Aaron Darling

Aaron Darling

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Aaron Darling

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

Plasmid 2019 03 15;102:56-61. Epub 2019 Mar 15.

The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia.

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http://dx.doi.org/10.1016/j.plasmid.2019.03.002DOI Listing
March 2019

CAMISIM: simulating metagenomes and microbial communities.

Microbiome 2019 02 8;7(1):17. Epub 2019 Feb 8.

Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany.

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http://dx.doi.org/10.1186/s40168-019-0633-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368784PMC
February 2019

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

Gut Pathog 2019 13;11. Epub 2019 Feb 13.

1ithree institute, University of Technology Sydney, Broadway Street, Ultimo, 2007 Australia.

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http://dx.doi.org/10.1186/s13099-019-0288-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373042PMC
February 2019

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

Genome Biol 2019 02 26;20(1):46. Epub 2019 Feb 26.

The ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia.

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http://dx.doi.org/10.1186/s13059-019-1643-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391755PMC
February 2019

Local and relaxed clocks: the best of both worlds.

PeerJ 2018 3;6:e5140. Epub 2018 Jul 3.

ithree institute, University of Technology Sydney, Sydney, Australia.

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http://dx.doi.org/10.7717/peerj.5140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6034591PMC
July 2018

Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo.

Syst Biol 2018 05;67(3):503-517

Program in Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/sysbio/syx087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920340PMC
May 2018

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 05 5;6(1):85. Epub 2018 May 5.

Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia.

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http://dx.doi.org/10.1186/s40168-018-0463-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935925PMC
May 2018

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

Gigascience 2018 02;7(2)

The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2077, Australia.

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http://dx.doi.org/10.1093/gigascience/gix103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827349PMC
February 2018

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

Genome Biol 2017 09 21;18(1):181. Epub 2017 Sep 21.

Department of Medicine, University of Chicago, Chicago, USA.

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http://dx.doi.org/10.1186/s13059-017-1309-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607848PMC
September 2017

Evaluation of ddRADseq for reduced representation metagenome sequencing.

PeerJ 2017 19;5:e3837. Epub 2017 Sep 19.

The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia.

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http://dx.doi.org/10.7717/peerj.3837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609526PMC
September 2017

A longitudinal study of the diabetic skin and wound microbiome.

PeerJ 2017 20;5:e3543. Epub 2017 Jul 20.

The i3 institute, University of Technology Sydney, Sydney, New South Wales, Australia.

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http://dx.doi.org/10.7717/peerj.3543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522608PMC
July 2017

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

BMC Evol Biol 2017 05 25;17(1):118. Epub 2017 May 25.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.

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http://dx.doi.org/10.1186/s12862-017-0965-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445350PMC
May 2017

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

PeerJ 2016 20;4:e2492. Epub 2016 Sep 20.

The i3 Institute, University of Technology Sydney , Sydney, NSW , Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036073PMC
http://dx.doi.org/10.7717/peerj.2492DOI Listing
October 2016

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

F1000Res 2015 30;4:1377. Epub 2015 Nov 30.

ithree institute, University of Technology Sydney, Sydney, NSW 2007, Australia.

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http://dx.doi.org/10.12688/f1000research.7281.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798154PMC
March 2016

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients.

Front Microbiol 2015 22;6:1532. Epub 2016 Jan 22.

Department of Otolaryngology, Mona Vale Hospital Sydney, NSW, Australia.

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http://dx.doi.org/10.3389/fmicb.2015.01532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722142PMC
February 2016

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

Bioinformatics 2015 Feb 22;31(4):587-9. Epub 2014 Oct 22.

Genome Center, University of California Davis, Davis, CA 95616, USA and ithree institute, University of Technology Sydney, New South Wales, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btu661DOI Listing
February 2015

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

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

PLoS Genet 2014 Nov 13;10(11):e1004784. Epub 2014 Nov 13.

Microbiology Graduate Group, University of California, Davis, Davis, California, United States of America; Genome Center, University of California, Davis, Davis, California, United States of America; Department of Biomedical Engineering, University of California, Davis, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230888PMC
November 2014

The genome of Clostridium difficile 5.3.

Gut Pathog 2014 Feb 24;6(1). Epub 2014 Feb 24.

ithree institute, University of Technology Sydney, Broadway Street, 2007 Ultimo, Australia.

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http://dx.doi.org/10.1186/1757-4749-6-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234979PMC
February 2014

PhyloSift: phylogenetic analysis of genomes and metagenomes.

PeerJ 2014 9;2:e243. Epub 2014 Jan 9.

Department of Evolution and Ecology, University of California , Davis, CA , United States of America ; Department of Medical Microbiology and Immunology, University of California , Davis, CA , United States of America.

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http://dx.doi.org/10.7717/peerj.243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897386PMC
January 2014

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

PLoS One 2013 25;8(4):e62510. Epub 2013 Apr 25.

Department of Medical Microbiology and Immunology and Department of Evolution and Ecology, University of California Davis, Davis, California, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062510PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636077PMC
November 2013

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

Genome Announc 2013 Jun 27;1(3). Epub 2013 Jun 27.

University of California Davis Genome Center, Davis, California, USA.

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http://dx.doi.org/10.1128/genomeA.00325-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675516PMC
June 2013

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

Genome Announc 2013 May 9;1(3). Epub 2013 May 9.

University of California, Davis, Genome Center, Davis, California, USA.

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http://dx.doi.org/10.1128/genomeA.00172-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650433PMC
May 2013

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

Genome Announc 2013 May 9;1(3). Epub 2013 May 9.

University of California, Davis, Genome Center, Davis, California, USA.

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http://dx.doi.org/10.1128/genomeA.00197-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650439PMC
May 2013

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

Genome Announc 2013 May 16;1(3). Epub 2013 May 16.

University of California Davis, Genome Center, Davis, California, USA.

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http://dx.doi.org/10.1128/genomeA.00244-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656209PMC
May 2013

An integrated pipeline for de novo assembly of microbial genomes.

PLoS One 2012 13;7(9):e42304. Epub 2012 Sep 13.

Genome Center, University of California Davis, Davis, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042304PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441570PMC
March 2013

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

Genome Announc 2013 Mar 21;1(2):e0008613. Epub 2013 Mar 21.

University of California at Davis, Genome Center, Davis, California, USA.

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http://dx.doi.org/10.1128/genomeA.00086-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622973PMC
March 2013

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

Genome Announc 2013 Mar 21;1(2):e0012013. Epub 2013 Mar 21.

University of California at Davis, Genome Center, Davis, California, USA.

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http://dx.doi.org/10.1128/genomeA.00120-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622984PMC
March 2013

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

BMC Genomics 2012 Jun 19;13:256. Epub 2012 Jun 19.

Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1PG, UK.

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http://dx.doi.org/10.1186/1471-2164-13-256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505186PMC
June 2012

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.

Syst Biol 2012 May 22;61(3):539-42. Epub 2012 Feb 22.

Department of Biodiversity Informatics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden.

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http://dx.doi.org/10.1093/sysbio/sys029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329765PMC
May 2012

Patterns of gene flow define species of thermophilic Archaea.

PLoS Biol 2012 Feb 21;10(2):e1001265. Epub 2012 Feb 21.

Department of Microbiology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283564PMC
February 2012

Mauve assembly metrics.

Bioinformatics 2011 Oct 2;27(19):2756-7. Epub 2011 Aug 2.

Genome Center, University of California-Davis, Davis, CA 95616, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179657PMC
October 2011

The rise and fall of breakpoint reuse depending on genome resolution.

BMC Bioinformatics 2011 Oct 5;12 Suppl 9:S1. Epub 2011 Oct 5.

Department of Infectious Diseases, Mount Sinai School of Medicine, NY, NY 10029, USA.

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http://dx.doi.org/10.1186/1471-2105-12-S9-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283316PMC
October 2011

Inference of homologous recombination in bacteria using whole-genome sequences.

Genetics 2010 Dec 5;186(4):1435-49. Epub 2010 Oct 5.

Department of Statistics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1534/genetics.110.120121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998322PMC
December 2010

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

PLoS One 2010 Jun 25;5(6):e11147. Epub 2010 Jun 25.

Genome Center and Department of Computer Science, University of Wisconsin, Madison, Wisconsin, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011147PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892488PMC
June 2010

Metagenomic sequencing of an in vitro-simulated microbial community.

PLoS One 2010 Apr 16;5(4):e10209. Epub 2010 Apr 16.

Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010209PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855710PMC
April 2010

Lateral transfer of genes and gene fragments in prokaryotes.

Genome Biol Evol 2009 Nov 4;1:429-38. Epub 2009 Nov 4.

Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, Queensland, Australia.

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http://gbe.oxfordjournals.org/content/1/429.full.pdf
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http://gbe.oxfordjournals.org/cgi/doi/10.1093/gbe/evp044
Publisher Site
http://dx.doi.org/10.1093/gbe/evp044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817436PMC
November 2009

A novel heuristic for local multiple alignment of interspersed DNA repeats.

IEEE/ACM Trans Comput Biol Bioinform 2009 Apr-Jun;6(2):180-9

Institut Pasteur, CNRS and UPMC University, Paris, France.

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http://dx.doi.org/10.1109/TCBB.2009.9DOI Listing
August 2009

Reordering contigs of draft genomes using the Mauve aligner.

Bioinformatics 2009 Aug 10;25(16):2071-3. Epub 2009 Jun 10.

Genome Evolution Laboratory, University of Wisconsin-Madison, 425G Henry Mall Suite 4400V, Madison, WI 53706, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723005PMC
August 2009

Phylogenetic and molecular analysis of hydrogen-producing green algae.

J Exp Bot 2009 2;60(6):1691-702. Epub 2009 Apr 2.

School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia.

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http://dx.doi.org/10.1093/jxb/erp052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671627PMC
July 2009

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

Genome Biol Evol 2009 Jun 22;1:153-64. Epub 2009 Jun 22.

Bioinformatics group, Alfréd Rényi Institute of Mathematics, Hungarian Academy of Sciences, Budapest, Hungary.

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https://academic.oup.com/gbe/article/doi/10.1093/gbe/evp015/
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http://dx.doi.org/10.1093/gbe/evp015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817410PMC
June 2009

Are protein domains modules of lateral genetic transfer?

PLoS One 2009 20;4(2):e4524. Epub 2009 Feb 20.

The University of Queensland, Institute for Molecular Biosciences, and ARC Centre of Excellence in Bioinformatics, Brisbane, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004524PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639706PMC
April 2009

Seevolution: visualizing chromosome evolution.

Bioinformatics 2009 Apr 20;25(7):960-1. Epub 2009 Feb 20.

Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btp096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660879PMC
April 2009

In silico identification of genes in bacteriophage DNA.

Methods Mol Biol 2009 ;502:57-89

Public Health Agency of Canada, Laboratory for Foodborne Diseases, Guelph, Ontario, Canada.

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http://dx.doi.org/10.1007/978-1-60327-565-1_6DOI Listing
March 2009

Inferring genomic flux in bacteria.

Genome Res 2009 Feb 17;19(2):306-17. Epub 2008 Nov 17.

Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom.

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http://dx.doi.org/10.1101/gr.082263.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652212PMC
February 2009

Genome rearrangement by the double cut and join operation.

Methods Mol Biol 2008 ;452:385-416

Department of Physics, Columbia University, New York, NY, USA.

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http://link.springer.com/10.1007/978-1-60327-159-2_18
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http://dx.doi.org/10.1007/978-1-60327-159-2_18DOI Listing
July 2008

Dynamics of genome rearrangement in bacterial populations.

PLoS Genet 2008 Jul 18;4(7):e1000128. Epub 2008 Jul 18.

ARC Center of Excellence in Bioinformatics, The University of Queensland, St. Lucia, Queensland, Australia.

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https://dx.plos.org/10.1371/journal.pgen.1000128
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http://dx.doi.org/10.1371/journal.pgen.1000128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483231PMC
July 2008

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

Genome Biol 2006 31;7(5):R44. Epub 2006 May 31.

Department of Mathematics, Lincoln Drive, University of Wisconsin, Madison WI 53706, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2006-7-5-r44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779527PMC
August 2006

Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Genome Res 2004 Jul;14(7):1394-403

Department of Computer Science, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.2289704
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http://dx.doi.org/10.1101/gr.2289704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC442156PMC
July 2004

GRIL: genome rearrangement and inversion locator.

Bioinformatics 2004 Jan;20(1):122-4

Department of Computer Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg378DOI Listing
January 2004

ASAP, a systematic annotation package for community analysis of genomes.

Nucleic Acids Res 2003 Jan;31(1):147-51

Animal Health and Biomedical Sciences, University of Wisconsin-Madison, 656 Linden Dr Madison, WI 53706-1581, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165572PMC
http://dx.doi.org/10.1093/nar/gkg125DOI Listing
January 2003