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Recent Publications


Mohali-Castillo S*, Stewart JE*AcceptedCalonectria vigiensis sp. nov. (Hypocreales, Nectraceae) associated with dieback and sudden death symptoms Theobroma cacao from Merida state, Venezuela. Canadian Journal of Botany.

Dobbs JT, Kim M-S, Dudley NS, Jones TC, Yeh A, Dumroese RK, Cannon PG, Hauff RD, Klopfenstein NB, Wright S, Stewart JE*. Accepted with RevisionFusarium spp. diversity associated with symptomatic Acacia koa in Hawai’i. Forest Pathology.

Harris FDobbs JTAtkins DA, Ippolito JA*, Stewart JE*Accepted with Revision. Soil fertility interactions with Sinorhizobium-Legume symbiosis in a simulated Martian regolith. PlosOne.

Ata J, Burns KS, Marchetti S, Munck I, Beenken L, Worrall JJ, Stewart JE*2021. Molecular characterization and phylogenetic analyses of Lophodermella needle pathogens (Rhytismataceae) on Pinus species in the USA and Europe. PeerJ.

Miller ST, Sterle D, Minas IS, Stewart JE*2021. Exploring fungicides and sealants for management of Cytospora plurivora infections in western Colorado peach production systems. Crop Protection.

Sitz RA, Luna, EK, Ibarra Caballero, J, Tisserat, NA, Cranshaw, WS, Mckenna JR, Stolz J, Stewart, JE*. 2021. Eastern black walnut (Juglans nigra L.) originating from native range varies in response to inoculation with Geosmithia morbida. Frontiers in Forests and Global Change. 4: 12.

Antonin V, Stewart JE, Medel Ortiz R, Kim M-S, Bonello P. (Enrico), Klopfenstein NB. 2021Desarmillaria caespitosa (Physalacriaceae, Basidiomycota), a North-American vicariant of D. tabescens, its evidence and multigene phylogeny. Mycologia.

Atkins DH, Davis TS*, Stewart, JE*2021. Probability of occurrence and phenology of pine wilt disease transmission by insect vectors in the southern Rocky Mountains. Ecological Solutions and Evidence.


Dobbs, JT, Kim M-K, Dudley NS, Jones TC, Yeh A, Dumroese RK, Cannon PG, Hauff RD, Klopfenstein NB, Stewart JE*. 2020Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring. BMC Genomics.  

Geldert C, Abdo Z, Stewart JE, Seshardri A. 2020. Dietary supplementation with phytochemical improves diversity and abundance of honey bee gut microbiota. Applied Microbiology.

Copes, WE, Ibarra Caballero J, Babiker E, Stewart JE, Orner VA, Windham AS, Arias RS. 2020. Draft Genome Assembly of Passalora sequoia a needle blight pathogen on Leyland cypress. BMC Data Note. DOI: 10.21203/

Dudley, MM, Tisserat, NA, Jacobi, WR, Stewart JE. 2020. Pathogenicity and distribution of two species of Cytospora to quaking aspen (Populous tremuloides Michx.) in selected regions of the Rock Mountain and Midwest in the United States. Forest Ecology and Management.

Lalande BL, Hughes K, Jacobi WR, Tinkham W, Reich R, Stewart JE. 2020. Subalpine fir decline in Colorado is associated with stand density, warming climates and interactions among fungal diseases and the western balsam bark beetle. Forest Ecology and Management.

Stewart, JE, Harris, FL, Otto, K, Davis, TS. 2020. Responses of Engelmann spruce to inoculation with Leptographium abietinum, a symbiotic fungus of the North American spruce beetle. Canadian Journal of Forest Research.

Ibarra Caballero, JR, Ata JPLeddy, KA, Glenn, TC, Kieran TJ, Klopfenstein, NB, Kim M-S, Stewart, JE*. 2020. Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of distinct wood substrates. Fungal Biology.

Stewart JE*, Kim M-S, Hanna JW, Ota Y, Ata#, J, Otto^ K, Akiba, M, Atibalentia N, Brooks F, Chu LM, Chung C-L, Mohd Farid A, Hattori T, Huang Y-C, Kwan HS, Lam RYC, Lee H-H, Leung MWK, Lee SS, Liou R-F, Sahashi N, Schlub RL, Shuey L, Tang AMC, Tsai J-N, Cannon PG, Klopfenstein NB. 2020. Phylogenetic and population analyses of the invasive brown root-rot pathogen (Phellinus noxius) highlights the existence of three distinct populations with unique climate habitats. European Journal of Plant Pathology.


Delong, JA, Stewart, JE, Balencia-Botin, A, Pedley, KF, Buck, JW, Brewer, MT. 2019. Mining the Uromyces transveralis genome for molecular markers reveals a lack of genotypic diversity among gladioulus rust isolates. PeerJ.

Zeng, Y., Abdo, Z., Charkowski, A., Stewart, JE, Frost, K. 2019. Responses of bacterial and fungal community structure to different rates of 1,3-dichloropropene fumigation. Phytobiomes.

Sitz, R.A.#, Aquino, V., Tisserat, N.A., Stewart J.E., Cranshaw W.S. 2019. Insects visiting drippy blight diseased red oak trees are contaminated with the pathogenic bacterium Lonsdalea quercina subsp. quercina. Plant Disease.

Warwell, MV, McDonald, GI, Hanna, JW, Kim, M-S, #Lalande, B, Stewart, JE, Klopfenstein, NB. 2019. Armillaria altimontana is associated with unimpeded growth and survival of western white pine (Pinus monticola) planted in northern Idaho: Potential in situ biological control agent for Armillaria root disease caused by A. solidipes. Forests. 10: 294-298. 

Fonseca NR, ^Ibarra Caballero, JR, Stewart JE*, Kim M-S, Lucio MS. Guimarães, Alfenas, A.C., Klopfenstein, N.B2019. Transcriptome analysis of Podosphaera pannosa infecting Eucalyptus urophyllade novo assembly, expression profiling, secretome prediction and, discovery of SSR markers. Forest Pathology.

Ibarra Caballero, JR, Jeon, J, Lee Y-H, Fraedrich S, Kim, M-S, Stewart, JE. 2019Genomic comparisons of the laurel wilt pathogen, Raffaelea lauricola, and related tree pathogens highlight an arsenal of pathogenicity related genes. Fungal Biology and Genetics. 125: 84-92. 

Miller, ST, Otto, KL, Sterling, D, Minas, IS, Stewart, JE. 2019. Preventive chemical control of Cytospora canker in peaches in western Colorado. Plant Disease. 

Grünwald NJ, Forbes G, Stewart JE, Fieland V. 2019. Discovery Phytophthora urerae sp. nov., a new relative of the Irish famine pathogen Phytophthora infestans. Plant Pathology. 68: 557-565.


Davis TS, Stewart JE, Mann A, Ramey SM, Bradley C, Hofstetter RW. 2018. Evaluating ecological roles of Leptographium abietinum, a symbiotic fungus associated with North American spruce beetle. Fungal Ecology. doi: 10.1016/j.funeco.2018.04.008.

Davis, TS, Home, F.B, Yetter, JC, Stewart, JE. 2018. Engelmann spruce chemotypes and their effects on symbiotic fungi associated with North American spruce beetle. Journal of Chemical Ecology. 44: 601-610. 

Stewart, JE*, Kim M-S, Klopfenstein NB. 2018. Molecular genetic approaches towards understanding forest-associated fungi and their interactive roles within forest ecosystems. Current Forestry Reports. 1: 1-13.

Ritter, S.M., Hoffman, C.M., Stewart, JE, Zimmerman, T. 2018. The influence of prescribed crown fire on Lodgepole Pine Dwarf Mistletoe (Arceuthobium americanum) populations 33 years post-fire. Forest Pathology, 48: e12419.  

Sitz, R, Snelling, J., Ibarra Caballero, J., Zerillo, M., Alexander, K., Tisserat, N., Cranshaw, W., Stewart, JE. 2018. Drippy blight, a disease of red oaks in Colorado Produced from the combined effect of the scale insect Allokermes galliformis and the bacterium Lonsdalea quercina subsp. quercina. Arboriculture and Urban Forestry 44: 146-153. Journal Impact: 0.80


Jongbum, J, Ki-Tae K, H-J Song, G-W Lee, K Cheong, H Kim, G Choi, Y-H Lee, JE Stewart, NB Klopfenstein, M-S Kim. 2017. Draft Genome Sequence of the Fungus Associated with Oak-Wilt Mortality in South Korea, Raffaelea quercus-mongolicae KACC44405, Genome Announcements.

Ritter S, Hoffman C, Ex S, Stewart, JE. 2017. Impacts of lodgepole pine dwarf mistletoe (Arceuthobium americanum) infestation on stand structure and fuel load in lodgepole pine dominated forests in central Colorado. Botany. 95: 307-231.

Klopfenstein NB, JE Stewart, Y Ota, JW Hanna, BA Richardson, AL Ross-Davis, RD Elías-Román, K Korhonen, N Keča, E Iturritxa, D Alvarado-Rosales, H Solheim, NJ Brazee, P Łakomy, MR Cleary, E Hasegawa, T Kikuchi, F Garza-Ocañas, P Tsopelas, D Rigling, S Prospero, T Tsykun, JA Bérubé, FOP Stefani, S Jafarpour, V Antonín, M Tomšovský, GI McDonald, S Woodward, M-S Kim. 2017. Insights into the phylogeny of Northern Hemisphere Armillaria: split-network and Bayesian analyses of translation elongation factor 1-α gene sequences. Mycologia. In press.

Sitz, R.A., Luna, E.K., Ibarra Caballero, J., Tisserat, N.A., Cranshaw, W.S., Stewart, JE. 2017. Virulence of genetically distinct Geosmithia morbida isolates to black walnut and their response to co-inoculation with Fusarium solani. Plant Disease. 101: 116-120.


Stewart, J.E.K. Otto, Cline, G.A., Dumroese, R.K., Klopfenstein, N.B., Kim, M.-S. 2016. First Report of Fusarium proliferatrum causing Fusarium root disease on sugar pine (Pinus lambertiana) in a forest container nursery in California. Plant Disease. 100: 12.

Kolb, T.E., Fettig, C.J., Bentz, B.J., Stewart, J.E., Weed, A.S., Hicks, J.A., Aryes, M.P. 2016. Observed and anticipated impacts of drought on forests insects and diseases in the United States. Forest Ecology and Management.

Glenn, A.T., Davis, B., Minglu, G., Gold, S.E., Mitchell, T., Proctor, R., Stewart, J.E., Snook, M. 2016. Two horizontally transferred xenobiotic resistance gene clusters associate with detoxification of benzoxazolinones by Fusarium species. PlosOne.


Stewart, J.E., Brooks# K., Brannen, P.M, Cline, W.O., Brewer, M.T. 2015Extreme diversity found in the emerging pathogen of blueberry Exobasidium maculosum. PlosOne.

Stewart, J.E., Turner, A.N., Brewer, MT. 2015Evolutionary history and variation in host range in the Didymella bryoniae/Stagonosporopsis caricae species complex pathogenic to curcurbits and papaya. Fungal Biology. 119: 370-182.

Huang, F., Fu, Y., Nie, D., Stewart, J.E., Peever, T.L., Li, H. 2015. Phylogeographic analysis of Alternaria alternata causing brown spot of tangerines in China reveals previously unknown diversity. Fungal Biology. 119: 320-330.


Stewart, J.E., Kroese, D., Tabima, J.F., Larsen, M.M., Press, C.M., Zasada, I., Grünwald, N.J. 2014. Phytophthora rubi isolates collected from raspberry (Rubus idaeus) in the Western United States show no differentiation in pathogenicity, fungicide resistance or genetic structure. Plant Disease. 98: 1702-1706.

Schoebel, C.N., Stewart, J.E., Grünwald, N.J., Prospero, S. 2014. Population history and pathways of spread of the plant pathogen Phytophthora plurivora. PlosOne. e85368.

Stewart, J.E., Timmer, L.M., Lawrence, C.B., Pryor, B.M., Peever, T.L. 2014. Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen BMC Evolutionary Biology. 1: 38.


Stewart, J.E., Thomas# K.A., Lawrence, C.B., Pryor, B.M., Peever, T.L., 2013. Signatures of recombination in clonal lineages of the citrus brown spot pathogen, Alternaria alternata. Phytopathology. 103: 741-749.

Stewart, J.E., Andrew, M., Bao, X., Chilvers, M.I., Carris, L. M. Peever, T.L., 2013. Development and utility of sequence characterized amplified genomic regions for lower-level fungal systematics: Proof of principle using AlternariaAscochyta and Tilletia. Mycologia. doi: 10.3852/12-287.

Ross-Davis*, A.L., Stewart*, J.E., Hanna, J.W., Kim, M.-S., Cronn, R., Rai, H., Richardson, B.R. McDonald, G.I., and Klopfenstein, N.B.2013. Transcriptome characterization of an Armillaria root disease pathogen reveals candidate pathogenicity-related genes. Forest Pathology. doi: 10.1111/efp.12056


Kim, M.-S., Stewart, J.E., Dumroese, R.K., and Klopfenstein, N.B. 2012. Occurrence of Fusarium commune in forest nurseries. Journal of Phytopathology. 160: 112-114.

Stewart, J.E., Abdo, Z., Dumroese, R.K., Klopfenstein, N.B., Kim, M.-S. 2012. Pathogenicity of Fusarium oxysporum and F. commune to Douglas-fir (Pseudotsuga menziesii) seedlings. Forest Pathology. DOI: 10.1111/j.1439-0329.2011.00746.x.

Humann, J.L., Wildung, M., Cheng, C-H, Lee, T., Stewart, J.E., Drew, J.C., Triplett, E.W., Main, D., B.K. Schroeder. 2011. Complete genome of the onion pathogen Enterobacter cloacae EcWSU1. Standards in Genomic Sciences. 5:3 ISSN 1944-3277 doi:10.4056/sigs.2174950.

Stewart*, J.E., Kawabe*, M., Abdo, Z., Arie, T., Peever T.L. 2011. Contrasting codon usage patterns and purifying selection at the mating locus in putatively asexual Alternaria fungal species. PLoS One. 6: e20083.

Akamastu, H.O., Chilvers, M.I., Stewart, J.E., Peever, T.L. 2010. Identification and function of a polyketide synthase gene responsible for 1,8-dihydrozynaphtahlene-melanin pigment biosynthesis in Ascochyta rabiei. Current Genetics. 56: 349-360.

Chilvers, M.I., Rogers, J.D., Dugan, F.M., Stewart, J.E., Chen W., Peever, T.L. 2009. Didymella pisi sp. nov., the teleomorph of Ascochyta pisi. Mycological Research. 113: 391-400.

Stewart, J.E., M.-S. Kim, R.L. James, R.K. Dumroese, N. B. Klopfenstein. 2006. Molecular characterization of Fusarium oxysporum and Fusarium commune from a conifer nursery. Phytopathology. 96.1124-1133.

McDonald, G.I., Tanimoto, P.D., Rice, T.M., Stewart, J.E., Tonn, J.R., Hall, D.E., Zambino, P.J., Klopfenstein, N.B., Kim, M.-S. 2005. Root Disease Analyzer – Armillaria Response Tool (ART). In: Sutherland, E.K., Black, A.E., eds. Science Synthesis and Integration. Environmental Consequences Fact Sheet: 13. Research Note RMRS-RN-23-13-WWW. Fort Collins, CO: U.S. Dept. of Agriculture, Forest Service, Rocky Mountain Research Station.

Rippy, R. C.; Stewart, J.E.; Zambino, P.J.; Klopfenstein, N. B.; Tirocke, J. M.; Kim, M.-S.; Thies, W. G. 2005. Root diseases in coniferous forests of the Inland West: potential implications of fuels treatments. Gen. Tech. Rep. RMRS-GTR-141. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 32 p.

Stewart, J.E., S. Halik, and D.R. Bergdahl. 2004. Viability of Sirococcus clavigignenti  juglandacearum conidia on exoskeletons of three coleopteran species.  Plant Dis. 88:1085-1091.

Stewart, J.E., S. Halik, and D.R. Bergdahl 2003. Viability of conidiospores of the butternut canker fungus on potential beetle vectorsNorthern Nut Growers Association Annual Report. 94:1-8.