Armaleo, D., Müller, O., Lutzoni, F., Andrésson, Ó. S., Blanc, G., Bode, H. B., … & Joneson, S. (2019). The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerataBMC genomics20(1), 605.

Olarte, R. A., Menke, J., Zhang, Y., Sullivan, S., Slot, J. C., Huang, Y., … & Bushley, K. E. (2019). Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatumBMC genomics20(1), 120.

Slot, J. C., & Gluck-Thaler, E. (2019). Metabolic gene clusters, fungal diversity, and the generation of accessory functionsCurrent opinion in genetics & development58, 17-24.

Farinas, C., Gluck-Thaler, E., Slot, J. C., & Hand, F. P. (2019). Whole-Genome Sequence of the Phlox Powdery Mildew Pathogen Golovinomyces magnicellulatus Strain FPH2017-1Microbiology resource announcements8(36), e00852-19.

Boyce, G., Gluck-Thaler, E., Slot, J. C., Stajich, J. E., Davis, W. J., James, T. Y., … & Kasson, M. T. (2018). Discovery of psychoactive plant and mushroom alkaloids in behavior-modifying fungal cicada pathogens. Fungal Ecology 41, 147-164.

Gluck-Thaler, E., Vijayakumar, V., & Slot, J. (2018). Fungal adaptation to plant defenses through convergent assembly of metabolic modules. Molecular ecology, 27(24), 5120-5136.

Blei, F., Fricke, J., Wick, J., Slot, J., & Hoffmeister, D. (2018). Iterative L‐tryptophan methylation in Psilocybe evolved by sub‐domain duplication. ChemBioChem.

Reynolds, H. T., Vijayakumar, V., Gluck-Thaler, E., Korotkin, H. B., Matheny, P. B., & Slot, J. C. (2018). Horizontal gene cluster transfer increased hallucinogenic mushroom diversity. Evolution Letters.

Gluck-Thaler, Emile, and Jason C. Slot. (2018). “Specialized plant biochemistry drives gene clustering in fungi.” The ISME Journal.

Sipos, G., A. N. Prasanna, M. C. Walter, E. O’Connor, B. Bálint, K. Krizsán, B. Kiss, J. Hess, T. Varga, J. C. Slot, R. Riley, B. Bóka, D. Rigling, K. Barry, J. Lee, S. Mihaltcheva, K. LaButti, A. Lipzen, R. Waldron, N. M. Moloney, C. Sperisen, L. Kredics, C. Vágvölgyi, A. Patrignani, D. Fitzpatrick, I. Nagy, S. Doyle, J. B. Anderson, I. V. Grigoriev, U. Güldener, M. Münsterkötter, and L. G. Nagy. (2017). Genome Expansion and Lineage-Specific Genetic Innovations in the Forest Pathogenic Fungi Armillaria. Nature Ecology & Evolution.

Slot, J. C. (2017). Fungal Gene Cluster Diversity and EvolutionAdvances in Genetics.

Nagy, L. G., Tóth, R., Kiss, E., Slot, J., Gácser, A., & Kovács, G. M. (2017). Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases. Microbiology spectrum, 5(4).

Reynolds, H. T., Slot, J. C., Divon, H. H., Lysøe, E., Proctor, R. H., & Brown, D. W. (2017). Differential retention of gene functions in a secondary metabolite cluster. Mol Biol Evol, msx145.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW. (2016). Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A.  113(35):9882-7.

Reynolds, H.T., H.A. Barton , and J.C. Slot. (2016). Phylogenomic analysis supports a recent change in nitrate assimilation in the White-nose Syndrome pathogen, Pseudogymnoascus destructansFungal Ecology, 23, 20-29.

Staehlin, B.M, J.G. Gibbons, A. Rokas, T.V. O’Halloran, and J.C. Slot. (2016). “Evolution of a Heavy Metal Homeostasis/Resistance Island Reflects Increasing Copper Stress in Enterobacteria.” Genome Biology and Evolution 8 (3): 811-826.

Gluck-Thaler, E. and J.C. Slot. Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens. (2015). PLoS Pathogens 11 (10): e1005156.

Elmore, M. H., K. L. McGary, J. H. Wisecaver, J.C. Slot, D. M. Geiser, S. Sink, K. O’Donnell, and A. Rokas. (2015). Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. Genome Biology and Evolution 7 (3): 789–800.

Wisecaver, J.H., J.C. Slot, A. Rokas. (2014). The Evolution of Fungal Metabolic Pathways. PLoS Genetics 10 (12): e1004816.

Greene, G.H., K.L. McGary, A. Rokas, J.C. Slot. (2014). Ecology drives the distribution of specialized tyrosine metabolism modules in fungi. Gen Biol Evol 6: 121-132.

McGary, K. L., J. C. Slot, and A. Rokas. (2013). The Physical Linkage of Metabolic Genes in Fungi is an Adaptation against the Accumulation of Toxic Intermediate Compounds. Proc Nat Acad Sci 110(28), 11481–11486.

Campbell, M.A., M. Staats, J.A.L. van Kan, A. Rokas and J.C. Slot. (2013). Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia 105:1126-1134.

Bradshaw, R.E., J. C. Slot, G. G. Moore, P. Chettri, P. J.G.M. de Wit, K. C. Ehrlich, A. R. D. Ganley, M. A. Olson, A. Rokas, I. Carbone, M. P. Cox. (2013). Fragmentation of an Aflatoxin-Like Gene Cluster in a Forest Pathogen. New Phytol 198:525-35.

Gibbons, J. G., L. Salichos, J. C. Slot, D.C. Rinker, K.L. McGary, J.G. King, M. A. Klich, D. L. Tabb, W. H. McDonald, and A. Rokas. (2012). The evolutionary imprint of domestication on microbe genome variation and function. Curr Biol 22:1-7.

Zhang, H., A. Rokas and J. C. Slot. (2012). Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes. PLoS ONE 7: e41903

League, G., J. C. Slot, and A. Rokas. (2012). The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces. FEMS Yeast Res 12(7):859-63

Floudas, D., (and 70 others, inc. J. C. Slot). (2012). The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes. Science 336: 1715.

Stergiopoulos, I., Y.A. Kourmpetis, J. C. Slot, F.T. Bakker, P.J.G.M. De Wit, and A. Rokas. (2012). In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins. Mol Biol Evol 29(11): 3371-3384.

Campbell, M. A., A. Rokas, and J. C. Slot. (2012). Horizontal transfer and death of a fungal secondary metabolic gene cluster. Gen Biol Evol, 4(3), 289–293.

Slot, J. C. and A. Rokas. (2011). Horizontal transfer of a large and highly toxic secondary metabolite gene cluster between fungi. Curr Biol 21(2): 134-9. Faculty of 1000 recommended. Current Biology Dispatch by T.A. Richards: doi: 10.1016/j.cub.2011.01.028

Slot, J. C. and A. Rokas. (2010). Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc Nat Acad Sci 107(22): 10136-10141.

Slot, J. C., K. N. Hallstrom, P. B. Matheny, K. Hosaka, G. Mueller, D. L. Robertson, and D. S. Hibbett. (2010). Phylogenetic, structural and functional diversification of nitrate transporters in three ecologically diverse clades of mushroom forming fungi. Fungal Ecology 3(3):160-177.

Slot, J. C., and D. S. Hibbett. (2007). Horizontal Transfer of a Nitrate Assimilation Gene Cluster and Ecological Transitions in Fungi: A Phylogenetic Study. PLoS ONE 2:e1097.

Slot, J. C., K. N. Hallstrom, P. B. Matheny, and D. S. Hibbett. (2007). Diversification of NRT2 and the Origin of Its Fungal Homolog. Mol Biol Evol 24:1731-1743.

Matheny, P. B., Z. Wang, M. Binder, J. M. Curtis, Y. W. Lim, R. H. Nilsson, K. W. Hughes, V. Hofstetter, J. F. Ammirati, C. L. Schoch, E. Langer, G. Langer, D. J. McLaughlin, A. W. Wilson, T. Froslev, Z. W. Ge, R. W. Kerrigan, J. C. Slot, Z. L. Yang, T. J. Baroni, M. Fischer, K. Hosaka, K. Matsuura, M. T. Seidl, J. Vauras, and D. S. Hibbett. (2007). Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phylogenet Evol 43:430-451.

Matheny, P. B., Curtis, J. M., Hoffstetter, V., Aime, M. C., Moncalvo, J. M., Ge, Z. W., Yang, Z. L., Slot, J. C., et al. (2006). Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98(6): 982-995.

James, T. Y., F. Kauff, C. L. Schoch, P. B. Matheny, V. Hofstetter, C. J. Cox, G. Celio, C. Gueidan, E. Fraker, J. Miadlikowska, H. T. Lumbsch, A. Rauhut, V. Reeb, A. E. Arnold, A. Amtoft, J. E. Stajich, K. Hosaka, G. H. Sung, D. Johnson, B. O’Rourke, M. Crockett, M. Binder, J. M. Curtis, J. C. Slot, et al. (2006). Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822.

Yang, Z. L., P.B. Matheny, Z. Ge, J. C. Slot, and D. S. Hibbett. (2005). New Asian species of the genus Anamika (euagarics, hebelomatoid clade) based on morphology and ribosomal DNA sequences. Mycol Res 109(11):1259-1267