Justin P. Shaffer
Justin P. Shaffer
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Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions
L Narunsky-Haziza, GD Sepich-Poore, I Livyatan, O Asraf, C Martino, ...
Cell 185 (20), 3789-3806. e17, 2022
Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity
RC Kaplan, Z Wang, M Usyk, D Sotres-Alvarez, ML Daviglus, ...
Genome biology 20, 1-21, 2019
Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome
BC Taylor, F Lejzerowicz, M Poirel, JP Shaffer, L Jiang, A Aksenov, ...
Msystems 5 (2), e00901-19, 2020
An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae)
JP Shaffer, JM U'Ren, RE Gallery, DA Baltrus, AE Arnold
Frontiers in microbiology 8, 350, 2017
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range …
Z Chen, L Pham, TC Wu, G Mo, Y Xia, PL Chang, D Porter, T Phan, H Che, ...
Genome research 30 (6), 898-909, 2020
Bacterial endosymbionts: master modulators of fungal phenotypes
SJ Araldi-Brondolo, J Spraker, JP Shaffer, EH Woytenko, DA Baltrus, ...
Microbiology spectrum 5 (5), 10.1128/microbiolspec. funk-0056-2016, 2017
Diversity, specificity, and phylogenetic relationships of endohyphal bacteria in fungi that inhabit tropical seeds and leaves
JP Shaffer, C Sarmiento, PC Zalamea, RE Gallery, AS Davis, DA Baltrus, ...
Frontiers in Ecology and Evolution 4, 116, 2016
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment
C Marotz, P Belda-Ferre, F Ali, P Das, S Huang, K Cantrell, L Jiang, ...
Microbiome 9 (1), 1-15, 2021
Microbiome metadata standards: report of the national microbiome data collaborative’s workshop and follow-on activities
P Vangay, J Burgin, A Johnston, KL Beck, DC Berrios, K Blumberg, ...
MSystems 6 (1), 10.1128/msystems. 01194-20, 2021
Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California
TL Alderete, RB Jones, JP Shaffer, EA Holzhausen, WB Patterson, ...
Gut Microbes 13 (1), 1961203, 2021
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
JP Shaffer, LF Nothias, LR Thompson, JG Sanders, RA Salido, ...
Nature microbiology 7 (12), 2128-2150, 2022
Enhancing untargeted metabolomics using metadata-based source annotation
JM Gauglitz, KA West, W Bittremieux, CL Williams, KC Weldon, ...
Nature biotechnology 40 (12), 1774-1779, 2022
A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities
JP Shaffer, CS Carpenter, C Martino, RA Salido, JJ Minich, MK Bryant, ...
Biotechniques 73 (1), 34-46, 2022
Context-dependent and variable effects of endohyphal bacteria on interactions between fungi and seeds
JP Shaffer, PC Zalamea, C Sarmiento, RE Gallery, JW Dalling, AS Davis, ...
Fungal Ecology 36, 117-127, 2018
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities
JP Shaffer, C Marotz, P Belda-Ferre, C Martino, S Wandro, M Estaki, ...
Biotechniques 70 (3), 149-159, 2021
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment
JJ Minich, F Ali, C Marotz, P Belda-Ferre, L Chiang, JP Shaffer, ...
Microbiome 9, 1-13, 2021
Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo …
Z Chen, L Pham, TC Wu, G Mo, Y Xia, P Chang, D Porter, T Phan, H Che, ...
BioRxiv, 852947, 2019
Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy
Q Zhu, S Huang, A Gonzalez, I McGrath, D McDonald, N Haiminen, ...
Msystems 7 (2), e00167-22, 2022
Soil-borne fungi influence seed germination and mortality, with implications for coexistence of desert winter annual plants
YM Li, JP Shaffer, B Hall, H Ko
PLoS One 14 (10), e0224417, 2019
OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures
Q Zhu, S Huang, A Gonzalez, I McGrath, D McDonald, N Haiminen, ...
bioRxiv, 2021.04. 04.438427, 2021
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Artículos 1–20