Donovan Parks

Donovan Parks

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Donovan Parks

Donovan Parks

Publications by authors named "Donovan Parks"

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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

Bioinformatics 2019 Nov 15. Epub 2019 Nov 15.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btz848DOI Listing
November 2019

Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).

ISME J 2019 Nov 21. Epub 2019 Nov 21.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.

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http://dx.doi.org/10.1038/s41396-019-0556-zDOI Listing
November 2019

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.

Nat Microbiol 2019 08 20;4(8):1306-1315. Epub 2019 May 20.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1038/s41564-019-0448-zDOI Listing
August 2019

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.

Nucleic Acids Res 2019 05;47(9):4442-4448

Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.

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http://dx.doi.org/10.1093/nar/gkz246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511854PMC
May 2019

An evolving view of methane metabolism in the Archaea.

Nat Rev Microbiol 2019 04 21;17(4):219-232. Epub 2019 Jan 21.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.

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http://dx.doi.org/10.1038/s41579-018-0136-7DOI Listing
April 2019

The importance of designating type material for uncultured taxa.

Syst Appl Microbiol 2019 Jan 18;42(1):15-21. Epub 2018 Jul 18.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.syapm.2018.07.003DOI Listing
January 2019

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.

Nat Biotechnol 2018 11 27;36(10):996-1004. Epub 2018 Aug 27.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, Australia.

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http://dx.doi.org/10.1038/nbt.4229DOI Listing
November 2018

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Nat Microbiol 2018 Feb;3(2):253

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.

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http://dx.doi.org/10.1038/s41564-017-0083-5DOI Listing
February 2018

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Nat Microbiol 2017 Nov 11;2(11):1533-1542. Epub 2017 Sep 11.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia.

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http://dx.doi.org/10.1038/s41564-017-0012-7DOI Listing
November 2017

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria.

Science 2017 03;355(6332):1436-1440

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.

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http://dx.doi.org/10.1126/science.aal3794DOI Listing
March 2017

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota.

Nat Microbiol 2016 Oct 3;1:16170. Epub 2016 Oct 3.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia.

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http://dx.doi.org/10.1038/nmicrobiol.2016.170DOI Listing
October 2016

Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

Front Microbiol 2016 8;7:731. Epub 2016 Jun 8.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia.

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http://dx.doi.org/10.3389/fmicb.2016.00731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4897734PMC
July 2016

A catalogue of 136 microbial draft genomes from Red Sea metagenomes.

Sci Data 2016 07 5;3:160050. Epub 2016 Jul 5.

Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1038/sdata.2016.50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4932879PMC
July 2016

Genome-Based Microbial Taxonomy Coming of Age.

Cold Spring Harb Perspect Biol 2016 Jun 1;8(6). Epub 2016 Jun 1.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia.

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http://dx.doi.org/10.1101/cshperspect.a018085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888819PMC
June 2016

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

Mol Biol Evol 2016 Apr 28;33(4):915-27. Epub 2015 Nov 28.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia

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http://dx.doi.org/10.1093/molbev/msv281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776705PMC
April 2016

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres.

Front Microbiol 2015 7;6:1469. Epub 2016 Jan 7.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Genomics and Computational Biology, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia.

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http://dx.doi.org/10.3389/fmicb.2015.01469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704652PMC
January 2016

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

Science 2015 Oct;350(6259):434-8

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia. Advanced Water Management Centre, University of Queensland, St Lucia 4072, Queensland, Australia.

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http://authors.library.caltech.edu/61783/2/aac7745-Evans-SM.
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http://www.sciencemag.org/cgi/doi/10.1126/science.aac7745
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http://dx.doi.org/10.1126/science.aac7745DOI Listing
October 2015

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Genome Res 2015 Jul 14;25(7):1043-55. Epub 2015 May 14.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia; Advanced Water Management Centre, The University of Queensland, St. Lucia, QLD 4072, Queensland, Australia.

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http://dx.doi.org/10.1101/gr.186072.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484387PMC
July 2015

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.

PeerJ 2015 21;3:e968. Epub 2015 May 21.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia ; Institute for Molecular Bioscience, The University of Queensland , St Lucia, QLD , Australia.

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http://dx.doi.org/10.7717/peerj.968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451040PMC
June 2015

A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes.

Microbiome 2015 25;3. Epub 2015 Feb 25.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland Australia ; DOE Joint Genome Institute, Walnut Creek, CA USA.

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http://dx.doi.org/10.1186/s40168-015-0067-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379614PMC
April 2015

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking.

PeerJ 2015 27;3:e740. Epub 2015 Jan 27.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland , Australia ; Institute for Molecular Bioscience, The University of Queensland , St. Lucia, Queensland , Australia.

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http://dx.doi.org/10.7717/peerj.740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312070PMC
February 2015

STAMP: statistical analysis of taxonomic and functional profiles.

Bioinformatics 2014 Nov 23;30(21):3123-4. Epub 2014 Jul 23.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Advanced Water Management Centre, The University of Queensland, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia and Dalhousie University, Halifax, Nova Scotia, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609014PMC
November 2014

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

PeerJ 2014 30;2:e603. Epub 2014 Sep 30.

Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia ; Advanced Water Management Center (AWMC), The University of Queensland , St Lucia, QLD , Australia.

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http://dx.doi.org/10.7717/peerj.603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183954PMC
October 2014

An expanded genomic representation of the phylum cyanobacteria.

Genome Biol Evol 2014 May;6(5):1031-45

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.

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http://dx.doi.org/10.1093/gbe/evu073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040986PMC
May 2014

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

ISME J 2013 Jan 2;7(1):173-83. Epub 2012 Aug 2.

Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.

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http://dx.doi.org/10.1038/ismej.2012.88DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526167PMC
January 2013

Measuring community similarity with phylogenetic networks.

Mol Biol Evol 2012 Dec 21;29(12):3947-58. Epub 2012 Aug 21.

Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.

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http://dx.doi.org/10.1093/molbev/mss200DOI Listing
December 2012

Rapid identification of high-confidence taxonomic assignments for metagenomic data.

Nucleic Acids Res 2012 Aug 24;40(14):e111. Epub 2012 Apr 24.

Faculty of Computer Science, Dalhousie University, 6050 University Avenue, PO BOX 15000, Halifax, NS B3H 4R2, Canada.

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http://dx.doi.org/10.1093/nar/gks335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413139PMC
August 2012

Classifying short genomic fragments from novel lineages using composition and homology.

BMC Bioinformatics 2011 Aug 9;12:328. Epub 2011 Aug 9.

Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, Canada.

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http://dx.doi.org/10.1186/1471-2105-12-328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173459PMC
August 2011

Identifying biologically relevant differences between metagenomic communities.

Bioinformatics 2010 Mar 3;26(6):715-21. Epub 2010 Feb 3.

Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1W5.

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http://dx.doi.org/10.1093/bioinformatics/btq041DOI Listing
March 2010

GenGIS: A geospatial information system for genomic data.

Genome Res 2009 Oct 27;19(10):1896-904. Epub 2009 Jul 27.

Dalhousie University, Halifax, Nova Scotia, Canada.

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http://dx.doi.org/10.1101/gr.095612.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765287PMC
October 2009

SeqMonitor: influenza analysis pipeline and visualization.

PLoS Curr 2009 Sep 22;1:RRN1040. Epub 2009 Sep 22.

Faculty of Computer Science, Dalhousie University, Halifax, NS.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762774PMC
http://dx.doi.org/10.1371/currents.rrn1040DOI Listing
September 2009

Tracking the evolution and geographic spread of Influenza A.

PLoS Curr 2009 Aug 27;1:RRN1014. Epub 2009 Aug 27.

Faculty of Computer Science, Dalhousie University and Dalhousie University.

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http://dx.doi.org/10.1371/currents.RRN1014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762414PMC
August 2009