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Michael Shaffer
Michael Shaffer
Gates Medical Research Institute
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Year
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ...
PeerJ Preprints, 2018
13809*2018
DRAM for distilling microbial metabolism to automate the curation of microbiome function
M Shaffer, MA Borton, BB McGivern, AA Zayed, SL La Rosa, LM Solden, ...
Nucleic Acids Research 48 (16), 8883-8900, 2020
4142020
Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders
DW Kang, ZE Ilhan, NG Isern, DW Hoyt, DP Howsmon, M Shaffer, ...
Anaerobe 49, 121-131, 2018
3132018
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men
AJS Armstrong, M Shaffer, NM Nusbacher, C Griesmer, S Fiorillo, ...
Microbiome 6 (1), 1-16, 2018
1302018
Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties
CP Neff, ME Rhodes, KL Arnolds, CB Collins, J Donnelly, N Nusbacher, ...
Cell Host & Microbe 20 (4), 535-547, 2016
1192016
Complexities of gut microbiome dysbiosis in the context of HIV infection and antiretroviral therapy
SX Li, AJS Armstrong, CP Neff, M Shaffer, CA Lozupone, BE Palmer
Clinical Pharmacology & Therapeutics 99 (6), 600-611, 2016
772016
Microbiome and metabolome data integration provides insight into health and disease
M Shaffer, AJS Armstrong, VV Phelan, N Reisdorph, CA Lozupone
Translational Research 189, 51-64, 2017
722017
Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection
SX Li, S Sen, JM Schneider, KN Xiong, NM Nusbacher, N Moreno-Huizar, ...
PLoS pathogens 15 (4), e1007611, 2019
672019
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data
M Shaffer, K Thurimella, K Quinn, K Doenges, X Zhang, S Bokatzian, ...
BMC bioinformatics 20 (1), 1-11, 2019
402019
Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands
M Shaffer, C Lozupone
mSystems 3 (1), e00192-17, 2018
322018
SCNIC: Sparse correlation network investigation for compositional data
M Shaffer, K Thurimella, JD Sterrett, CA Lozupone
Molecular Ecology Resources 23 (1), 312-325, 2023
212023
Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus
C Putonti, B Nowicki, M Shaffer, Y Fofanov, S Nowicki
BMC evolutionary biology 13 (1), 1-12, 2013
112013
Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments
JA Rodríguez-Ramos, MA Borton, BB McGivern, GJ Smith, LM Solden, ...
Msystems 7 (4), e00516-22, 2022
82022
Optimization of proteomics sample preparation for identification of host and bacterial proteins in mouse feces
M Baniasad, Y Kim, M Shaffer, A Sabag-Daigle, I Leleiwi, RA Daly, ...
Analytical and Bioanalytical Chemistry 414 (7), 2317-2331, 2022
62022
ORT: A workflow linking genome-scale metabolic models with reactive transport codes
RL Rubinstein, MA Borton, H Zhou, M Shaffer, DW Hoyt, J Stegen, ...
Bioinformatics 38 (3), 778-784, 2022
62022
Human-gut phages harbor sporulation genes
D Schwartz, J Rodriguez-Ramos, M Shaffer, R Flynn, RA Daly, K Wrighton, ...
bioRxiv, 2023.01. 19.524802, 2023
32023
Targeted curation of the gut microbial gene content modulating human cardiovascular disease
MA Borton, M Shaffer, DW Hoyt, R Jiang, J Ellenbogen, SO Purvine, ...
bioRxiv, 2022.06. 20.496735, 2022
32022
Exposing New Taxonomic Variation with Inflammation-A Murine Model-Specific Genome Database for Gut Microbiome Researchers
I Leleiwi, J Rodriguez-Ramos, M Shaffer, A Sabag-Daigle, K Kokkinias, ...
bioRxiv, 2022.10. 24.513540, 2022
22022
kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase
M Shaffer, MA Borton, B Bolduc, P Ghadermazi, J Edirisinghe, JP Faria, ...
bioRxiv, 2022.03. 13.484145, 2022
2*2022
Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments
JA Rodríguez-Ramos, MA Borton, BB McGivern, GJ Smith, LM Solden, ...
12021
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