Philip Hugenholtz

Philip Hugenholtz

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Philip Hugenholtz

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Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice.

Gut Microbes 2020 Jan 13:1-17. Epub 2020 Jan 13.

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

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http://dx.doi.org/10.1080/19490976.2019.1705729DOI Listing
January 2020

Defining the human gut host-phage network through single-cell viral tagging.

Nat Microbiol 2019 12 5;4(12):2192-2203. Epub 2019 Aug 5.

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/10.1038/s41564-019-0526-2DOI Listing
December 2019

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

Functional effects of the microbiota in chronic respiratory disease.

Lancet Respir Med 2019 Oct 8;7(10):907-920. Epub 2019 Apr 8.

Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia; Centre for Inflammation, Centenary Institute, and University of Technology Sydney, NSW, Australia. Electronic address:

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http://dx.doi.org/10.1016/S2213-2600(18)30510-1DOI Listing
October 2019

Evolution of photosynthesis and aerobic respiration in the cyanobacteria.

Free Radic Biol Med 2019 Aug 29;140:200-205. Epub 2019 Mar 29.

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

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https://linkinghub.elsevier.com/retrieve/pii/S08915849183230
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http://dx.doi.org/10.1016/j.freeradbiomed.2019.03.029DOI Listing
August 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

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments.

Nat Microbiol 2019 06 11;4(6):1014-1023. Epub 2019 Mar 11.

School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.

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http://www.nature.com/articles/s41564-019-0391-z
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http://dx.doi.org/10.1038/s41564-019-0391-zDOI Listing
June 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

IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota.

Ann Rheum Dis 2019 04 30;78(4):494-503. Epub 2019 Jan 30.

Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia

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http://dx.doi.org/10.1136/annrheumdis-2018-214381DOI 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

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes.

mBio 2018 10 9;9(5). Epub 2018 Oct 9.

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

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http://mbio.asm.org/lookup/doi/10.1128/mBio.01432-18
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http://dx.doi.org/10.1128/mBio.01432-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178618PMC
October 2018

Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.

Environ Sci Technol 2018 05 16;52(9):5386-5397. Epub 2018 Apr 16.

Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia.

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http://dx.doi.org/10.1021/acs.est.7b04273DOI Listing
May 2018

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo.

Sci Rep 2018 05 25;8(1):8128. Epub 2018 May 25.

School of Biological Sciences, University of Auckland, Auckland, New Zealand.

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http://dx.doi.org/10.1038/s41598-018-26484-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970201PMC
May 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

Atmospheric trace gases support primary production in Antarctic desert surface soil.

Nature 2017 12 6;552(7685):400-403. Epub 2017 Dec 6.

School of Biotechnology and Biomolecular Sciences, Australian Centre for Astrobiology, UNSW Sydney, Randwick, New South Wales 2052, Australia.

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http://dx.doi.org/10.1038/nature25014DOI Listing
December 2017

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

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for digestion.

PeerJ 2017 16;5:e4075. Epub 2017 Nov 16.

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

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http://dx.doi.org/10.7717/peerj.4075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697889PMC
November 2017

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.

Nat Microbiol 2017 Oct 28;2(10):1344-1349. Epub 2017 Aug 28.

Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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http://dx.doi.org/10.1038/s41564-017-0010-9DOI Listing
October 2017

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence.

Nat Commun 2017 08 9;8(1):215. Epub 2017 Aug 9.

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

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http://dx.doi.org/10.1038/s41467-017-00262-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548757PMC
August 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

Microbiomes in respiratory health and disease: An Asia-Pacific perspective.

Respirology 2017 02;22(2):240-250

Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia.

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http://dx.doi.org/10.1111/resp.12971DOI Listing
February 2017

Emerging pathogenic links between microbiota and the gut-lung axis.

Nat Rev Microbiol 2017 01 3;15(1):55-63. Epub 2016 Oct 3.

Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia.

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http://www.nature.com/articles/nrmicro.2016.142
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http://dx.doi.org/10.1038/nrmicro.2016.142DOI Listing
January 2017

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics.

PeerJ 2016 22;4:e2486. Epub 2016 Sep 22.

Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036114PMC
http://dx.doi.org/10.7717/peerj.2486DOI Listing
October 2016

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

Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57.

Stand Genomic Sci 2016 6;11(1):60. Epub 2016 Sep 6.

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/10.1186/s40793-016-0189-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012032PMC
September 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

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community.

PLoS One 2015 11;10(11):e0142720. Epub 2015 Nov 11.

Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142720PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641665PMC
June 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

The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application.

Environ Microbiol 2016 05 30;18(5):1338-51. Epub 2015 Jul 30.

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

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http://doi.wiley.com/10.1111/1462-2920.12925
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http://dx.doi.org/10.1111/1462-2920.12925DOI Listing
May 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

Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma.

Eur Respir J 2016 Mar 2;47(3):792-800. Epub 2015 Dec 2.

Respiratory and Sleep Medicine, School of Medicine and Public Health, Centre for Asthma and Respiratory Disease, The University of Newcastle, Callaghan, Australia Woolcock Institute of Medical Research, Glebe, Australia.

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http://dx.doi.org/10.1183/13993003.00405-2015DOI Listing
March 2016

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.

Front Microbiol 2016 25;7:211. Epub 2016 Feb 25.

Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands.

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http://dx.doi.org/10.3389/fmicb.2016.00211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766312PMC
March 2016

Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions.

Microb Ecol 2016 Feb 26;71(2):494-504. Epub 2015 Jun 26.

CSIRO Agriculture, St Lucia, QLD, 4067, Australia.

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http://dx.doi.org/10.1007/s00248-015-0641-4DOI Listing
February 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

Discovery of a novel methanogen prevalent in thawing permafrost.

Nat Commun 2014 ;5:3212

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

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http://dx.doi.org/10.1038/ncomms4212DOI Listing
October 2015

Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients.

PeerJ 2015 15;3:e1223. Epub 2015 Sep 15.

Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland , Brisbane, Queensland , Australia ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland , Brisbane, Queensland , Australia.

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http://dx.doi.org/10.7717/peerj.1223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579023PMC
September 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

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

J Microbiol Biol Educ 2015 May 1;16(1):50-60. Epub 2015 May 1.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland 4072, Australia ; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1128/jmbe.v16i1.816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416505PMC
May 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

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.

Sci Rep 2015 Mar 2;5:8678. Epub 2015 Mar 2.

School of Agriculture and Food Sciences, The University of Queensland, St. Lucia QLD, 4072, Australia.

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http://dx.doi.org/10.1038/srep08678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155403PMC
March 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

Effects of sample treatments on genome recovery via single-cell genomics.

ISME J 2014 Dec 13;8(12):2546-9. Epub 2014 Jun 13.

DOE Joint Genome Institute, Walnut Creek, CA, USA.

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http://dx.doi.org/10.1038/ismej.2014.92DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260712PMC
December 2014

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

JTD special edition 'Hot Topics in COPD'-The microbiome in COPD.

J Thorac Dis 2014 Nov;6(11):1525-31

1 Qld Lung Transplant Service, The Prince Charles Hospital, Brisbane, Australia ; 2 School of Medicine, The University of Queensland, Brisbane, Australia ; 3 Centre for Asthma & Respiratory Disease, University of Newcastle, Newcastle, Australia ; 4 Hunter Medical Research Institute, Newcastle, Australia ; 5 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.3978/j.issn.2072-1439.2014.11.08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255167PMC
November 2014

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters.

ISME J 2014 Oct 17;8(10):2015-28. Epub 2014 Apr 17.

1] Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia [2] Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.

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http://dx.doi.org/10.1038/ismej.2014.50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184015PMC
October 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

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.

Nature 2014 Sep 13;513(7517):242-5. Epub 2014 Jul 13.

1] Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA [2] Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85719, USA.

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http://www.nature.com/doifinder/10.1038/nature13459
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http://dx.doi.org/10.1038/nature13459DOI Listing
September 2014

Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties.

PLoS One 2013 16;8(10):e76751. Epub 2013 Oct 16.

Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076751PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797743PMC
August 2014

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

Microbiome 2014 7;2:11. Epub 2014 Apr 7.

Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia ; Advanced Water Management Center, Level 4, Gehrmann Laboratories Building (60), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1186/2049-2618-2-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021573PMC
August 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

In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery.

Methods Enzymol 2013 ;531:3-19

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/10.1016/B978-0-12-407863-5.00001-0DOI Listing
April 2014

Genome Sequence of Enterotoxigenic Escherichia coli Strain B2C.

Genome Announc 2014 Apr 10;2(2). Epub 2014 Apr 10.

School of Medical Sciences, Griffith Health Centre, Griffith University, Gold Coast Campus, Queensland, Australia.

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http://dx.doi.org/10.1128/genomeA.00247-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983298PMC
April 2014

A new species of Burkholderia isolated from sugarcane roots promotes plant growth.

Microb Biotechnol 2014 Mar 19;7(2):142-54. Epub 2013 Dec 19.

School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Qld, 4072, Australia; ARC Centre of Excellence in Bioinformatics, The University of Queensland, St. Lucia, Qld, 4072, Australia.

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http://doi.wiley.com/10.1111/1751-7915.12105
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http://dx.doi.org/10.1111/1751-7915.12105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937718PMC
March 2014

Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal.

ISME J 2013 Dec 25;7(12):2301-14. Epub 2013 Jul 25.

Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin at Madison, Madison, WI, USA.

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http://dx.doi.org/10.1038/ismej.2013.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834850PMC
December 2013

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage.

Nature 2013 Aug 28;500(7464):567-70. Epub 2013 Jul 28.

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

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http://dx.doi.org/10.1038/nature12375DOI Listing
August 2013

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.

Nat Biotechnol 2013 Jun 26;31(6):533-8. Epub 2013 May 26.

Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark.

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http://dx.doi.org/10.1038/nbt.2579DOI Listing
June 2013

Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data.

PLoS Comput Biol 2013 Apr 11;9(4):e1003031. Epub 2013 Apr 11.

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/10.1371/journal.pcbi.1003031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623719PMC
April 2013