Author details

Full Name

Aaron E Darling

Affiliation

ORCID

Career Start Year

2003

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37099595	Fidelity of hyperbolic space for Bayesian phylogenetic inference.		2023
36972309	Rhometa: Population recombination rate estimation from metagenomic read datasets.		2023
37491320	Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics.	Microbiome	2023
35014949	Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.	Microbial genomics	2022
34370660	Post-weaning shifts in microbiome composition and metabolism revealed by over 25â¿¿000 pig gut metagenome-assembled genomes.	Microbial genomics	2021
34080630	A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen.	GigaScience	2021
33649565	Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.	Nat Protoc	2021
34311761	STRONG: metagenomics strain resolution on assembly graphs.		2021
34301928	Strainberry: automated strain separation in low-complexity metagenomes using long reads.	Nature Communications	2021
32650022	Human milk oligosaccharide profiles and allergic disease up to 18 years.	Journal of Allergy and Clinical Immunology	2021
34634030	qc3C: Reference-free quality control for Hi-C sequencing data.	PLoS Computational Biology	2021
32512857	Whole Genome Sequencing Analysis of Porcine Faecal Commensal Carrying Class 1 Integrons from Sows and Their Offspring.	Microorganisms	2020
32029559	Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor.	Microbiology Resource Announcements	2020
32051187	TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance.	Genome Res	2020
32686595	ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex.	Emerging Microbes and Infections	2020
30885788	Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids.	Plasmid	2019
31759226	Molecular techniques and their limitations shape our view of the holobiont.		2019
31976168	Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics.	PeerJ	2019
31181071	Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment.	PLoS One	2019
30808380	bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.		2019
30805030	High contiguity genome sequence of a multidrug-resistant hospital isolate of .	Gut Pathogens	2019
30736849	CAMISIM: simulating metagenomes and microbial communities.	Microbiome	2019
29729663	Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.	Microbiome	2018
30002973	Local and relaxed clocks: the best of both worlds.	PeerJ	2018
30086128	Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota.	PLoS Biol	2018
29186587	Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals.	Systematic Biology	2018
29703152	Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes.	BMC Genomics	2018
29244177	Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo.	Systematic Biology	2018
29149264	Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.	GigaScience	2018
29306352	Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26.	Microbial genomics	2017
28948110	Evaluation of ddRADseq for reduced representation metagenome sequencing.	PeerJ	2017
28545432	The impact of migratory flyways on the spread of avian influenza virus in North America.	BMC Evol Biol	2017
28934976	DESMAN: a new tool for de novo extraction of strains from metagenomes.		2017
28967888	Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.	Nat Methods	2017
28878043	The rapid evolution of in ventilator-associated pneumonia patients leads to attenuated virulence.	Open Biology	2017
28740749	A longitudinal study of the diabetic skin and wound microbiome.	PeerJ	2017
27688981	A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq.	PeerJ	2016
26971047	Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease.	BMC Microbiology	2016
27843713	Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C).	PeerJ	2016
26020012	Swabs to genomes: a comprehensive workflow.	PeerJ	2015
25888127	Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.	BMC Genomics	2015
25338718	A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.		2015
25858832	Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome.	Genome Announc	2015
26834708	Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients.	Frontiers in Microbiology	2015
27006753	Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges.	F1000Research	2015
26568374	Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis.	Genome Biol Evol	2015
24918035	Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.	PeerJ	2014
25273068	Alignathon: a competitive assessment of whole-genome alignment methods.	Genome Res	2014
25393412	Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.	PLoS Genet	2014
24482762	PhyloSift: phylogenetic analysis of genomes and metagenomes.	PeerJ	2014