Author

J. P. Shaffer

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Ecology· 2 Microbiology· 2

Signature Assays, Organisms & Methods

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Assay:metagenomics· 3 Research Focus:benchmarking· 2 Approach:experimental assay· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

G. Humphrey· 3 shared K. Sanders· 3 shared R. A. Salido· 3 shared A. D. Swafford· 2 shared C. Marotz· 2 shared C. Martino· 2 shared C. S. Carpenter· 2 shared G. Ackermann· 2 shared

Activity by Year

2020-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersEcology

G. Humphrey

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Author profile →

4 papers

Recent·Most cited

A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities

J. P. Shaffer, C. S. Carpenter, C. P. Martino, R. A. Salido, M. Bryant, K. Sanders, T. Schwartz, G. Humphrey, A. D. Swafford, R. Knight

The paper compares six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing, finding the MagMAX Microbiome kit performs best across multiple criteria.

bioRxiv · Mar 7, 2022Microbiology

Transcriptional profiles of a foliar fungal endophyte (Pestalotiopsis, Ascomycota) and its endohyphal bacterium (Luteibacter, Gammaproteobacteria) in co-culture support sulfur exchange and growth regulation

J. P. Shaffer, M. E. Carter, J. E. Spraker, M. Clark, B. Smith, K. L. Hockett, D. A. Baltrus, E. Arnold

This study uses dual RNA-seq to compare gene expression of a foliar fungal endophyte and its endohyphal bacterium in co-culture and axenic conditions, revealing sulfur exchange and potential role of type VI secretion system in symbiosis.

bioRxiv · Nov 24, 2021 · PreprintMicrobiology

Multi-omics profiling of Earth's biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

J. P. Shaffer, L.-F. Nothias, L. R. Thompson, S. G. Jon, R. A. Salido, S. P. Couvillion, A. D. Brejnrod, S. Huang, F. Lejzerowicz, N. Haiminen, H. L. Lutz, Q. Zhu, C. Martino, J. T. Morton, S. Karthikeyan, , St

The paper performs a multi-omics meta-analysis of microbial and metabolite data from diverse environments, revealing patterns of diversity and co-occurrence across biomes.

bioRxiv · Jun 4, 2021Ecology

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

J. P. Shaffer, C. Marotz, P. Belda-Ferre, C. Martino, S. Wandro, M. Estaki, R. A. Salido, C. S. Carpenter, L. S. Zaramela, J. J. Minich, M. B. Bryant, K. Sanders, S. Fraraccio, G. Ackermann, G. Humphrey, , R. Knight

The paper compares DNA/RNA extraction protocols for microbial community sequencing, finding one protocol equivalent or better than a standard DNA-only method for RNA-based organisms.

bioRxiv · Nov 13, 2020Ecology