|Microbiome datasets are compositional: and this is not optional|
GB Gloor, JM Macklaim, V Pawlowsky-Glahn, JJ Egozcue
Frontiers in microbiology 8, 2224, 2017
|Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis|
AD Fernandes, JN Reid, JM Macklaim, TA McMurrough, DR Edgell, ...
Microbiome 2 (1), 1-13, 2014
|Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products|
GB Gloor, R Hummelen, JM Macklaim, RJ Dickson, AD Fernandes, ...
PLoS One 5 (10), e15406, 2010
|Microbiota of human breast tissue|
C Urbaniak, J Cummins, M Brackstone, JM Macklaim, GB Gloor, ...
Applied and environmental microbiology 80 (10), 3007-3014, 2014
|Deep sequencing of the vaginal microbiota of women with HIV|
R Hummelen, AD Fernandes, JM Macklaim, RJ Dickson, J Changalucha, ...
PloS one 5 (8), e12078, 2010
|Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis|
JM Macklaim, AD Fernandes, JM Di Bella, JA Hammond, G Reid, ...
Microbiome 1 (1), 1-11, 2013
|ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq|
AD Fernandes, JM Macklaim, TG Linn, G Reid, GB Gloor
PLoS One 8 (7), e67019, 2013
|At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1|
JM Macklaim, GB Gloor, KC Anukam, S Cribby, G Reid
Proceedings of the National Academy of Sciences 108 (Supplement 1), 4688-4695, 2011
|Vaginal microbiome and epithelial gene array in post-menopausal women with moderate to severe dryness|
R Hummelen, JM Macklaim, JE Bisanz, JA Hammond, A McMillan, ...
PloS one 6 (11), e26602, 2011
|Changes in vaginal microbiota following antimicrobial and probiotic therapy|
JM Macklaim, JC Clemente, R Knight, GB Gloor, G Reid
Microbial ecology in health and disease 26 (1), 27799, 2015
|A multi-platform metabolomics approach identifies highly specific biomarkers of bacterial diversity in the vagina of pregnant and non-pregnant women|
A McMillan, S Rulisa, M Sumarah, JM Macklaim, J Renaud, JE Bisanz, ...
Scientific reports 5 (1), 1-14, 2015
|Microbiota at multiple body sites during pregnancy in a rural Tanzanian population and effects of Moringa-supplemented probiotic yogurt|
JE Bisanz, MK Enos, G PrayGod, S Seney, JM Macklaim, S Chilton, ...
Applied and environmental microbiology 81 (15), 4965-4975, 2015
|Persistence of the oral probiotic Streptococcus salivarius M18 is dose dependent and megaplasmid transfer can augment their bacteriocin production and adhesion characteristics|
JP Burton, PA Wescombe, JM Macklaim, MHC Chai, K MacDonald, ...
Plos one 8 (6), e65991, 2013
|Adhesion of Lactobacillus iners AB-1 to human fibronectin: a key mediator for persistence in the vagina?|
A McMillan, JM Macklaim, JP Burton, G Reid
Reproductive Sciences 20 (7), 791-796, 2013
|Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman|
KC Anukam, JM Macklaim, GB Gloor, G Reid, J Boekhorst, B Renckens, ...
PloS one 8 (3), e59239, 2013
|Subinhibitory antibiotic therapy alters recurrent urinary tract infection pathogenesis through modulation of bacterial virulence and host immunity|
LW Goneau, TJ Hannan, RA MacPhee, DJ Schwartz, JM Macklaim, ...
MBio 6 (2), e00356-15, 2015
|Responders and non-responders to probiotic interventions: How can we improve the odds?|
G Reid, E Gaudier, F Guarner, GB Huffnagle, JM Macklaim, AM Munoz, ...
Gut Microbes 1 (3), 200, 2010
|Compositional uncertainty should not be ignored in high-throughput sequencing data analysis|
GB Gloor, JM Macklaim, M Vu, AD Fernandes
Austrian Journal of Statistics 45 (4), 73-87, 2016
|Displaying variation in large datasets: plotting a visual summary of effect sizes|
GB Gloor, JM Macklaim, AD Fernandes
Journal of Computational and Graphical Statistics 25 (3), 971-979, 2016
|Exploring a road map to counter misconceptions about the cervicovaginal microbiome and disease|
JM Macklaim, CR Cohen, G Donders, GB Gloor, JE Hill, GP Parham, ...
Reproductive sciences 19 (11), 1154-1162, 2012