Curriculum Vitae
C. Alisha Quandt | Assistant Professor | [email protected] | https://quandtmycology.weebly.com/ | Twitter: @alisha_quandt
EDUCATION
Oregon State University
Ph.D. in Botany and Plant Pathology 2008 - 2014
Dissertation: “Systematic, genomic, and transcriptomic analysis of mycoparasitic Tolypocladium species and their Elaphomyces hosts.”
Advisor: Joey Spatafora, Professor, Botany and Plant Pathology
University of South Carolina
South Carolina Honors College
B.S. Biological Sciences 2002 - 2006
Magna cum Laude
Minor: Chemistry
PROFESSIONAL EXPERIENCE
University of Colorado Boulder
Assistant Professor 2018 - Present
Ecology and Evolutionary Biology Department
University of Michigan
NSF Postdoctoral Research Fellow in Biology 2016 - 2017
Advisor: Tim James, Associate Professor, Ecology and Evolutionary Biology
University of Michigan
Postdoctoral Research Fellow 2014 - 2015
Advisor: Tim James, Associate Professor, Ecology and Evolutionary Biology
GRANTS and FELLOWSHIPS
Co-PI, USDA-ARS National Sclerotinia Initiative Grant, CU Boulder 2021
Co-PI, DOE Joint Genome Institute Community Science Program, CU Boulder 2020
Co-PI, USDA-ARS National Sclerotinia Initiative Grant, CU Boulder 2020
PI, NSF DEB SBS Grant, CU Boulder 2020
Co-PI, USDA-ARS National Sclerotinia Initiative Grant, CU Boulder 2019
NSF Postdoctoral Research Fellowship in Biology, University of Michigan 2016 - 2017
NSF Doctoral Dissertation Improvement Grant, Oregon State University 2013
Mycological Society of America Graduate Fellowship, Oregon State University 2013
Graduate Student Association Travel Grant, Botany & Plant Path. Dept. 2013
Anita Summers Travel Grant, Botany & Plant Path. Dept., Oregon State University 2013
Anita Summers Travel Grant, Botany & Plant Path. Dept., Oregon State University 2012
NSF Graduate Research Fellowship, Oregon State University 2010 - 2013
NSF East Asia and the Pacific Summer Institute, Anhui Agricultural University, China 2010
Howard Hughes Undergraduate Research Fellowship, University of South Carolina 2005 - 2006
AWARDS
Postdoc Poster Award, Genetics Society of America, Fungal Genetics Conference 2017
Mycological Society of America Mentor Travel Award, MSA annual meeting 2013
Visiting Scientist Award of the Lab of Excellence ARBRE, INRA-Nancy, France 2013
Mycological Society of America Oral Presentation Award, MSA annual meeting 2012
Mycological Society of America Mentor Travel Award, MSA annual meeting 2012
PEER REVIEWED PUBLICATIONS (†Undergraduate Mentee, ‡Postdoctoral Mentee)
23. Quandt, CA, and D Haelewaters. “Phylogenetic advances in Leotiomycetes, an understudied clade of taxonomically and ecologically diverse fungi.” Encyclopedia of Mycology: www.sciencedirect.com/science/article/pii/B9780128199909000524
22. Ciobanu, D, Clum, A, Ahrendt, SA, Andreoupoulos, W, Salamov, A, Chan, S, Quandt, CA, Foster, B, Meier-Kolthoff, JP, Tang, Y-T, Longcore, JE, Benny, GL, Smith, ME, Bauer, D, Deshpande, S, Barry, K, Copeland, A, Singer, S, Woyke, T, Grigoriev, I, James, TY, and J-F Cheng. “A Single-Cell Genomics Pipeline for Environmental Microbial Eukaryotes.” 2021 iScience 24(4): 102290.
21. Pogoda, CS, Reinert, S, Talukder, ZI, Corwin, J, Money, KL, Collier-zans, ECE, Underwood, W, Gulya, TJ, Quandt, CA, Kane, NC, and BC Hulke. “Heritable associations with microbial communities contribute to host-pathogen interactions.” In review. Biorxiv: https://doi.org/10.1101/2020.07.16.207597
20. Grupe, AC‡ and CA Quandt. “A growing pandemic: a review of Nosema parasites in globally distributed domesticated and native bees.” 2020 PLOS Pathogens 16(6): e1008580.
**Popular press for Grupe & Quandt 2020: CU Boulder Today, Daily Mail U.K., CBS Denver, Science Daily, Earth, Down to Earth, Radio-1190, Daily Camera
19. Davis, WJ, Jeronimo, GH, Simmons, DR, Quandt, CA, and TY James. “Revisiting the aquatic phycomycete flora of the Douglas Lake region since the time of Dogma and Sparrow.” 2019 Philippine Journal of Systematic Biology 13 (2): 1-14.
18. 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.
17. Olarte, RA, Menke, J, Zhang Y, Sullivan, S, Slot, J, Huang, YJ, Badalamenti, JP, Quandt, CA, Spatafora, JW, and KE Bushley. “Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum.” 2019 BMC Genomics 20: 120.
16. 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. **Cover Article
15. 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.
14. Quandt, CA, Beaudet, D, Corsaro, D, Walochnik, J, Michel, R, Corradi, N, and TY James. “The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, unveils alternative adaptations to obligate intracellular parasitism.” 2017 eLife 6: e29594.
13. Kepler, RM, Luangsa-ard, JJ, Hywel-Jones, NL, Quandt, CA, Sung, G-H, Rehner, SA, Aime, MC, Henkel, TW, Sanjuan, T, Zare, R, Chen, M, Rossman, AY, Spatafora, JW, and B Shrestha. "A phylogenetic-based nomenclature for Cordycipitaceae (Hypocreales)." 2017 IMA Fungus 8(2): 335-353.
12. Letcher, PM, Longcore, JE, Quandt, CA, da Silva Leite, D, TY James, and MJ Powell. "Morphological, molecular, and ultrastructural characterization of Rozella rhizoclosmatii, a new species in Cryptomycota." 2017 Fungal Biology 121: 1-10.
11. Peter, M, Kohler, A, Ohm, R, Kuo, A, Krüzmann, J, Morin, E, Arend, M, Barry, KW, Binder, M, Choi, C Clum, A, Copeland, A, Grisel, N, Haridas, S, Kipfer, T, LaButti, K, Lindquist, E, Lipzen, A, Maire, R, Meier, B, Mihaltcheva, S, Molinier, V, Murat, C, Pöggeler, S, Quandt, CA, Sperisen, C, Tritt, A, Tisserant, E, Crous, PW, Henrissat, B, Nehls, U, Egli, S, Spatafora, JW, Grigoriev, IV, and FM Martin. “Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.” 2016 Nature Communications 7: 12662.
10. Johnson, D, Zemenick, KA, Malloure, B, Quandt, CA, and TY James. “Fine scale spatial genetic structure of a fungal parasite of coffee scale insects.” 2016 Journal of Invertebrate Pathology 139:34-41.
9. 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.
8. Spatafora, JW, Quandt, CA, Kepler, RM, Sung, G-H, Shrestha, B, Hywel-Jones, NL, and JJ Luangsa-ard. “New 1F1N species combinations in Ophiocordycipitaceae (Hypocreales).” 2015 IMA Fungus 6(2): 357-362.
7. 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.
6. 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.
5. 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.
4. Bushley, KE, Raja, R, Jaiswal, P, Elser, J, Cumbie, JS, Boyd, A, Owensby, CA*, Knaus, BJ, McPhail, KL, and JW Spatafora. “Draft genome sequence of the Cyclosporin producing fungus Tolypocladium inflatum reveals complex patterns of secondary metabolite evolution and expression.” 2013 PLOS Genetics 9: e1003496.
3. Kepler, RM, Ban, S, Nakagiri, A, Bischoff, J, Hywel-Jones, N, Owensby, CA*, and JW Spatafora. “The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: an application of one fungus one name.” 2013 Fungal Biology 117: 611-622.
2. Spatafora, JW, Owensby, CA*, Douhan, GW, Boehm, EWA, and CL Schoch. “Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes).” 2012 Mycologia. 104: 758-765.
1. Schoch, CL, Crous, PW, Groenwald, JZ, Boehm, EWA, Burgess, TI, De Gruyter, J, De Hoog, GS, Dixon, LJ, Grube, M, Gueidan, C, Harada, Y, Hatakeyama, S, Hirayama, K, Hosoya, T, Huhndorf, SM, Hyde, KD, Jones, EBG, Kohlmeyer, J, Kruys, A, Lucking, R, Lumbsch, HT, Marvanova, L, Mbatchou, JS, McVay, AH, Miller, AN, Mugambi, GK, Muggia, L, Nelsen, MP, Nelson, P, Owensby, CA*, Phillips, AJL, Phongpaichit, S, Pointing, SB, Pujade-Renaud, V, Raja, HA, Rivas Plata, E, Robbertse, B, Ruibal, C, Sakayaroj, J, Sano, T, Selbmann, L, Shearer, CA, Shirozu, T, Slippers, B, Suetrong, S, Tanaka, K, Volkmann-Kohlmeyer, B, Wingfield, MJ, Wood, AR, Woudenberg, JHC, Yonezawa, H, Zhang, Y, and JW Spatafora. “A class-wide phylogenetic assessment of the Dothideomycetes.” 2009 Studies in Mycology. 64:1-16.
TEACHING EXPERIENCE
University of Colorado Boulder
- Microbiology – EBIO 3400 Spring 2020
- Mycology – EBIO 4460/5460 Fall 2019
- Microbiology – EBIO 3400 Spring 2019
- Mycology – EBIO 4460/5460 Fall 2018
- Microbiology – EBIO 3400 Spring 2018
- Teaching Assistant – Introductory Mycology (Split Grad/Undergrad) Fall 2013
- Teaching Assistant – Biology for Majors I, II, and III 2008-2009
- Marshall Islands High School – Life Science 2007-2008
- Utrok Elementary School – English as a Foreign Language 2006-2007
MENTORING EXPERIENCE
University of Colorado Boulder:
Graduate Students:
Tina Jones – EBIO Ph.D. student 2018-present
Kyle Schütz – EBIO Ph.D. student 2020-present
Undergraduate Students:
Isaac Dickerson – EBIO major Spring 2020
Sallie Tucker – EBIO major Spring 2020
Candice Perrotta – EBIO major, Biological Sciences Initiative (BSI) Summer Scholar 2019
Beck Glaser – EBIO major 2019
Miklos Eger – EBIO major Spring 2019
Sam Swisher – MCDB major Fall 2018
Postdoctoral Scholars:
Arthur Grupe, Ph.D. 2019-present
University of Michigan:
Alex Glasco – Undergraduate Research Opportunity Program (UROP) student 2016-2017
Ellen James – UROP student 2015-2016
Oregon State University:
Will Patterson – Computer science undergraduate 2014
INVITED PRESENTATIONS
"Hidden fungi: ecology and evolution of cryptic intracellular parasites.” 2020, Biology Department, Stanford University.
“Diversity, Mind Control, and Host Jumping in Cordyceps-like fungi.” 2019, Telluride Mushroom Festival, Telluride, CO.
“Hidden fungi: diversity and abundance of the enigmatic Cryptomycota across habitats and niches.” 2019, Fungal Genetics Conference, Pacific Grove, CA.
"Life on the inside: how cryptic Fungi became intracellular parasites across eukaryotic kingdoms.” 2018, Microbiology and Immunology Department, Montana State University.
"Shared versus independent losses: evolutionary consequences of intracellular parasitism in cryptic Fungi.” 2018, 11th International Mycological Congress, San Juan, Puerto Rico.
"Life on the inside: the evolutionary consequences of intracellular parasitism in cryptic Fungi." 2018, Plant and Microbial Biology Department, University of California Berkeley.
"Insect pathogens and mycoparasites: host jumping within Tolypocladium." 2014, 10th International Mycological Congress, Bangkok, Thailand.
“Phylogenomics of secondary metabolism in entomopathogenic and mycoparasitic fungi.” 2012, Oregon State University, Center for Genome Research and Biocomputing Fall Conference, Corvallis, OR.
OTHER PRESENTATIONS
Oral, “Isolation and characterization of bacterial communities associated with sunflower resistance to Sclerotinia stalk rot.” 2020, National Sclerotinia Initiative Annual Meeting, Fargo, ND.
Poster, “Hidden fungi: diversity and abundance of the enigmatic fungal phylum, Cryptomycota, across habitats and niches.” 2019, Front Range Microbiome Symposium, Fort Collins, CO.
Poster, "Assessment of microbiome variation in the predatory snail genus, Conus, using museum preserved specimens." 2017, Mycological Society of America Annual Meeting, Athens, GA.
Oral and Poster, "The intestinal fungal community (mycobiome) of marine snails in the genus Conus." 2017, Fungal Genetics Conference, Pacific Grove, CA.
Poster, "The genome of Paramicrosporidium saccamoebae highlights alternate adaptations to obligate intracellular parasitism in Cryptomycota and Microsporidia evolution." 2017, Fungal Genetics Conference, Pacific Grove, CA.
**Winner Poster Presentation Award.
Oral, "Genome sequence of amoeba parasite links Cryptomycota and Microsporidia." 2016, Mycological Society of America Annual Meeting, Berkeley, CA.
Oral and Poster, "Known unknowns: exploring the evolution, genomics, and diversity of cryptic early diverging fungi." 2015, Fungal Genetics Conference, Pacific Grove, CA.
Oral, “Comparative transcriptomics of host recognition in the mycoparasite Elaphocordyceps ophioglossoides.” 2013, Mycological Society of America Annual Meeting, Austin, TX.
Oral and Poster, “Phylogenomics unveils secondary metabolites specific to mycoparasitic lineages in Hypocreales.” 2013. Fungal Genetics Conference, Pacific Grove, CA.
Oral, “Complex patterns of secondary metabolite evolution in the genus Elaphocordyceps.” 2012, Yale University, Mycological Society of America Annual Meeting, New Haven, CT.
**Winner Oral Presentation Award.
Poster, “Using comparative genomics to examine inter-kingdom host-jumping and mycoparasitism in the genus Elaphocordyceps.” 2012, JGI User Meeting, Oakland, CA.
Poster, “The genome sequence of the truffle pathogen Elaphocordyceps ophioglossoides provides insights into its metabolic potential.” 2011, Asian Mycological Congress, Incheon, South Korea.
SERVICE TO PROFESSION
Mycological Society of America
Karling Lecture Committee (2018-2021, Committee Chair 2020-2021)
Councilor, Genetics/ Molecular Biology (2018-2020)
Poster and Oral Presentation Judge, Annual Meetings (2016, 2017, 2018)
Genetics Society of America
Poster Presentation Judge, 30th Fungal Genetics Conference (2019)
Front Range Microbiome Symposium
Poster Presentation Judge, 1st annual symposium (2019)
Review Editor
Frontiers in Cellular and Infection Microbiology (2019 – present)
Review Editor
Frontiers in Fungal Biology (2020 – present)
Symposium Organizer
“Metagenomes: whole fungal genomes from complex samples.” 11th International Mycological Congress, July 2018, San Juan, Puerto Rico.
Ad hoc Grant Reviewer
National Science Foundation – Division of Environmental Biology
Reviewer
Mycologia, Fungal Biology, Fungal Ecology, Nature Ecology and Evolution, Molecular Ecology, Current Biology, Nature Communications, BMC Evolutionary Biology, Molecular Biology and Evolution, Eukaryotic Microbiology, IMA Fungus, G3: Genes|Genomes|Genetics, Frontiers in Cellular and Infection Microbiology, Mycological Progress, The Fungal Kingdom (Book, ASM Press), International Journal of Systematic and Evolutionary Microbiology
SERVICE TO DEPARTMENT
University of Colorado Boulder, Ecology and Evolutionary Biology Department:
Executive Committee Member 2018 – 2019
EBIO Spring Symposium Presentation Judge 2018, 2019
Graduate Student Committee Member: 11 EBIO PhD students, 2 EBIO MA students
Oregon State University, Botany and Plant Pathology Department:
Faculty Promotion and Tenure, Student Subcommittee, Chair 2013
Graduate Studies Admissions Committee Member 2010 - 2011
Graduate Student Association Vice President 2009 – 2010
SERVICE TO UNIVERSITY
University of Colorado Boulder:
Departmental Representative, Boulder Faculty Assembly (BFA) 2020 – present
Speaker, “Preparing for the Academic Job Market”, Graduate Teacher Program June 2019
Affiliations
Center for Microbial Exploration Faculty Member 2019 – present
IQBio Faculty Member 2018 – present
Workshops and Training
University of Colorado Boulder:
Faculty Teaching and Excellence Program (FTEP) Early Career Faculty Lunch October 2019
EBIO Diversity & Inclusion Seminar, Faculty Participant 2018 – present
FTEP Summer Assessment Institute June 2018
LEAP Introductory Leadership Workshop May 2018
University of Michigan:
Implementing Inclusive Teaching Principles in Your Courses Sept 2017
Professional Workshops:
NSF Future of Systematics, Gainesville, FL Jan 2020
Marine Fungi Workshop at Marine Biological Laboratory, Woods Hole, MA May 2018
DIVERSITY, EQUITY, & INCLUSION
Publications
Branco, S, Moore, G, Shay, R, CA Quandt, and AE Arnold. “Increasing MSA Diversity Via Interchange, Ambassadorship, and Recruitment: an Opportunity to Diversify and Promote Inclusion Throughout our MSA Community”. MSA Inoculum October 2020. Available: https://files.constantcontact.com/8b73de79701/758be6af-f081-4172-a2ea-4480cacc5179.pdf
EBIO Diversity & Inclusion Seminar, Faculty Participant 2018 – present
Action-oriented group, including creation of new departmental guide on Inclusive Practices in Hiring
Association for Women in Science (AWIS), Panelist 2017
Panel discussion with female postdocs in STEM fields for University of Michigan grad students.
AWIS Mentoring Circle, Member 2017
Biweekly meetings discussing topics, experiences of women in STEM with grad students/ postdocs.
FEMMES Volunteer Educator 2015-2016
Community education events with Females Excelling More in Math Engineering and the Sciences (FEMMES) program in Ann Arbor, MI.
COMMUNITY OUTREACH
Invited Speaker 2020
Lecture on cordyceps-like fungi for the Colorado Mycological Society, Denver, CO
Invited Speaker 2019
Lecture on cordyceps-like fungi at the Telluride Mushroom Festival, Telluride, CO
Guest Lecturer 2016
Lecture and demonstration on Fungi for 7th & 8th grade science classes at Ann Arbor Open School.
Guest Lecturer 2016
Two Lectures on “Ectomycorrhizal Fungi” and “Fungi and Food Security” for Advanced Placement (AP) Environmental Science classes at Pioneer High School in Ann Arbor, MI.
Volunteer Reader 2012-2014
Weekly Start Making a Reader Today (SMART) reading program in Oregon public schools.
Volunteer Educator 2008-2013
Discovery Days at OSU, Semiannual Science Education Event for Elementary Students.
Volunteer Educator 2011-2012
Winter Wonderings program for gifted 3rd-4th grade students, Oregon State University Pre-college Programs.
MEMBERSHIPS
Mycological Society of America – 2009 – present
Genetics Society of America – 2013 – present
Society of Systematic Biologists – 2020 – present