transposon mutagenesis approach comparing multiple datasets identifies novel mechanisms of action and resistance to triclosan

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Metagenomics Strain Resolution on Assembly Graphs

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The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America

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Porcine commensal Escherichia coli: A reservoir for class 1 integrons associated with IS26

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Evaluation of ddRADseq for reduced representation metagenome sequencing

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Genomes from Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment

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Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes

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Trial by phylogenetics - Evaluating the Multi-Species Coalescent for evolutionary inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae).

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Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit

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Community composition and development of the post-weaning piglet gut microbiome

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