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omicplotR: visualizing omic datasets as compositions.

Giguere DJ, Macklaim JM, Lieng BY, Gloor GB.

BMC Bioinformatics. 2019 Nov 15;20(1):580. doi: 10.1186/s12859-019-3174-x.


Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease.

Laforet M, McMurrough TA, Vu M, Brown CM, Zhang K, Junop MS, Gloor GB, Edgell DR.

Nucleic Acids Res. 2019 Nov 18;47(20):10830-10841. doi: 10.1093/nar/gkz866.


Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing.

Hamilton TA, Pellegrino GM, Therrien JA, Ham DT, Bartlett PC, Karas BJ, Gloor GB, Edgell DR.

Nat Commun. 2019 Oct 4;10(1):4544. doi: 10.1038/s41467-019-12448-3.


Targeted sequencing reveals expanded genetic diversity of human transfer RNAs.

Berg MD, Giguere DJ, Dron JS, Lant JT, Genereaux J, Liao C, Wang J, Robinson JF, Gloor GB, Hegele RA, O'Donoghue P, Brandl CJ.

RNA Biol. 2019 Nov;16(11):1574-1585. doi: 10.1080/15476286.2019.1646079. Epub 2019 Aug 13.


A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease.

Wootton DG, Cox MJ, Gloor GB, Litt D, Hoschler K, German E, Court J, Eneje O, Keogan L, Macfarlane L, Wilks S, Diggle PJ, Woodhead M, Moffatt MF, Cookson WOC, Gordon SB.

Sci Rep. 2019 Feb 20;9(1):2388. doi: 10.1038/s41598-018-38090-5.


A new genomic blueprint of the human gut microbiota.

Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD, Finn RD.

Nature. 2019 Apr;568(7753):499-504. doi: 10.1038/s41586-019-0965-1. Epub 2019 Feb 11.


Unaccounted risk of cardiovascular disease: the role of the microbiome in lipid metabolism.

Joris BR, Gloor GB.

Curr Opin Lipidol. 2019 Apr;30(2):125-133. doi: 10.1097/MOL.0000000000000582.


Acceptor Stem Differences Contribute to Species-Specific Use of Yeast and Human tRNASer.

Berg MD, Genereaux J, Zhu Y, Mian S, Gloor GB, Brandl CJ.

Genes (Basel). 2018 Dec 7;9(12). pii: E612. doi: 10.3390/genes9120612.


Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases.

McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR.

Nucleic Acids Res. 2018 Dec 14;46(22):11990-12007. doi: 10.1093/nar/gky976.


From RNA-seq to Biological Inference: Using Compositional Data Analysis in Meta-Transcriptomics.

Macklaim JM, Gloor GB.

Methods Mol Biol. 2018;1849:193-213. doi: 10.1007/978-1-4939-8728-3_13.


Comparative Genomic and Phenotypic Analysis of the Vaginal Probiotic Lactobacillus rhamnosus GR-1.

Petrova MI, Macklaim JM, Wuyts S, Verhoeven T, Vanderleyden J, Gloor GB, Lebeer S, Reid G.

Front Microbiol. 2018 Jun 15;9:1278. doi: 10.3389/fmicb.2018.01278. eCollection 2018.


Mediterranean Diet Score: Associations with Metabolic Products of the Intestinal Microbiome, Carotid Plaque Burden, and Renal Function.

Pignanelli M, Just C, Bogiatzi C, Dinculescu V, Gloor GB, Allen-Vercoe E, Reid G, Urquhart BL, Ruetz KN, Velenosi TJ, Spence JD.

Nutrients. 2018 Jun 16;10(6). pii: E779. doi: 10.3390/nu10060779.


Pilot assessment of probiotics for pregnant women in Rwanda.

McMillan A, Rulisa S, Gloor GB, Macklaim JM, Sumarah M, Reid G.

PLoS One. 2018 Jun 18;13(6):e0195081. doi: 10.1371/journal.pone.0195081. eCollection 2018.


Data on the gut and saliva microbiota from a cohort of atherosclerosis patients determined by 16S rRNA gene sequencing.

Gloor GB, Wong RG, Allen-Vercoe E, Dinculescu V, Pignanelli M, Bogiatzi C, Reid G, Spence JD.

Data Brief. 2018 May 11;19:481-485. doi: 10.1016/j.dib.2018.05.032. eCollection 2018 Aug.


Microbiome Datasets Are Compositional: And This Is Not Optional.

Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ.

Front Microbiol. 2017 Nov 15;8:2224. doi: 10.3389/fmicb.2017.02224. eCollection 2017. Review.


Evaluation of sampling and storage procedures on preserving the community structure of stool microbiota: A simple at-home toilet-paper collection method.

Al KF, Bisanz JE, Gloor GB, Reid G, Burton JP.

J Microbiol Methods. 2018 Jan;144:117-121. doi: 10.1016/j.mimet.2017.11.014. Epub 2017 Nov 16.


The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young.

Bian G, Gloor GB, Gong A, Jia C, Zhang W, Hu J, Zhang H, Zhang Y, Zhou Z, Zhang J, Burton JP, Reid G, Xiao Y, Zeng Q, Yang K, Li J.

mSphere. 2017 Sep 27;2(5). pii: e00327-17. doi: 10.1128/mSphere.00327-17. eCollection 2017 Sep-Oct.


Lactobacillus rhamnosus GR-1 Attenuates Induction of Hypertrophy in Cardiomyocytes but Not through Secreted Protein MSP-1 (p75).

Ettinger G, Burton JP, Gloor GB, Reid G.

PLoS One. 2017 Jan 13;12(1):e0168622. doi: 10.1371/journal.pone.0168622. eCollection 2017.


Impact of birth weight and postnatal diet on the gut microbiota of young adult guinea pigs.

Al K, Sarr O, Dunlop K, Gloor GB, Reid G, Burton J, Regnault TR.

PeerJ. 2017 Jan 3;5:e2840. doi: 10.7717/peerj.2840. eCollection 2017.


The acute effects of inulin and resistant starch on postprandial serum short-chain fatty acids and second-meal glycemic response in lean and overweight humans.

Rahat-Rozenbloom S, Fernandes J, Cheng J, Gloor GB, Wolever TM.

Eur J Clin Nutr. 2017 Feb;71(2):227-233. doi: 10.1038/ejcn.2016.248. Epub 2016 Dec 14.


Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease.

Wolfs JM, Hamilton TA, Lant JT, Laforet M, Zhang J, Salemi LM, Gloor GB, Schild-Poulter C, Edgell DR.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):14988-14993. doi: 10.1073/pnas.1616343114. Epub 2016 Dec 12.


Population Differences at MHC Do Not Explain Enhanced Resistance of Song Sparrows to Local Parasites.

Slade JW, Sarquis-Adamson Y, Gloor GB, Lachance MA, MacDougall-Shackleton EA.

J Hered. 2017 Mar 1;108(2):127-134. doi: 10.1093/jhered/esw082.


Chemical composition of preen wax reflects major histocompatibility complex similarity in songbirds.

Slade JW, Watson MJ, Kelly TR, Gloor GB, Bernards MA, MacDougall-Shackleton EA.

Proc Biol Sci. 2016 Nov 16;283(1842). pii: 20161966.


Expanding the UniFrac Toolbox.

Wong RG, Wu JR, Gloor GB.

PLoS One. 2016 Sep 15;11(9):e0161196. doi: 10.1371/journal.pone.0161196. eCollection 2016.


Post-acquisition filtering of salt cluster artefacts for LC-MS based human metabolomic studies.

McMillan A, Renaud JB, Gloor GB, Reid G, Sumarah MW.

J Cheminform. 2016 Sep 6;8(1):44. doi: 10.1186/s13321-016-0156-0. eCollection 2016.


Research Priorities in the Field of Posttraumatic Pain and Disability: Results of a Transdisciplinary Consensus-Generating Workshop.

Walton DM, Elliott JM, Lee J, Loh E, MacDermid JC, Schabrun S, Siqueira WL, Corneil BD, Aal B, Birmingham T, Brown A, Cooper LK, Dickey JP, Dixon SJ, Fraser DD, Gati JS, Gloor GB, Good G, Holdsworth D, McLean SA, Millard W, Miller J, Sadi J, Seminowicz DA, Shoemaker JK, Siegmund GP, Vertseegh T, Wideman TH.

Pain Res Manag. 2016;2016:1859434. doi: 10.1155/2016/1859434. Epub 2016 Jun 14.


New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA.

Asemaninejad A, Weerasuriya N, Gloor GB, Lindo Z, Thorn RG.

PLoS One. 2016 Jul 8;11(7):e0159043. doi: 10.1371/journal.pone.0159043. eCollection 2016.


The Microbiota of Breast Tissue and Its Association with Breast Cancer.

Urbaniak C, Gloor GB, Brackstone M, Scott L, Tangney M, Reid G.

Appl Environ Microbiol. 2016 Jul 29;82(16):5039-48. doi: 10.1128/AEM.01235-16. Print 2016 Aug 15.


The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals.

Bisanz JE, Suppiah P, Thomson WM, Milne T, Yeoh N, Nolan A, Ettinger G, Reid G, Gloor GB, Burton JP, Cullinan MP, Stebbings SM.

PeerJ. 2016 Jun 9;4:e2095. doi: 10.7717/peerj.2095. eCollection 2016.


A human gut ecosystem protects against C. difficile disease by targeting TcdA.

Martz SL, Guzman-Rodriguez M, He SM, Noordhof C, Hurlbut DJ, Gloor GB, Carlucci C, Weese S, Allen-Vercoe E, Sun J, Claud EC, Petrof EO.

J Gastroenterol. 2017 Apr;52(4):452-465. doi: 10.1007/s00535-016-1232-y. Epub 2016 Jun 21.


Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data.

Gloor GB, Reid G.

Can J Microbiol. 2016 Aug;62(8):692-703. doi: 10.1139/cjm-2015-0821. Epub 2016 Apr 12. Review.


It's all relative: analyzing microbiome data as compositions.

Gloor GB, Wu JR, Pawlowsky-Glahn V, Egozcue JJ.

Ann Epidemiol. 2016 May;26(5):322-9. doi: 10.1016/j.annepidem.2016.03.003. Epub 2016 Apr 2. Review.


Human milk microbiota profiles in relation to birthing method, gestation and infant gender.

Urbaniak C, Angelini M, Gloor GB, Reid G.

Microbiome. 2016 Jan 6;4:1. doi: 10.1186/s40168-015-0145-y.


Administration of defined microbiota is protective in a murine Salmonella infection model.

Martz SL, McDonald JA, Sun J, Zhang YG, Gloor GB, Noordhof C, He SM, Gerbaba TK, Blennerhassett M, Hurlbut DJ, Allen-Vercoe E, Claud EC, Petrof EO.

Sci Rep. 2015 Nov 4;5:16094. doi: 10.1038/srep16094.


A multi-platform metabolomics approach identifies highly specific biomarkers of bacterial diversity in the vagina of pregnant and non-pregnant women.

McMillan A, Rulisa S, Sumarah M, Macklaim JM, Renaud J, Bisanz JE, Gloor GB, Reid G.

Sci Rep. 2015 Sep 21;5:14174. doi: 10.1038/srep14174.


Changes in vaginal microbiota following antimicrobial and probiotic therapy.

Macklaim JM, Clemente JC, Knight R, Gloor GB, Reid G.

Microb Ecol Health Dis. 2015 Aug 14;26:27799. doi: 10.3402/mehd.v26.27799. eCollection 2015.


Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt.

Bisanz JE, Enos MK, PrayGod G, Seney S, Macklaim JM, Chilton S, Willner D, Knight R, Fusch C, Fusch G, Gloor GB, Burton JP, Reid G.

Appl Environ Microbiol. 2015 Aug;81(15):4965-75. doi: 10.1128/AEM.00780-15. Epub 2015 May 15.


Subinhibitory antibiotic therapy alters recurrent urinary tract infection pathogenesis through modulation of bacterial virulence and host immunity.

Goneau LW, Hannan TJ, MacPhee RA, Schwartz DJ, Macklaim JM, Gloor GB, Razvi H, Reid G, Hultgren SJ, Burton JP.

mBio. 2015 Mar 31;6(2). pii: e00356-15. doi: 10.1128/mBio.00356-15.


Is there a role for probiotics in the prevention of preterm birth?

Yang S, Reid G, Challis JR, Kim SO, Gloor GB, Bocking AD.

Front Immunol. 2015 Feb 17;6:62. doi: 10.3389/fimmu.2015.00062. eCollection 2015. Review.


Systematic investigation of hierarchical phosphorylation by protein kinase CK2.

St-Denis N, Gabriel M, Turowec JP, Gloor GB, Li SS, Gingras AC, Litchfield DW.

J Proteomics. 2015 Apr 6;118:49-62. doi: 10.1016/j.jprot.2014.10.020. Epub 2014 Nov 5.


Randomized open-label pilot study of the influence of probiotics and the gut microbiome on toxic metal levels in Tanzanian pregnant women and school children.

Bisanz JE, Enos MK, Mwanga JR, Changalucha J, Burton JP, Gloor GB, Reid G.

mBio. 2014 Oct 7;5(5):e01580-14. doi: 10.1128/mBio.01580-14.


A systems biology approach investigating the effect of probiotics on the vaginal microbiome and host responses in a double blind, placebo-controlled clinical trial of post-menopausal women.

Bisanz JE, Seney S, McMillan A, Vongsa R, Koenig D, Wong L, Dvoracek B, Gloor GB, Sumarah M, Ford B, Herman D, Burton JP, Reid G.

PLoS One. 2014 Aug 15;9(8):e104511. doi: 10.1371/journal.pone.0104511. eCollection 2014.


Effect of chemotherapy on the microbiota and metabolome of human milk, a case report.

Urbaniak C, McMillan A, Angelini M, Gloor GB, Sumarah M, Burton JP, Reid G.

Microbiome. 2014 Jul 11;2:24. doi: 10.1186/2049-2618-2-24. eCollection 2014.


Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping.

Kernohan KD, Vernimmen D, Gloor GB, Bérubé NG.

Nucleic Acids Res. 2014 Jul;42(13):8356-68. doi: 10.1093/nar/gku564. Epub 2014 Jul 2.


Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues.

McMurrough TA, Dickson RJ, Thibert SM, Gloor GB, Edgell DR.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):E2376-83. doi: 10.1073/pnas.1322352111. Epub 2014 May 27.


Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.

Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB.

Microbiome. 2014 May 5;2:15. doi: 10.1186/2049-2618-2-15. eCollection 2014.


Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendations from an African workshop.

Reid G, Nduti N, Sybesma W, Kort R, Kollmann TR, Adam R, Boga H, Brown EM, Einerhand A, El-Nezami H, Gloor GB, Kavere II, Lindahl J, Manges A, Mamo W, Martin R, McMillan A, Obiero J, Ochieng' PA, Onyango A, Rulisa S, Salminen E, Salminen S, Sije A, Swann JR, van Treuren W, Waweru D, Kemp SJ.

Microbiome. 2014 Apr 16;2:12. doi: 10.1186/2049-2618-2-12. eCollection 2014.


Evidence for greater production of colonic short-chain fatty acids in overweight than lean humans.

Rahat-Rozenbloom S, Fernandes J, Gloor GB, Wolever TM.

Int J Obes (Lond). 2014 Dec;38(12):1525-31. doi: 10.1038/ijo.2014.46. Epub 2014 Mar 19.


Probiotic administration attenuates myocardial hypertrophy and heart failure after myocardial infarction in the rat.

Gan XT, Ettinger G, Huang CX, Burton JP, Haist JV, Rajapurohitam V, Sidaway JE, Martin G, Gloor GB, Swann JR, Reid G, Karmazyn M.

Circ Heart Fail. 2014 May;7(3):491-9. doi: 10.1161/CIRCHEARTFAILURE.113.000978. Epub 2014 Mar 13.


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