Author

R. Riley

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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Microbiology· 5 Evolutionary Biology· 2 Bioengineering· 1 Cell Biology· 1 Physiology· 1

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Approach:experimental assay· 5 Research Focus:cell type annotation· 4 Approach:statistical model· 4 Assay:whole-genome sequencing· 4 Assay:DNA methylation· 3 Research Focus:gene regulatory network inference· 3 Assay:metagenomics· 3 Research Focus:chromatin & epigenetic regulation· 2

Frequent Co-Authors

A. Lipzen· 5 shared B. Henrissat· 4 shared E. Drula· 3 shared I. V. Grigoriev· 3 shared J. Pangilinan· 3 shared K. LaButti· 3 shared S. Miyauchi· 3 shared A. Clum· 2 shared

Activity by Year

2018-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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5 shared papersMicrobiology

A. Lipzen

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Author profile →

10 papers

Recent·Most cited

Multi-omics analysis of a traditional fermented food reveals a byproduct-associated subpopulation of Neurospora intermedia for waste-to-food upcycling

V. Maini Rekdal, J. M. Villalobos-Escobedo, N. Rodriguez-Valeron, M. Olaizola Garcia, D. Prado Vasquez, A. Rosales, P. M. Sorensen, E. E. K. Baidoo, A. Calheiros de Carvalho, R. Riley, A. Lipzen, G. He, M. Yan, S. Haridas, C. Daum, , J. D. Keasling

This study uses multi-omics analysis to characterize Neurospora intermedia in oncom, revealing its role in byproduct conversion and potential for waste-to-food upcycling.

bioRxiv · Jul 24, 2024 · PreprintMicrobiology

Viral gene drive spread during herpes simplex virus 1 infection in mice

M. Walter, A. K. Haick, R. Riley, P. A. Massa, D. E. Strongin, L. M. Klouser, M. A. Loprieno, L. Stensland, T. K. Santo, M. Aubert, M. P. Taylor, K. R. Jerome, E. Verdin

This study demonstrates that a viral gene drive can spread in vivo during HSV-1 infection in mice by promoting co-infection and recombination.

bioRxiv · Dec 7, 2023Microbiology

A standardized quantitative analysis strategy for stable isotope probing metagenomics

D. Vyshenska, P. Sampara, K. Singh, A. Tomatsu, W. B. Kauffman, E. Nuccio, S. J. Blazewicz, J. Pett-Ridge, N. Varghese, M. Kellom, A. Clum, R. Riley, S. Roux, E. A. Eloe-Fadrosh, R. M. Ziels, R. R. Malmstrom

This paper introduces a standardized analysis framework and R package for quantifying isotopic enrichment in SIP metagenomics to identify active microbial genomes.

bioRxiv · Dec 20, 2022Microbiology

HT-SIP: A semi-automated Stable Isotope Probing pipeline identifies interactions in the hyphosphere of arbuscular mycorrhizal fungi

E. E. Nuccio, S. J. Blazewicz, M. Lafler, A. N. Campbell, A. Kakouridis, J. A. Kimbrel, J. Wollard, D. Vyshenska, R. Riley, A. Tomatsu, R. Hestrin, R. Malmstrom, M. K. Firestone, J. Pett-Ridge

The paper introduces a semi-automated DNA-SIP pipeline to improve efficiency and reproducibility in microbial community studies, demonstrating its application in analyzing the hyphosphere of arbuscular mycorrhizal fungi.

bioRxiv · Jul 1, 2022 · PreprintMicrobiology

Genetic determinants of endophytism in the Arabidopsis root mycobiome

F. Mesny, S. Miyauchi, T. Thiergart, B. Pickel, L. Atanasova, M. Karlsson, B. Hüttel, K. W. Barry, S. Haridas, C. Chen, D. Bauer, W. Andreopoulos, J. Pangilinan, K. LaButti, R. Riley, , S. Hacquard

The paper identifies genetic factors associated with endophytism in Arabidopsis root fungi, showing specific gene families linked to aggressive colonization and plant health.

bioRxiv · Apr 28, 2021Microbiology

Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?

B. P. Looney, S. Miyauchi, E. Morin, P.-E. Courty, A. P. Kohler, E. Lindquist, A. Kuo, K. LaButti, J. Pangilinan, A. Lipzen, R. Riley, W. Andreopoulos, G. He, J. Johnson, M. Nolan, , F. M. Martin

This study identifies genomic features of the transition to ectomycorrhizal habit in Russulaceae fungi, finding gene loss, TE expansion, and secreted protein associations with TE nests.

bioRxiv · Feb 23, 2021 · PreprintEvolutionary Biology

Stress reactivity elicits a tissue-specific reduction in telomere length in ageing zebrafish (Danio rerio)

J. R. Evans, J. V. Torres-Perez, M. E. Miletto Petrazzini, R. Riley, C. H. Brennan

This study shows that stress-reactivity in ageing zebrafish is inversely related to telomere length in heart tissue but not brain tissue.

bioRxiv · Apr 17, 2020Physiology

Alpha-ketoglutarate, an endogenous metabolite, extends lifespan and compresses morbidity in aging mice

A. Asadi Shahmirzadi, D. Edgar, C.-Y. Liao, Y.-M. Hsu, M. Lucanic, A. Asadi Shahmirzadi, C. Wiley, R. Riley, G. Gan, C. Kuehnemann, D. Bhaumik, G. J. Lithgow, B. K. Kennedy

This study shows that alpha-ketoglutarate extends lifespan and healthspan in aging mice by reducing frailty and inflammatory factors.

bioRxiv · Oct 4, 2019Cell Biology

The genome of Auriculariopsis ampla sheds light on fruiting body development and wood-decay of bark-inhabiting fungi

E. Almasi, N. Sahu, K. Krizsan, B. Balint, G. M. Kovacs, B. Kiss, J. Cseklye, E. Drula, B. Henrissat, I. Nagy, M. Chovatia, C. Adam, K. LaButti, A. Lipzen, R. Riley, , L. G. Nagy

This study sequenced the genome of Auriculariopsis ampla and analyzed its transcriptome to uncover genetic features related to wood-decay and fruiting body development in fungi.

bioRxiv · Feb 14, 2019 · PreprintEvolutionary Biology

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass.

S. Miyauchi, A. Rancon, E. Drula, D. Chaduli, A. Favel, S. Grisel, B. Henrissat, I. Herpoël-Gimbert, F. J. Ruiz-Duenas, D. Chevret, M. Hainaut, J. Lin, M. Wang, J. Pangilinan, A. Lipzen, , M.-N. Rosso

This study identifies the oxidative enzyme systems in Polyporus brumalis that enable efficient lignin degradation during wheat straw fermentation.

bioRxiv · Apr 6, 2018Bioengineering