Author

J. M. Allen

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· 5 Evolutionary Biology· 2 Immunology· 2 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 8 Research Focus:ecology & biodiversity· 4 Research Focus:host-pathogen & immune response· 4 Assay:metagenomics· 4 Organism:mouse· 2 Organism:multiple species· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

T. Levi· 3 shared D. E. Soltis· 2 shared D. W. Yu· 2 shared K. P. Johnson· 2 shared M. C. Kasperek· 2 shared M. E. Caetano-Silva· 2 shared M. T. Bailey· 2 shared P. C. Brewster· 2 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 10 mutual co-author links

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3 shared papersEcology

T. Levi

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10 papers

Recent·Most cited

Aging amplifies a gut microbiota immunogenic signature linked to heightened inflammation

M. E. Caetano-Silva, A. Shrestha, A. F. Duff, D. Kontic, P. C. Brewster, M. C. Kasperek, C. H. Lin, D. A. Wainwright, D. H. Saavedra, J. A. Woods, M. T. Bailey, T. W. Buford, J. M. Allen

This study shows that aging alters gut microbiota immunogenicity, increasing TLR4 activation and inflammation, and that these changes are linked to heightened host inflammation.

bioRxiv · Mar 22, 2024Immunology

Microbial aromatic amino acid metabolism is modifiable in fermented food matrices to promote bioactivity

M. C. Kasperek, A. Velasquez Galeas, M. E. Caetano-Silva, Z. Xie, A. V. Ulanov, M. R. La Frano, S. Devkota, M. J. Miller, J. M. Allen

This study identifies aryl-lactates as bioactive metabolites in fermented foods and shows their production can be enhanced to boost AhR receptor activity.

bioRxiv · Dec 21, 2023Microbiology

Nano-computed tomography reveals repeated phenotypic divergence in parasites to escape host defense

S. Kolencik, E. L. Stanley, A. Punnath, A. R. Grant, J. Dona, K. P. Johnson, J. M. Allen

The paper uses nano-computed tomography to analyze morphological traits of feather lice across different host habitats, finding strong associations between morphology and host-specific adaptations.

bioRxiv · Jan 21, 2023 · PreprintEvolutionary Biology

Psychological stress disrupts intestinal epithelial cell function and mucosal integrity through microbe and host-directed processes

J. M. Allen, A. Mackos, R. M. Jaggers, P. C. Brewster, M. Webb, C.-H. Lin, C. Ladaika, P. White, B. R. Loman, M. T. Bailey

This study shows that psychological stress disrupts intestinal epithelial cell function and mucosal integrity in mice, mediated by microbiota and host stress signals.

bioRxiv · Oct 25, 2021Immunology

Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites

B. M. Boyd, N.-P. Nguyen, J. M. Allen, R. M. Waterhouse, K. B. Vo, A. D. Sweet, D. H. Clayton, S. E. Bush, M. D. Shapiro, K. P. Johnson

This study shows that long-distance dispersal of pigeons and doves created new ecological opportunities for their parasites to speciate through host-switching, but this opportunity decreased over time as cospeciation became more common.

bioRxiv · Aug 2, 2021Evolutionary Biology

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

C. Earl, M. W. Belitz, S. W. Laffan, V. Barve, N. Barve, D. E. Soltis, J. M. Allen, P. S. Soltis, B. D. Mishler, A. Y. Kawahara, R. P. Guralnick

This study compares spatial phylogenetic patterns of butterflies and flowering plants in North America, finding divergent biodiversity patterns and suggesting differences in habitat conservation.

bioRxiv · Jul 22, 2020Ecology

Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats

A. L. Massey, G. Roffler, T. Vermeul, J. M. Allen, T. Levi

This study compares mechanical sorting and DNA metabarcoding for analyzing wolf scat diets, finding metabarcoding reveals greater diversity and accuracy in identifying prey species.

bioRxiv · Dec 13, 2019 · PreprintEcology

Environmental DNA facilitates accurate, indigenous-led, inexpensive, and multi-year population estimates of millions of Eulachon fish

M. Pochardt, J. M. Allen, T. Hart, S. D. L. Miller, D. W. Yu, T. Levi

This study shows that environmental DNA (eDNA) can accurately estimate eulachon fish populations over multiple years, with high predictive power compared to mark-recapture methods, at a lower cost.

bioRxiv · Sep 25, 2019 · PreprintEcology

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

D. Li, L. Trotta, H. E. Marx, J. M. Allen, M. Sun, D. E. Soltis, P. S. Soltis, R. P. Guralnick, B. H. Baiser

This paper compares purpose-built and synthesis phylogenies for community phylogenetic analyses, finding synthesis trees yield comparable results with less effort.

bioRxiv · May 7, 2019Ecology

Environmental DNA for the enumeration and management of Pacific salmon

T. Levi, J. M. Allen, D. Bell, J. Joyce, J. R. Russell, D. A. Tallmon, S. C. Vulstek, C. Yang, D. W. Yu

This study demonstrates that flow-corrected environmental DNA (eDNA) rates can accurately track daily numbers of returning and outmigrating Pacific salmon spawners and smolts.

bioRxiv · Dec 6, 2018Ecology