Alisha headshot
Ph.D. Oregon State University, 2014 • Assistant Professor

Ramaley N344

Research Interests

I'm interested in all aspects of fungal biology. My research is focused on addressing three fundamental questions in mycology: (1) How do fungi evolve the ability to switch hosts or adapt to utilize various substrates? (2) How do fungi interact with other microorganisms? and (3) Where are potential unexplored habitats of novel fungal diversity? Genomics, metagenomics, transcriptomics, phylogenetics, and molecular community ecology are tools that I combine with computational biology to address these larger interests in fungal evolutionary biology.

Selected Publications

Amend, A, Burgaud, G, Cunliff, M, Edgcomb, VP, Ettinger, CL, Gutiérrez, MH, Heitman, J,Hom, EFY, Ianiri, G, Jones, AC, Kagami, M, Picard, KT, Quandt, CA, Raghukumar, S, Riquellme, M, Stajich, J, Vargas-Muñiz, J, Walker, A, Yarden, O, and AS Gladfelter. “Fungi in the marine environment: open questions and unsolved problems.” 2019 mBio 10: e01189-18.

Ahrendt, SR, Quandt, CA, Ciobanu, D, Clum, A, Salamov, A, Andreopoulos, W, Cheng, J-F, Woyke, T, Pelin, A, Henrissat, B, Reynolds, NK, Benny, GL, Smith, ME, James, TY, and IV Grigoriev. “Leveraging single-cell genomics to expand the Fungal Tree of Life.”  2018 Nature Microbiology 3: 1417-1428.

Quandt, CA, Patterson, W, and JW Spatafora. "Harnessing the power of phylogenomics to disentangle the directionality and signatures of interkingdom host-jumping in the fungal genus Tolypocladium." 2018 Mycologia 110: 104-117.

Quandt, CA, Beaudet, D, Corsaro, D, Walochnik, J, Michel, R, Corradi, N, and TY James. "The genome of an intranuclear parasite unveils alternative adaptations to obligate intracellular parasitism." 2017 eLife 6:e29594.

Quandt, CA, Di, Y, Elser, J, Jaiswal, P, and JW Spatafora. "Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides." 2016, G3: Genes | Genomes | Genetics 6(3): 731-741.

Quandt, CA, Bushley, KE, and JW Spatafora. "The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal Peptaibiotics." 2015, BMC Genomics 16: 553.

Quandt, CA, Kohler, A, Hesse, C, Sharpton, T, Martin, F, and JW Spatafora. "Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria rich microbiome." 2015, Environmental Microbiology 17(8): 2952-2968. 

Quandt, CA, Kepler, RM, Gams, W, Araújo, JPM, Ban, S, Evans, HC, Humber, R, Hywel-Jones, N, Li, Z, Luangsa-ard, JJ, Rehner, SA, Sanjuan, T, Sato, H, Shrestha, B, Sung, G-H, Yao, Y-J, Zare, R, and JW Spatafora. “Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium.” 2014, IMA Fungus 5: 121-134.