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Genome-Based Microbial Taxonomy Coming of Age.

Hugenholtz P, Skarshewski A, Parks DH.

Cold Spring Harb Perspect Biol. 2016 Mar 17. pii: a018085. doi: 10.1101/cshperspect.a018085. [Epub ahead of print]


A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres.

Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P.

Front Microbiol. 2016 Jan 7;6:1469. doi: 10.3389/fmicb.2015.01469. eCollection 2015.


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

Yeoh YK, Sekiguchi Y, Parks DH, Hugenholtz P.

Mol Biol Evol. 2016 Apr;33(4):915-27. doi: 10.1093/molbev/msv281. Epub 2015 Nov 28.


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

Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW.

Science. 2015 Oct 23;350(6259):434-8. doi: 10.1126/science.aac7745.


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

Soo RM, Woodcroft BJ, Parks DH, Tyson GW, Hugenholtz P.

PeerJ. 2015 May 21;3:e968. doi: 10.7717/peerj.968. eCollection 2015.


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

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW.

Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. Epub 2015 May 14.


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

Abdul Rahman N, Parks DH, Willner DL, Engelbrektson AL, Goffredi SK, Warnecke F, Scheffrahn RH, Hugenholtz P.

Microbiome. 2015 Feb 25;3:5. doi: 10.1186/s40168-015-0067-8. eCollection 2015.


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

Sekiguchi Y, Ohashi A, Parks DH, Yamauchi T, Tyson GW, Hugenholtz P.

PeerJ. 2015 Jan 27;3:e740. doi: 10.7717/peerj.740. eCollection 2015.


STAMP: statistical analysis of taxonomic and functional profiles.

Parks DH, Tyson GW, Hugenholtz P, Beiko RG.

Bioinformatics. 2014 Nov 1;30(21):3123-4. doi: 10.1093/bioinformatics/btu494. Epub 2014 Jul 23.


An expanded genomic representation of the phylum cyanobacteria.

Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P.

Genome Biol Evol. 2014 May;6(5):1031-45. doi: 10.1093/gbe/evu073.


GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MG, Beiko RG.

PLoS One. 2013 Jul 29;8(7):e69885. doi: 10.1371/journal.pone.0069885. Print 2013.


Measuring community similarity with phylogenetic networks.

Parks DH, Beiko RG.

Mol Biol Evol. 2012 Dec;29(12):3947-58. doi: 10.1093/molbev/mss200. Epub 2012 Aug 21.


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

Parks DH, Beiko RG.

ISME J. 2013 Jan;7(1):173-83. doi: 10.1038/ismej.2012.88. Epub 2012 Aug 2.


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

MacDonald NJ, Parks DH, Beiko RG.

Nucleic Acids Res. 2012 Aug;40(14):e111. doi: 10.1093/nar/gks335. Epub 2012 Apr 24.


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

Parks DH, MacDonald NJ, Beiko RG.

BMC Bioinformatics. 2011 Aug 9;12:328. doi: 10.1186/1471-2105-12-328.


Toll-like receptor 3 upregulation by type I interferon in healthy and scleroderma dermal fibroblasts.

Agarwal SK, Wu M, Livingston CK, Parks DH, Mayes MD, Arnett FC, Tan FK.

Arthritis Res Ther. 2011 Jan 11;13(1):R3. doi: 10.1186/ar3221.


Identifying biologically relevant differences between metagenomic communities.

Parks DH, Beiko RG.

Bioinformatics. 2010 Mar 15;26(6):715-21. doi: 10.1093/bioinformatics/btq041. Epub 2010 Feb 3.


Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF.

Appl Environ Microbiol. 2009 Dec;75(23):7537-41. doi: 10.1128/AEM.01541-09. Epub 2009 Oct 2.


GenGIS: A geospatial information system for genomic data.

Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S, Beiko RG.

Genome Res. 2009 Oct;19(10):1896-904. doi: 10.1101/gr.095612.109. Epub 2009 Jul 27.


Saline irrigation to facilitate unfolding of selected full-thickness skin grafts.

Chen TM, Wanitphakdeedecha R, Nguyen TH, Parks DH.

Int J Dermatol. 2008 Aug;47(8):869-70. doi: 10.1111/j.1365-4632.2008.03592.x. No abstract available.

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