Lista de obras - Aaron Earl Darling - Dominio Público Uruguay

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

artículo científico publicado en 2014

A longitudinal study of the diabetic skin and wound microbiome.

artículo científico publicado en 2017

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

artículo científico publicado en 2016

A novel heuristic for local multiple alignment of interspersed DNA repeats

artículo científico publicado en 2009

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

artículo científico publicado en 2014

ASAP, a systematic annotation package for community analysis of genomes

artículo científico publicado en 2003

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

artículo científico publicado en 2006

Alignathon: a competitive assessment of whole-genome alignment methods

artículo científico publicado en 2014

An integrated pipeline for de novo assembly of microbial genomes

artículo científico publicado en 2012

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

artículo científico publicado en 2018

Analyzing patterns of microbial evolution using the mauve genome alignment system

artículo científico publicado en 2007

Are protein domains modules of lateral genetic transfer?

artículo científico publicado en 2009

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

artículo científico publicado en 2011

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

artículo científico publicado en 2011

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

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

artículo científico publicado en 2003

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

article

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

artículo científico publicado en 2017

Critical Assessment of Metagenome Interpretation: the second round of challenges

artículo científico publicado en 2022

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

Dynamics of genome rearrangement in bacterial populations

artículo científico publicado en 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

artículo científico publicado en 2017

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

artículo científico publicado en 2009

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

artículo científico publicado en 2007

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

artículo científico publicado en 2019

Evaluation of ddRADseq for reduced representation metagenome sequencing.

artículo científico publicado en 2017

GRIL: genome rearrangement and inversion locator

article

Genome rearrangement by the double cut and join operation

artículo científico publicado en 2008

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

artículo científico publicado en 2006

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

artículo científico publicado en 2019

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

artículo científico publicado en 2012

In Sffamily Identification of Genes in Bacteriophage DNA

article

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

artículo científico publicado en 2013

Inference of homologous recombination in bacteria using whole-genome sequences

artículo científico publicado en 2010

Inferring genomic flux in bacteria

artículo científico publicado en 2008

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

artículo científico publicado en 2013

Insights into the phylogeny and coding potential of microbial dark matter

artículo científico publicado en 2013

Lateral transfer of genes and gene fragments in prokaryotes

artículo científico publicado en 2009

Local and relaxed clocks: the best of both worlds

artículo científico publicado en 2018

Mauve assembly metrics

artículo científico publicado en 2011

Mauve: multiple alignment of conserved genomic sequence with rearrangements

artículo científico publicado en 2004

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

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

artículo científico publicado en 2020

Metagenomic sequencing of an in vitro-simulated microbial community

artículo científico publicado en 2010

Molecular techniques and their limitations shape our view of the holobiont

artículo científico publicado en 2019

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

artículo científico publicado en 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.

artículo científico publicado en 2018

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

artículo científico publicado en 2018

Online Bayesian phylogenetic inference: theoretical foundations via Sequential Monte Carlo

artículo científico publicado en 2017

Patterns of gene flow define species of thermophilic Archaea

artículo científico publicado en 2012

PhyloSift: phylogenetic analysis of genomes and metagenomes

artículo científico publicado en 2014

Phylogenetic and molecular analysis of hydrogen-producing green algae

artículo científico publicado en 2009

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

artículo científico publicado en 2014

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

artículo científico publicado el 25 de abril de 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.

artículo científico publicado en 2017

Progressive genome-wide introgression in agricultural Campylobacter coli

artículo científico publicado en 2012

Reordering contigs of draft genomes using the Mauve aligner

artículo científico publicado en 2009

Seevolution: visualizing chromosome evolution

artículo científico publicado en 2009

Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 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

artículo científico publicado en 2015

Swabs to genomes: a comprehensive workflow

The Amphimedon queenslandica genome and the evolution of animal complexity ⬇️

artículo científico publicado en 2010

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

The common oceanographer: crowdsourcing the collection of oceanographic data

artículo científico publicado en 2014

The genome of Clostridium difficile 5.3.

artículo científico publicado en 2014

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

The rise and fall of breakpoint reuse depending on genome resolution

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado en 2021

Lista de obras de 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.