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Items: 23


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.


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.


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.


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.


The lectin-like protein 1 in Lactobacillus rhamnosus GR-1 mediates tissue-specific adherence to vaginal epithelium and inhibits urogenital pathogens.

Petrova MI, Lievens E, Verhoeven TL, Macklaim JM, Gloor G, Schols D, Vanderleyden J, Reid G, Lebeer S.

Sci Rep. 2016 Nov 21;6:37437. doi: 10.1038/srep37437.


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.


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.


Microbiota of human breast tissue.

Urbaniak C, Cummins J, Brackstone M, Macklaim JM, Gloor GB, Baban CK, Scott L, O'Hanlon DM, Burton JP, Francis KP, Tangney M, Reid G.

Appl Environ Microbiol. 2014 May;80(10):3007-14. doi: 10.1128/AEM.00242-14. Epub 2014 Mar 7.


Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis.

Macklaim JM, Fernandes AD, Di Bella JM, Hammond JA, Reid G, Gloor GB.

Microbiome. 2013 Apr 12;1(1):12. doi: 10.1186/2049-2618-1-12.


ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.

Fernandes AD, Macklaim JM, Linn TG, Reid G, Gloor GB.

PLoS One. 2013 Jul 2;8(7):e67019. doi: 10.1371/journal.pone.0067019. Print 2013.


Persistence of the oral probiotic Streptococcus salivarius M18 is dose dependent and megaplasmid transfer can augment their bacteriocin production and adhesion characteristics.

Burton JP, Wescombe PA, Macklaim JM, Chai MH, Macdonald K, Hale JD, Tagg J, Reid G, Gloor GB, Cadieux PA.

PLoS One. 2013 Jun 13;8(6):e65991. doi: 10.1371/journal.pone.0065991. Print 2013.


Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman.

Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J, Renckens B, van Hijum SA, Siezen RJ.

PLoS One. 2013;8(3):e59239. doi: 10.1371/journal.pone.0059239. Epub 2013 Mar 19.


Adhesion of Lactobacillus iners AB-1 to human fibronectin: a key mediator for persistence in the vagina?

McMillan A, Macklaim JM, Burton JP, Reid G.

Reprod Sci. 2013 Jul;20(7):791-6. doi: 10.1177/1933719112466306. Epub 2012 Nov 30.


Exploring a road map to counter misconceptions about the cervicovaginal microbiome and disease.

Macklaim JM, Cohen CR, Donders G, Gloor GB, Hill JE, Parham GP, Ravel J, Spear G, van de Wijgert J, Reid G.

Reprod Sci. 2012 Nov;19(11):1154-62. doi: 10.1177/1933719112446075. Epub 2012 May 21. Review.


Vaginal microbiome and epithelial gene array in post-menopausal women with moderate to severe dryness.

Hummelen R, Macklaim JM, Bisanz JE, Hammond JA, McMillan A, Vongsa R, Koenig D, Gloor GB, Reid G.

PLoS One. 2011;6(11):e26602. doi: 10.1371/journal.pone.0026602. Epub 2011 Nov 2.


Responders and non-responders to probiotic interventions: how can we improve the odds?

Reid G, Gaudier E, Guarner F, Huffnagle GB, Macklaim JM, Munoz AM, Martini M, Ringel-Kulka T, Sartor B, Unal R, Verbeke K, Walter J; International Scientific Association for Probiotics and Prebiotics.

Gut Microbes. 2010 May-Jun;1(3):200-4. doi: 10.4161/gmic.1.3.12013.


At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1.

Macklaim JM, Gloor GB, Anukam KC, Cribby S, Reid G.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4688-95. doi: 10.1073/pnas.1000086107. Epub 2010 Nov 8.


Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products.

Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, MacPhee R, Reid G.

PLoS One. 2010 Oct 26;5(10):e15406. doi: 10.1371/journal.pone.0015406.


Deep sequencing of the vaginal microbiota of women with HIV.

Hummelen R, Fernandes AD, Macklaim JM, Dickson RJ, Changalucha J, Gloor GB, Reid G.

PLoS One. 2010 Aug 12;5(8):e12078. doi: 10.1371/journal.pone.0012078.

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