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Items: 40

1.

Mucosal associated invariant T cells and Vδ2+ γδ T cells in community acquired pneumonia: association of abundance in sputum with clinical severity and outcome.

Hannaway RF, Wang X, Schneider M, Slow S, Cowan J, Brockway B, Schofield MR, Morgan XC, Murdoch DR, Ussher JE.

Clin Exp Immunol. 2019 Oct 6. doi: 10.1111/cei.13377. [Epub ahead of print]

PMID:
31587268
2.

Diverse hydrogen production and consumption pathways influence methane production in ruminants.

Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI.

ISME J. 2019 Oct;13(10):2617-2632. doi: 10.1038/s41396-019-0464-2. Epub 2019 Jun 26.

3.

Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand.

Rushton-Green R, Darnell RL, Taiaroa G, Carter GP, Cook GM, Morgan XC.

Appl Environ Microbiol. 2019 Jun 17;85(13). pii: e00137-19. doi: 10.1128/AEM.00137-19. Print 2019 Jul 1.

4.

Oral probiotics reduce halitosis in patients wearing orthodontic braces: a randomized, triple-blind, placebo-controlled trial.

Benic GZ, Farella M, Morgan XC, Viswam J, Heng NC, Cannon RD, Mei L.

J Breath Res. 2019 May 31;13(3):036010. doi: 10.1088/1752-7163/ab1c81.

PMID:
31022704
5.

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N.

Cell. 2019 Jan 24;176(3):649-662.e20. doi: 10.1016/j.cell.2019.01.001. Epub 2019 Jan 17.

6.

Invited Commentary: Improving the Accessibility of Human Microbiome Project Data Through Integration With R/Bioconductor.

Griffith JC, Morgan XC.

Am J Epidemiol. 2019 Jun 1;188(6):1027-1030. doi: 10.1093/aje/kwz007.

PMID:
30649168
7.

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.

Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB.

PeerJ. 2019 Jan 4;7:e6160. doi: 10.7717/peerj.6160. eCollection 2019.

8.

Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT.

Murphy R, Morgan XC, Wang XY, Wickens K, Purdie G, Fitzharris P, Otal A, Lawley B, Stanley T, Barthow C, Crane J, Mitchell EA, Tannock GW.

Benef Microbes. 2019 Feb 8;10(1):5-17. doi: 10.3920/BM2017.0191. Epub 2018 Dec 21.

PMID:
30574802
9.

Microbial biogeography of 925 geothermal springs in New Zealand.

Power JF, Carere CR, Lee CK, Wakerley GLJ, Evans DW, Button M, White D, Climo MD, Hinze AM, Morgan XC, McDonald IR, Cary SC, Stott MB.

Nat Commun. 2018 Jul 23;9(1):2876. doi: 10.1038/s41467-018-05020-y.

10.

bioBakery: a meta'omic analysis environment.

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C.

Bioinformatics. 2018 Apr 1;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754.

11.

Experimental design and quantitative analysis of microbial community multiomics.

Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C.

Genome Biol. 2017 Nov 30;18(1):228. doi: 10.1186/s13059-017-1359-z. Review.

12.

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice.

Yasuda K, Hsu T, Gallini CA, Mclver LJ, Schwager E, Shi A, DuLong CR, Schwager RN, Abu-Ali GS, Franzosa EA, Garrett WS, Huttenhower C, Morgan XC.

mSystems. 2017 Aug 8;2(4). pii: e00047-17. doi: 10.1128/mSystems.00047-17. eCollection 2017 Jul-Aug.

13.

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment.

Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, DuLong C, Baranowski C, Gevers D, Green JL, Morgan XC, Spengler JD, Huttenhower C.

mSystems. 2016 Jun 28;1(3). pii: e00018-16. eCollection 2016 May-Jun.

14.

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone.

Lee KC, Stott MB, Dunfield PF, Huttenhower C, McDonald IR, Morgan XC.

Appl Environ Microbiol. 2016 May 31;82(12):3572-81. doi: 10.1128/AEM.00139-16. Print 2016 Jun 15.

15.

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.

Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C.

Genome Med. 2016 Feb 17;8(1):17. doi: 10.1186/s13073-016-0271-6.

16.

Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).

Lee KC, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB.

Stand Genomic Sci. 2015 Nov 14;10:101. doi: 10.1186/s40793-015-0099-5. eCollection 2015.

17.

Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus.

Houghton KM, Morgan XC, Lagutin K, MacKenzie AD, Vyssotskii M, Mitchell KA, McDonald IR, Morgan HW, Power JF, Moreau JW, Hanssen E, Stott MB.

Int J Syst Evol Microbiol. 2015 Dec;65(12):4479-87. doi: 10.1099/ijsem.0.000598. Epub 2015 Sep 14.

PMID:
26374291
18.

A reproducible approach to high-throughput biological data acquisition and integration.

Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C.

PeerJ. 2015 Mar 31;3:e791. doi: 10.7717/peerj.791. eCollection 2015.

19.

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C.

Nat Rev Microbiol. 2015 Jun;13(6):360-72. doi: 10.1038/nrmicro3451. Epub 2015 Apr 27. Review.

20.

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C.

Genome Biol. 2015 Apr 8;16:67. doi: 10.1186/s13059-015-0637-x.

21.

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque.

Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, Miller AD, Westmoreland SV, Mansfield KG, Vallender EJ, Miller GM, Rowlett JK, Gevers D, Huttenhower C, Morgan XC.

Cell Host Microbe. 2015 Mar 11;17(3):385-391. doi: 10.1016/j.chom.2015.01.015. Epub 2015 Feb 26.

22.

Determining microbial products and identifying molecular targets in the human microbiome.

Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower C.

Cell Metab. 2014 Nov 4;20(5):731-741. doi: 10.1016/j.cmet.2014.10.003. Epub 2014 Nov 4. Review.

23.

Relating the metatranscriptome and metagenome of the human gut.

Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38. doi: 10.1073/pnas.1319284111. Epub 2014 May 19.

24.

The treatment-naive microbiome in new-onset Crohn's disease.

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ.

Cell Host Microbe. 2014 Mar 12;15(3):382-392. doi: 10.1016/j.chom.2014.02.005.

25.

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission.

Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JE, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WS.

ISME J. 2014 Jul;8(7):1403-17. doi: 10.1038/ismej.2014.3. Epub 2014 Feb 6.

26.

Meta'omic analytic techniques for studying the intestinal microbiome.

Morgan XC, Huttenhower C.

Gastroenterology. 2014 May;146(6):1437-1448.e1. doi: 10.1053/j.gastro.2014.01.049. Epub 2014 Jan 28. Review.

PMID:
24486053
27.

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes.

Lee KC, Morgan XC, Dunfield PF, Tamas I, McDonald IR, Stott MB.

ISME J. 2014 Jul;8(7):1522-33. doi: 10.1038/ismej.2013.251. Epub 2014 Jan 30.

28.

Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils.

Crowe MA, Power JF, Morgan XC, Dunfield PF, Lagutin K, Rijpstra IC, Vyssotski GN, Sinninghe Damste JS, Houghton KM, Ryan JL, Stott MB.

Int J Syst Evol Microbiol. 2014 Jan;64(Pt 1):220-7. doi: 10.1099/ijs.0.055079-0. Epub 2013 Sep 18. Erratum in: Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):1074. Rijpstra, W I C [removed]; Vyssotski, G N S [added].

PMID:
24048862
29.

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.

Segata N, Börnigen D, Morgan XC, Huttenhower C.

Nat Commun. 2013;4:2304. doi: 10.1038/ncomms3304.

30.

Functional profiling of the gut microbiome in disease-associated inflammation.

Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C.

Genome Med. 2013 Jul 31;5(7):65. doi: 10.1186/gm469. eCollection 2013. Review.

31.

Computational meta'omics for microbial community studies.

Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C.

Mol Syst Biol. 2013 May 14;9:666. doi: 10.1038/msb.2013.22. Review.

32.

Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions.

Lee KC, Herbold CW, Dunfield PF, Morgan XC, McDonald IR, Stott MB.

Appl Environ Microbiol. 2013 Apr;79(7):2484-7. doi: 10.1128/AEM.03333-12. Epub 2013 Feb 1.

33.

Chapter 12: Human microbiome analysis.

Morgan XC, Huttenhower C.

PLoS Comput Biol. 2012;8(12):e1002808. doi: 10.1371/journal.pcbi.1002808. Epub 2012 Dec 27.

34.

Biodiversity and functional genomics in the human microbiome.

Morgan XC, Segata N, Huttenhower C.

Trends Genet. 2013 Jan;29(1):51-8. doi: 10.1016/j.tig.2012.09.005. Epub 2012 Nov 7. Review.

35.

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.

Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C.

Genome Biol. 2012 Apr 16;13(9):R79. doi: 10.1186/gb-2012-13-9-r79.

36.

Electing a candidate: a speculative history of the bacterial phylum OP10.

Dunfield PF, Tamas I, Lee KC, Morgan XC, McDonald IR, Stott MB.

Environ Microbiol. 2012 Dec;14(12):3069-80. doi: 10.1111/j.1462-2920.2012.02742.x. Epub 2012 Apr 13.

PMID:
22497633
37.

Fatty Acids of Chthonomonas calidirosea, of a novel class Chthonomonadetes from a recently described phylum Armatimonadetes.

Vyssotski M, Lee KC, Lagutin K, Ryan J, Morgan XC, Stott MB.

Lipids. 2011 Dec;46(12):1155-61. doi: 10.1007/s11745-011-3597-2. Epub 2011 Jul 31.

PMID:
21805326
38.

Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10.

Lee KC, Dunfield PF, Morgan XC, Crowe MA, Houghton KM, Vyssotski M, Ryan JL, Lagutin K, McDonald IR, Stott MB.

Int J Syst Evol Microbiol. 2011 Oct;61(Pt 10):2482-90. doi: 10.1099/ijs.0.027235-0. Epub 2010 Nov 19.

PMID:
21097641
39.
40.

Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.

Kim J, Bhinge AA, Morgan XC, Iyer VR.

Nat Methods. 2005 Jan;2(1):47-53. Epub 2004 Dec 21.

PMID:
15782160

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