Núñez-Pons, L., Cunning, R., Nelson, C. E., Amend, A. S., Sogin, E. M., Gates, R., & Ritson-Williams, R. (2023). Hawaiian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses. Science of The Total Environment889, 164040.

Steinbach, R. M., El Baidouri, F., Mitchison-Field, L. M., Lim, F. Y., Ekena, J., Vogt, E. J.,Galdfelter, A., Theberge, A.B., & Amend, A. S. (2023). Malassezia is widespread and has undescribed diversity in the marine environment. Fungal Ecology65, 101273.

Darcy, J. L.†, Amend, A. S., Swift, S. O., Sommers, P. S., & Lozupone, C. A. (2022). specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data. Environmental Microbiome, 17(1), 1-12.

Amend, A. S., Swift, S. O., Darcy, J. L.†, Belcaid, M., Nelson, C. E., Buchanan, J., Cetraro, N., Fraiola, K., Frank, K., Kajihara, K., McDermot, T.G., McFall-Ngai, M.,  Medeiros, M., Mora, C., Nakayama, K.K., Nguyen, N.H., Rollins, R.L., Sadowski, P., Sparagon, W., Téfit, M.A., Yew, J.Y., Yogi, D.,& Hynson, N. A. (2022). A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes. Proceedings of the National Academy of Sciences119(33), e2204146119.

Boekhout,T.,  Amend, A.S., Mittelbach, M., Robert, V., Wang, Q. M., & Yurkov, A. (2021) Trends in yeast diversity discovery. Fungal Diversity, 114, 491-537

El Baidouri†, F., Zalar, P., James, T.Y., Gladfelter, A.S. & Amend, A. S. (2021) Evolution and Physiology of Amphibious Yeasts. Annual Review of Microbiology, 75:16.1-16.21

Steinbach, R. M., El Baidouri, F., Mitchison-Field, L. M., Lim, F. Y., Ekena, J., Vogt, E. J.,Galdfelter, A., Theberge, A.B., & Amend, A. S. (2023). Malassezia is widespread and has undescribed diversity in the marine environment. Fungal Ecology65, 101273.

Boraks, A.* & Amend, A. S. (2021) Fungi in soil and understory have coupled distribution patterns. PeerJ 9, e11915

Egan, C. P., Koko, J. H., Muir, C. D., Zahn, G., Swift, S. O., Amend, A. S., & Hynson, N. A. (2021). Restoration of the mycobiome of the endangered Hawaiian mint Phyllostegia kaalaensis increases its resistance to a common powdery mildew. Fungal Ecology, 52, 101070.

Boraks, A.*, Plunkett, G. M., Doro, T. M., Alo, F., Sam, C., Tuiwawa, M., Ticktin, T. & Amend, A. S. (2021). Scale-dependent influences of distance and vegetation on the composition of aboveground and belowground tropical fungal communities. Microbial Ecology81(4), 874-883.

Bernard, J., Wall, C. B., Costantini, M. S., Rollins, R. L., Atkins, M. L., Cabrera, F. P., Cetraro, N.D., Feliciano, C.K., Greene, A.L., Kitamura, P.K., Olmedo-Velarde, A., & Amend, A. S. (2021). Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. The ISME Journal15(4), 999-1009.

Tipton, L., Zahn, G. L.†, Darcy, J. L.†, Amend, A. S., & Hynson, N. A. (2021). Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography. Microbial Ecology, 1-10.

Chock, M. K. *, Hoyt, B.§, & Amend, A. S. (2021). Mycobiome transplant increases resistance to Austropuccinia psidii in an endangered Hawaiian plant. Phytobiomes Journal, 5(3), 326-334.

Darcy, J. L.†, Swift, S., Cobian, G.*, Zahn, G.†, Perry, B. A., & Amend, A. S. (2020). Fungal communities living within leaves of native Hawaiian dicots are structured by landscape-scale variables as well as by host plants. Molecular Ecology 29(16), 3102-3115.

Tipton, L., Zahn, G.†, Datlof, E., Kivlin, S. N., Sheridan, P., Amend, A. S., & Hynson, N. A. (2019). Fungal aerobiota are not affected by time nor environment over a 13-y time series at the Mauna Loa Observatory. Proceedings of the National Academy of Sciences, 116(51), 25728–25733. 

Vargas‐Gastélum, L.*, Chong‐Robles, J., Lago‐Lestón, A., Darcy, J. L.†, Amend, A. S., & Riquelme, M. (2019). Targeted ITS1 sequencing unravels the mycodiversity of deep‐sea sediments from the Gulf of Mexico. Environmental Microbiology, 21(11), 4046–4061. 

Cobian, G. M.*, Egan, C. P., & Amend, A. S. (2019). Plant–microbe specificity varies as a function of elevation. The ISME Journal, 13(11), 2778–2788.

Amend, A. S., Cobian, G. M.*, Laruson, A. J., Remple, K., Tucker, S. J., Poff, K. E., Antaky, C., Boraks, A.*, Jones, C. A., & Kuehu, D. (2019). Phytobiomes are compositionally nested from the ground up. PeerJ, 7, e6609. 

Zahn, Geoffrey†, & Amend, A. S. (2019). Foliar fungi alter reproductive timing and allocation in Arabidopsis under normal and water-stressed conditions. Fungal Ecology, 41, 101–106. 

Gladfelter, A. S., James, T. Y., & Amend, A. S. (2019). Marine fungi. Current Biology, 29(6), R191–R195 

Gladfelter, A. S., James, T. Y., & Amend, A. S. (2019). Marine fungi. Current Biology, 29(6), R191–R195 

Amend, A. S., Burgaud, G., Cunliffe, M., Edgcomb, V., Ettinger, C., Gutiérrez, M., Heitman, J., Hom, E., Ianiri, G., & Jones, A. (2019). Fungi in the marine environment: open questions and unsolved problems. mBio, 10: e01189-18

Hynson, N. A., Frank, K. L., Alegado, R. A., Amend, A. S., Arif, M., Bennett, G. M., Jani, A. J., Medeiros, M. C., Mileyko, Y., & Nelson, C. E. (2018). Synergy among microbiota and their Hosts: Leveraging the Hawaiian archipelago and local collaborative networks to address pressing questions in microbiome research. Msystems, 3(2).

Wainwright, B.J.†, Zahn, G.L. †, Arlyza, I.S. and Amend, A.S. (2018) Seagrass‐associated fungal communities follow Wallace’s line, but host genotype does not structure fungal community. Journal of Biogeography, 45(4), 762-770 

Zahn, G.†, & Amend, A. S. (2017) Foliar microbiome transplants confer disease resistance in a critically-endangered plant. PeerJ5, e4020.

Datlof, E.M., Amend, A.S., Earl, K. *, Hayward, J., Morden, C.W., Wade, R., Zahn, G. † and Hynson, N.A., (2017) Uncovering unseen fungal diversity from plant DNA banks. PeerJ5, e3730 

Wainwright, B.J†, G. Zahn†, H. Spadling, A. Sherwood, C. Smith A.S. Amend (2017) Fungi Associated with mesophotic macroalgae from the ʻAuʻau Channel, west Maui are differentiated by host and overlap terrestrial communities.  PeerJ, 5, e3532 

O’Rorke, R.†, B.S. Holland, G.M. Cobian*, K. Gaughen§, A.S. Amend  (2017) Not just browsing; an animal that grazes microbes facilitates community invasions and instability. ISME Journal, 11, 1788-1798

Price M.R., R. O’Rorke†, A.S. Amend, M.G. Hadfield (2016) Diet selection at three scales: implications for conservation of an endangered Hawaiian tree snail. Biotropica, 49(1) 130-136

O’Rorke, R†, B.S. Holland, G.M. Cobian*, K. Gaughen§, A.S. Amend (2016) Dietary preferences of Hawaiian tree snails to inform culture for conservation. Biological Conservation, 198 177-182

Tishammer K*, G.M. Cobian* and A.S. Amend (2015) Global Biogeography of Marine Fungi is Shaped by Environmental Determinates. Fungal Ecology, 19 39-46 

Amend A.S., A. Martiny, S. Allison, R. Berlemont, M. Goulden, Y. Lu, K.K. Treseder, C. Weihe and J.B.H. Martiny (2015) Microbial response to simulated global change is phylogenetically conserved and linked with functional potential, ISME Journal. 10 109-118 

Matulich K.L., C. Weihe, S.D. Allison, A.S. Amend, R. Berlemont, M.L. Goulden, S. Kimball, A.C. Martiny, J.B.H. Martiny (2015) Temporal variation overshadows the response of leaf litter microbial communities to simulated global change. ISME Journal, 9 2477-2489

Amend A.S., K. Matulich and J. Martiny (2015) Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities. Frontiers in microbiology, 6 109.

O’Rorke, R.†, G.M. Cobian*, B.S. Holland, M.R. Price, V. Costello and A.S. Amend (2015) Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured. Environmental Microbiology, 17(5) 1753-1764 

Amend, A.S. (2014) From dandruff to deep sea vents: Malassezia-like fungi are ecologically hyper-diverse. PLoS Pathogens, 10(8):e1004277 

Visagie, C.M., Y. Hirooka, J.B. Tanney, E. Whitfield, K. Mwange, M. Meijer, A.S. Amend, K.A. Seifert, and R.A. Samson (2014) Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world. Studies in Mycology, 78 63-139

Mouginot C., R. Kiwamura, K. Matulich, R. Berlemont, S.D. Allison, A.S. Amend, A.C. Martiny, (2014) Elemental stoichiometry of Fungi and Bacteria strains from grassland leaf litter. Soil Biology and Biochemistry, 76 278-285 

Adams RI, A.S. Amend, J.W. Taylor, T.D. Bruns (2013) A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust. Microbial Ecology, 66(4) 735-741

Bengtsson-Palme, J., M. Ryberg, M. Hartmann, S. Branco, Z. Wang, A. Godhe, P. DeWit, M. Sanchez-Garcia, I. Ebersberger, F. Sousa, A.S. Amend, A. Jumpponen, M. Unterseher, E. Kristiansson, K. Abarenkov,Y.J.K. Bertrand, K. Sanli, K. M. Eriksson, U. Vik, V. Veldre and R. H. Nilsson (2013) Improved software detection and extraction of internal transcribed spacer (ITS)1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution, 4(10) 914-919

Kerekes, J., M. Kaspari,  B. Stevenson, R. Henrik Nilsson, M. Hartmann, A.S. Amend, and T.D. Bruns (2013) Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest. Molecular Ecology, 22(10) 2827-2838

Salick, J., R. K. Moseley and contributing authors: A.S. Amend, D. Anderson, A. Byg, W. Law, Ma J., N.J. Ross, Y. Yongping (2012) Khawa Karpo conservation research. In: Salick, J., R. K. Moseley (Eds.) Khawa Karpo: Tibetan traditional knowledge and biodiversity conservation.  Missouri Botanical Garden Press, St. Louis, USA. 

Amend, A.S., T.A. Oliver, L.A. Amaral-Zettler, A. Boetius, J.A. Fuhrman, M.C. Horner-Devine, S.M. Huse, D.B.M. Welch, A.C. Martiny, A. Ramette, L. Zinger, M.L. Sogin, J.H. Martiny (2012) Macroecology of marine bacteria on a global scale. Journal of Biogeography, 40(4) 800-811.

Amend, A.S., D.J., Barshis, T.A. Oliver (2011) Community Structure, Transcriptomics and Phylogenetics of Symbiotic Coral-Associated Fungi Indicate Novel Nutritional Roles and Deep-Branching Lineages. ISME Journal, 6(7) 1291-1301 

Hynson, N.A., S. Mambelli, A.S. Amend, T.E. Dawson (2011) Measuring carbon gains from fungal networks in understory plants from the tribe Pyroleae (Ericaceae): a field manipulation and stable isotope approach. Oecologia, 169(2) 307-317 

Amend, A.S., K.A. Seifert, R. Samson, T. D. Bruns (2010) Indoor Fungal Assemblages are Geographically Patterned and More Diverse in Temperate Zones than the Tropics. Proceedings of the National Academy of Sciences USA, 107(31) 13748-13753 

Amend, A. S., K.A. Seifert, T. D. Bruns (2010) Quantifying Microbial Communities with 454 Pyrosequencing: Does Read Abundance Count? Molecular Ecology, 19(24) 5555-5565 

Nilsson, R.H., Veldre, V., Hartmann, M., Unterseher, M., Amend, A.S., Bergsten, J., Kristiansson, E., Ryberg, M., Jumpponen, A. & Abarenkov, K (2010) An Open Source Software Package for Rapid, Automated Extraction of ITS1 and ITS2 from Fungal ITS Sequences for use in High-Throughput Community Assays and Molecular Ecology.  Fungal Ecology, 3(4) 284-287 

Amend, A.S., Z. Fang, W. McClatchey (2010) Local Perceptions of Matsutake Mushroom Management, in NW Yunnan China. Biological Conservation, 143(1) 165-172 

Amend, A.S., M. Garbelotto, Z. Fang, S. Keeley (2010) Isolation by Landscape in Populations of the Prized Edible Mushroom Tricholoma matsutake. Conservation Genetics, 11(3) 795-802 

Amend, A.S., S. Keeley, M. Garbelotto (2009) Forest Age Correlates with Fine-Scale Spatial Structure of Matsutake Mycorrhizas. Mycological Research, 113(5) 541-550 

Salick, J., A.S. Amend, D. Anderson, B. Gunn, Z. Fang (2007) Tibetan Sacred Sites Conserve Old Growth Forests and Cover in the Eastern Himalayas.  Biodiversity and Conservation, 16(3) 693-706 

Salick, J., A. Byg, A.S. Amend, B. Gunn, H. Schmidt (2006) Tibetan Medicine Plurality.  Economic Botany, 60(3) 227-253 

Salick, J., Yang Y. P., A.S. Amend (2005) Tibetan land use and change near Khawa Karpo, Eastern Himalayas.  Economic Botany, 59(4) 312-325