GLOOR, Gregory

Professor
Schulich School of Medicine and Dentistry
Department of Biochemistry

B.Sc. (Hons) (University of Western Ontario): 1983
Ph.D. (Univeristy of Western Ontario): 1988
Post-Doctoral (University of Wisconsin-Madison): 1990


Research Summary:

I have an interest in functional characterization of complex systems. The major projects involve examining the composition and functional characteristics of microbial communities, and of coevolving networks in protein families.

We are examining the meta-transcriptome of vaginal, stool and maize microbial communities, and are connecting these results with those from other functional analyses such as metabolomics and proteomics. Interestingly, we have been able to show that many high-throughput sequencing experiments are best analyzed by combining Bayesian and compositional data approaches. It is crucial to understand that HTS generates data where the actual read count is irrelevant because the reads for a given sample have a constrained sum. The constant sum problem in statistical analyses was recognized by Karl Pearson in the 19th century, but was largely ignored until recently. Using standard statistical tools on these types of data, as is common in metagenomics and transcriptomics, results in data where the results are unstable to re-coding, permutation, sequencing depth, and sub-setting. Our approach is invariant to these since we convert the read counts to ratios that are stable no matter how the data is subset, rearranged or subdivided.

With this approach we have successfully examined meta-transcriptomic datasets, 16S rRNA gene sequencing datasets, in vitro selection (selex) datasets and shown that the basic approach is broadly generalizable across many different HTS study designs.


ALDEx2

We developed and maintain the ALDEx2 package which uses the principles of Compositional Data analysis coupled with Bayesian inference to determine differential abundance between groups for transcriptome and microbiome datasets: Fernandes et al, 2013, Fernandes et al, 2014. The ALDEx2 package is on Bioconductor.

The Effect plot

effect plot We have developed the 'effect plot', a useful graphical tool that shows the relationship between the within group dispersion and the between group difference. We find the plot to be a useful adjunct to Bland-Altman and Volcano plots: Gloor et al, 2015

In line barcodes and workflow for 16S rRNA gene sequencing

We developed an inline combinatorial barcoding system for the Illumina HiSeq and MiSeq platforms. ( Original publication Gloor et al, 2010, Current Tool Release, 8mer barcodes)


My Google Scholar profile

Recent Publications and Manuscripts:

1. St Denis, N and Gabriel, M and Turowec, J P and Gloor, G B and Li, S S-C and Gingras, A-C and Litchfield, D W , "Systematic investigation of hierarchical phosphorylation by protein kinase {CK2}", J. Proteomics, 118, [49-62], (2015).
2. Macklaim, Jean M and Clemente, Jose C and Knight, Rob and Gloor, Gregory B and Reid, Gregor , "Changes in vaginal microbiota following antimicrobial and probiotic therapy", Microb Ecol Health Dis, 26, [27799], (2015).
3. Yang S, Reid G, Challis JR, Kim SO, Gloor GB, Bocking AD. , "Is there a role for probiotics in the prevention of preterm birth?", Frontiers in Immunology, 17, [62], (2015).
4. Goneau LW, Hannan TJ, MacPhee RA, Schwartz DJ, Macklaim JM, Gloor GB, Razvi H, Reid G, Hultgren SJ, Burton JP. , "Subinhibitory antibiotic therapy alters recurrent urinary tract infection pathogenesis through modulation of bacterial virulence and host immunity.", MBio, 6, [ e00356-15], (2015).
5. Julia M Di Bella, Yige Bao, Gregory B Gloor, Jeremy P Burton, and Gregor Reid. , "High throughput sequencing methods and analysis for microbiome research.", J Microbiol Methods, 95, 3, [401-14], (2014).
6. RussellJDicksonandGregoryBGloor , "Bioinformatics identification of coevolving residues", Methods Mol Biol, 1123, [223-43], (2014).
7. Mariana Rosenthal, Allison E Aiello, Carol Chenoweth, Deborah Goldberg, Elaine Larson, Gregory Gloor, and Betsy Foxman , "Impact of technical sources of variation on the hand microbiome dynamics of healthcare workers", PLoS One, 9, 2, [e88999], (2014).
8. Xiaohong Tracey Gan, Grace Ettinger, Cathy X Huang, Jeremy P Burton, James V Haist, Venkatesh Rajapurohitam, James E Sidaway, Glynn Martin, Gregory B Gloor, Jonathan R Swann, Gregor Reid, and Morris Karmazyn , "Probiotic administration attenuates myocardial hypertrophy and heart failure following myocardial infarction in the rat.", Circ Heart Fail, 7, 3, [491-9], (2014).
9. S Rahat-Rozenbloom, J Fernandes, G B Gloor, and T M S Wolever , "Evidence for greater production of colonic short chain fatty acids in overweight than lean humans.", Int J Obes (Lond), Accepted: 2014-03-19
10. CamillaUrbaniak,JoanneCummins,MurielBrackstone,JeanMMacklaim,GregoryBGloor,Chwan- row K Baban, Leslie Scott, Deidre M O’Hanlon, Jeremy P Burton, Kevin P Francis, Mark Tangney, and Gregor Reid , "Microbiota of human breast tissue", Appl Environ Microbiol, 80, 10, [3007-14], (2014).


KEYWORDS: Computational Biology, Protein Evolution, Coevolution, Molecular Biology, High throughput sequencing, Genomics, Molecular genetics


Also from this web page:

faculty pic

Contact Info

Department of Biochemistry

MBL,
Rm #: C8
Telephone: 661-2111 x83526
Email: ggloor@uwo.ca