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Ibarra Caballero, JRJP Ata, KA Leddy, TC Glenn, TJ Kieran, NB Klopfenstein, M-S Kim and JE Stewart. 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 different wood substrates. Fungal Biology. https://

Stewart, JE, M-S Kim, Y Ota, N Sahashi, JW Hanna, M Akiba, JP Ata, N Atibalentja, F Brooks, C-L Chung, EK Dann, A Mohd Farid, T Hattori, SS Lee, K Otto, GS Pegg, RL Schlub, LS Shuey, AMC Tang, JN Tsai, PG Cannon and NB Klopfenstein. 2020. Phylogenetic and population analyses reveal three distinct lineages of the invasive brown-rot pathogen, Phellinus noxius, and bioclimatic modeling predicts differences in associated climate niches. European Journal of Plant Pathology.


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

Sitz, RA, Aquino, V., Tisserat NA, Stewart JE, Cranshaw WS. In press. 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. Accepted with revisions. Armillaria altimontanais associated with unimpeded growth andsurvival 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.

Fonseca NR, Ibarra Caballero, JR, Stewart JE, Kim M-S, Lucio MS. Guimarães, Alfenas, A.C., Klopfenstein, N.B. 2019Transcriptome analysis of Podosphaera pannosa infecting Eucalyptus urophylla: de novo assembly, expression profiling, secretome prediction and, discovery of SSR markers. Forest Pathology. DOI: 10.1111/efp.12508

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

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. 2018. Discovery Phytophthoraureraesp. nov., a new relative of the Irish famine pathogen Phytophthora infestans. Plant Pathology. Doi:10.1111/ppa.12968

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. doi: 10.1007/s10886-018-0961-1.

Stewart, JE, Kim M-S, Klopfenstein NB. 2018Molecular 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, In press. 

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 Allokermesgalliformisand the bacterium Lonsdalea quercina subsp. quercina. Arboriculture and Urban Forestry. 44: 146-153.

Stewart, JE, Ross-Davis, ALE, RN Graҫa, AC Alfenas, TL Peever, JW Hanna, E Pitman, JY Uchida, RD Hauff, CY Kadooka, M-S Kim, PG Cannon, S Namba,N Minato, S Simeto, CA Pérez, MB Rayamajhi, M Morán, DJ Lodge, M Arguedas, R Medel-Ortiz, MA López-Ramirez, P Tennant, M Glen, A McTaggart, NB Klopfenstein. 2017. Insights into the genetic diversity of Puccinia psidii in the Americas and Hawaii: Global implications for invasive threat assessments. Forest Pathology. DOI: 10.1111/efp.12378


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. 2015. Extreme diversity found in the emerging pathogen of blueberry Exobasidium maculosum. PlosOne.

Stewart, J.E., Turner, A.N., Brewer, MT. 2015. Evolutionary 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 Alternaria, Ascochyta 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 vectors. Northern Nut Growers Association Annual Report. 94:1-8.

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