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Items: 1 to 50 of 67

1.

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

Rinke C, Rubino F, Messer LF, Youssef N, Parks DH, Chuvochina M, Brown M, Jeffries T, Tyson GW, Seymour JR, Hugenholtz P.

ISME J. 2018 Oct 15. doi: 10.1038/s41396-018-0282-y. [Epub ahead of print]

PMID:
30323263
2.

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

Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P.

Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27.

PMID:
30148503
3.

The importance of designating type material for uncultured taxa.

Chuvochina M, Rinke C, Parks DH, Rappé MS, Tyson GW, Yilmaz P, Whitman WB, Hugenholtz P.

Syst Appl Microbiol. 2018 Jul 18. pii: S0723-2020(18)30200-5. doi: 10.1016/j.syapm.2018.07.003. [Epub ahead of print]

4.

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.

Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, Muir JG, Gibson PR, Cuív PÓ, Hugenholtz P, Tyson GW, Morrison M.

ISME J. 2018 Dec;12(12):2942-2953. doi: 10.1038/s41396-018-0225-7. Epub 2018 Aug 1.

PMID:
30068938
5.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
6.

Erratum: Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P.

Front Microbiol. 2018 Apr 18;9:772. doi: 10.3389/fmicb.2018.00772. eCollection 2018.

7.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

8.

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

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2018 Feb;3(2):253. doi: 10.1038/s41564-017-0083-5.

PMID:
29234139
9.

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

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2017 Nov;2(11):1533-1542. doi: 10.1038/s41564-017-0012-7. Epub 2017 Sep 11. Erratum in: Nat Microbiol. 2017 Dec 12;:.

PMID:
28894102
10.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893.

PMID:
28787424
11.

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P.

Front Microbiol. 2017 Apr 24;8:682. doi: 10.3389/fmicb.2017.00682. eCollection 2017. Erratum in: Front Microbiol. 2018 Apr 18;9:772.

12.

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

Soo RM, Hemp J, Parks DH, Fischer WW, Hugenholtz P.

Science. 2017 Mar 31;355(6332):1436-1440. doi: 10.1126/science.aal3794.

PMID:
28360330
13.

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota.

Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW.

Nat Microbiol. 2016 Oct 3;1:16170. doi: 10.1038/nmicrobiol.2016.170.

PMID:
27694807
14.

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

Haroon MF, Thompson LR, Parks DH, Hugenholtz P, Stingl U.

Sci Data. 2016 Jul 5;3:160050. doi: 10.1038/sdata.2016.50.

15.

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

Robbins SJ, Evans PN, Parks DH, Golding SD, Tyson GW.

Front Microbiol. 2016 Jun 8;7:731. doi: 10.3389/fmicb.2016.00731. eCollection 2016.

16.

Genome-Based Microbial Taxonomy Coming of Age.

Hugenholtz P, Skarshewski A, Parks DH.

Cold Spring Harb Perspect Biol. 2016 Jun 1;8(6). pii: a018085. doi: 10.1101/cshperspect.a018085. Review.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

PMID:
22915830
28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

PMID:
20130030
33.

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.

34.

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.

35.

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.

PMID:
18717877
36.

Pharmacokinetic evaluation of single-dose intravenous daptomycin in patients with thermal burn injury.

Mohr JF 3rd, Ostrosky-Zeichner L, Wainright DJ, Parks DH, Hollenbeck TC, Ericsson CD.

Antimicrob Agents Chemother. 2008 May;52(5):1891-3. doi: 10.1128/AAC.01321-07. Epub 2008 Feb 25.

37.

Whole-molecule approach for determining orientation at isotropic surfaces by nonlinear vibrational spectroscopy.

Hore DK, Beaman DK, Parks DH, Richmond GL.

J Phys Chem B. 2005 Sep 8;109(35):16846-51.

PMID:
16853143
38.

Gestational gigantomastia after reduction mammaplasty.

Vidaeff AC, Parks DH.

Plast Reconstr Surg. 2004 Mar;113(3):1086-7. Review. No abstract available.

PMID:
15108923
39.

Gigantomastia complicating mirror syndrome in pregnancy.

Vidaeff AC, Ross PJ, Livingston CK, Parks DH.

Obstet Gynecol. 2003 May;101(5 Pt 2):1139-42.

PMID:
12738130
40.

Prognostic indicators in the elderly patient with burns.

Covington DS, Wainwright DJ, Parks DH.

J Burn Care Rehabil. 1996 May-Jun;17(3):222-30.

PMID:
8736367
41.

Changing patterns in the epidemiology and treatment of zygoma fractures: 10-year review.

Covington DS, Wainwright DJ, Teichgraeber JF, Parks DH.

J Trauma. 1994 Aug;37(2):243-8.

PMID:
8064924
42.

Academic consequences of a trauma system failure.

Fischer RP, Pepe PE, Reed RL 2nd, Parks DH, Prentice FD, Mattox KL.

J Trauma. 1990 Jul;30(7):784-90; discussion 790-1.

PMID:
2380995
43.

Nasal surgery complications.

Teichgraeber JF, Riley WB, Parks DH.

Plast Reconstr Surg. 1990 Apr;85(4):527-31.

PMID:
2315392
44.

Timing of burn therapy in the pediatric patient.

Parks DH.

Clin Plast Surg. 1990 Jan;17(1):65-70.

PMID:
2302919
45.

Post-trauma reconstruction with free tissue transfer--analysis of 442 consecutive cases.

Melissinos EG, Parks DH.

J Trauma. 1989 Aug;29(8):1095-102; discussion 1102-3.

PMID:
2668546
46.

Primary skin closure in large myelomeningoceles.

Teichgraeber JF, Riley WB, Parks DH.

Pediatr Neurosci. 1989;15(1):18-22.

PMID:
2635770
47.

Structured exercise circuit program for burn patients.

Parrott M, Ryan R, Parks DH, Wainwright DJ.

J Burn Care Rehabil. 1988 Nov-Dec;9(6):666-8.

PMID:
3220877
48.

Optimal composition of burn resuscitation fluids.

Carvajal HF, Parks DH.

Crit Care Med. 1988 Jul;16(7):695-700.

PMID:
3371046
49.

Managing the difficult airway in patients with burns of the head and neck.

Larson SM, Parks DH.

J Burn Care Rehabil. 1988 Jan-Feb;9(1):55-6.

PMID:
3356740
50.

Evaluation of a caloric requirement formula in burned children treated with early excision.

Hildreth MA, Herndon DN, Parks DH, Desai MH, Rutan T.

J Trauma. 1987 Feb;27(2):188-9.

PMID:
3546712

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