List of works - Aaron Earl Darling

A draft genome of Escherichia coli sequence type 127 strain 2009-46

scientific article

A longitudinal study of the diabetic skin and wound microbiome.

scientific article

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq

scientific article

A novel heuristic for local multiple alignment of interspersed DNA repeats

scientific article

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

scientific article

ASAP, a systematic annotation package for community analysis of genomes

scientific article published on January 2003

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data

scientific article

Alignathon: a competitive assessment of whole-genome alignment methods

scientific article

An integrated pipeline for de novo assembly of microbial genomes

scientific article

Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes.

scientific article

Analyzing patterns of microbial evolution using the mauve genome alignment system

scientific article published on January 2007

Are protein domains modules of lateral genetic transfer?

scientific article

Assemblathon 1: a competitive assessment of de novo short read assembly methods

scientific article

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

scientific article published on 01 November 2019

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

scientific article

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients

scientific article

CAMISIM: simulating metagenomes and microbial communities

scientific article published on 08 February 2019

Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis

scientific article

Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.

scientific article published on 10 March 2015

Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease

scientific article

Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T

scientific article

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

article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022

DESMAN: a new tool for de novo extraction of strains from metagenomes.

scientific article published on 21 September 2017

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C).

scientific article published on 8 November 2016

Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders

scientific article

Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).

scientific article

Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).

scientific article published on 9 May 2013

Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).

scientific article published on 9 May 2013

Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria).

scientific article published on 27 June 2013

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).

scientific article

Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4.

scientific article

Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome

scientific article published on 9 April 2015

Dynamics of genome rearrangement in bacterial populations

scientific article published in 2008

Effective Online Bayesian Phylogenetics Via Sequential Monte Carlo With Guided Proposals

scholarly article published 2 June 2017

Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals

scientific article published on 27 November 2017

Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia

scientific article

Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria

scientific article

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

scientific article published on 18 December 2019

Evaluation of ddRADseq for reduced representation metagenome sequencing.

scientific article published on 19 September 2017

GRIL: genome rearrangement and inversion locator

article

Genome rearrangement by the double cut and join operation

scientific article

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli

scientific article

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment

scientific article published on 10 June 2019

High contiguity genome sequence of a multidrug-resistant hospital isolate of

scientific article published on 13 February 2019

Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids

scientific article published on 15 March 2019

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

scientific article

In Sffamily Identification of Genes in Bacteriophage DNA

article

Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic

scientific article published on 13 February 2013

Inference of homologous recombination in bacteria using whole-genome sequences

scientific article

Inferring genomic flux in bacteria

scientific article published on 17 November 2008

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence

scientific article (publication date: 12 February 2013)

Insights into the phylogeny and coding potential of microbial dark matter

scientific article

Lateral transfer of genes and gene fragments in prokaryotes

scientific article

Local and relaxed clocks: the best of both worlds

scientific article published on 03 July 2018

Mauve assembly metrics

scientific article

Mauve: multiple alignment of conserved genomic sequence with rearrangements

scientific article (publication date: July 2004)

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

scientific article

Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges

scientific article published on 30 November 2015

Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor

scientific article published on 06 February 2020

Metagenomic sequencing of an in vitro-simulated microbial community

scientific article

Molecular techniques and their limitations shape our view of the holobiont

scientific article published on 16 July 2019

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

scientific article (publication date: May 2012)

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.

scientific article

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

scientific article published on 7 August 2018

Online Bayesian phylogenetic inference: theoretical foundations via Sequential Monte Carlo

scientific article published on 13 December 2017

Patterns of gene flow define species of thermophilic Archaea

scientific article

PhyloSift: phylogenetic analysis of genomes and metagenomes

scientific article published on 9 January 2014

Phylogenetic and molecular analysis of hydrogen-producing green algae

scientific article (publication date: 2009)

Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response

scientific article

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices ⬇️

scientific article published on April 25, 2013

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

scholarly article published 3 July 2017

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

scientific article

Progressive genome-wide introgression in agricultural Campylobacter coli

scientific article published on 20 December 2012

Reordering contigs of draft genomes using the Mauve aligner

scientific article published on 10 June 2009

Seevolution: visualizing chromosome evolution

scientific article published on 20 February 2009

Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

scientific article

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.

scientific article published on 15 November 2017

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

scientific article published on 27 May 2014

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

Swabs to Genomes: A Comprehensive Workflow

article published in 2014

Swabs to genomes: a comprehensive workflow

scientific article

Swabs to genomes: a comprehensive workflow

The Amphimedon queenslandica genome and the evolution of animal complexity ⬇️

scientific article

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

The common oceanographer: crowdsourcing the collection of oceanographic data

scientific article

The genome of Clostridium difficile 5.3.

scientific article

The impact of migratory flyways on the spread of avian influenza virus in North America

scientific article

The rapid in vivo evolution of Pseudomonas aeruginosa in ventilator-associated pneumonia patients leads to attenuated virulence.

scientific article published on September 2017

The rise and fall of breakpoint reuse depending on genome resolution

scientific article

Visualization of Biomedical Data

scholarly article published 20 July 2018

Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups

scientific article published on 01 January 2020

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

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

scientific article published on 26 February 2019

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

scientific article (publication date: 25 June 2010)

qc3C: Reference-free quality control for Hi-C sequencing data

scientific article published on 11 October 2021

List of works by Aaron Earl Darling

A draft genome of Escherichia coli sequence type 127 strain 2009-46

A longitudinal study of the diabetic skin and wound microbiome.

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq

A novel heuristic for local multiple alignment of interspersed DNA repeats

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

ASAP, a systematic annotation package for community analysis of genomes

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data

Alignathon: a competitive assessment of whole-genome alignment methods

An integrated pipeline for de novo assembly of microbial genomes

Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes.

Analyzing patterns of microbial evolution using the mauve genome alignment system

Are protein domains modules of lateral genetic transfer?

Assemblathon 1: a competitive assessment of de novo short read assembly methods

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients

CAMISIM: simulating metagenomes and microbial communities

Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis

Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.

Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease

Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T

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

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Critical Assessment of Metagenome Interpretation: the second round of challenges

DESMAN: a new tool for de novo extraction of strains from metagenomes.

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C).

Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders

Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).

Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).

Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).

Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria).

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).

Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4.

Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome

Dynamics of genome rearrangement in bacterial populations

Effective Online Bayesian Phylogenetics Via Sequential Monte Carlo With Guided Proposals

Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals

Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia

Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

Evaluation of ddRADseq for reduced representation metagenome sequencing.

GRIL: genome rearrangement and inversion locator

Genome rearrangement by the double cut and join operation

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli

Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment

High contiguity genome sequence of a multidrug-resistant hospital isolate of

Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

In Sffamily Identification of Genes in Bacteriophage DNA

Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic

Inference of homologous recombination in bacteria using whole-genome sequences

Inferring genomic flux in bacteria

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence

Insights into the phylogeny and coding potential of microbial dark matter

Lateral transfer of genes and gene fragments in prokaryotes

Local and relaxed clocks: the best of both worlds

Mauve assembly metrics

Mauve: multiple alignment of conserved genomic sequence with rearrangements

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges

Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor

Metagenomic sequencing of an in vitro-simulated microbial community

Molecular techniques and their limitations shape our view of the holobiont

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae.

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

Online Bayesian phylogenetic inference: theoretical foundations via Sequential Monte Carlo

Patterns of gene flow define species of thermophilic Archaea

PhyloSift: phylogenetic analysis of genomes and metagenomes

Phylogenetic and molecular analysis of hydrogen-producing green algae

Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices ⬇️

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

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

Progressive genome-wide introgression in agricultural Campylobacter coli

Reordering contigs of draft genomes using the Mauve aligner

Seevolution: visualizing chromosome evolution

Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.