Dr. Rebecca Shapiro

I completed my Bachelor’s degree at McGill University in the Department of Biology, where I worked in labs studying cancer genetics, and Drosophila developmental biology. After that, I moved to Toronto to join the Department of Molecular Genetics at the University of Toronto as a doctoral candidate. At U of T, I worked with Dr. Leah Cowen, where I developed a strong interest in the biology of fungal pathogens. My PhD research focused on temperature stress and cellular morphogenesis in the pathogenic fungus Candida albicans. After completing my doctoral studies, I joined the lab of Dr. Jim Collins at MIT and the Broad Institute as a Banting Postdoctoral Fellow. During my postdoc, I learned new techniques focusing on CRISPR-based technologies, functional genomics, and microbial genomic analysis. My new research group at the University of Guelph will focus on studying microbial fungal pathogens and developing and employing CRISPR-based genomic technologies to allow us to better understand the biology and pathogenesis of these fungal species.

• BSc - McGill University, Biology
• PhD - University of Toronto, Molecular Genetics
• Postdoctoral Fellow - Broad Institute/MIT, Biological Engineering

Genomic technologies. To better study the biology and virulence of fungal pathogens, we are developing new genomic technology platforms for diverse fungal species. We are exploiting CRISPR-Cas9 based technologies to revolutionize the way we do high-throughput functional genomic analysis in fungal pathogens. This is enabling us to map genetic interactions, and uncover genetic factors and pathways that mediate important phenotypes associated with pathogenesis, antifungal drug resistance, and other biological processes.

Fungal pathogenesis. We are interested in microbial fungal pathogens, and the mechanisms by which they cause disease. Most of our work focuses on the human fungal pathogen Candida albicans, but we are also expanding our research to include other fungal pathogens of both humans and plants. We use genetics and systems-level analysis to assess cellular factors involved in fungal pathogenesis and virulence pathways - including cellular morphogenesis and biofilm formation.

Antifungal drug resistance. Resistance to antifungal drugs is a serious clinical concern. We study the mechanisms by which fungal pathogens evolve antifungal drug resistance, and identify genetic factors involved in mediating this resistance. Using experimental evolution, molecular genetic techniques, and whole genome sequencing analysis, we are building an understanding of how fungi evolve resistance to diverse classes of antifungal agents.

Complete list of publications available here

• Gervais NC, Rogers RKJ, Robin MR, and Shapiro RS. HyperdCas12a-based multiplexed genetic regulation in Candida albicans. Nucleic Acids Research (2025) doi.org/10.1093/nar/gkaf1402
• Gervais NC, Hendriks A, and Shapiro RS. Effective strategies for translating CRISPR-dCas systems to diverse microbes. ACS Synthetic Biology (2025) doi: 10.1021/acssynbio.5c00537
• Després PC*, Gervais NC*, Fogal M, Rogers RKJ, Cuomo CA, and Shapiro RS. Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9 reveals the functional impact of allelic variation. Genetics (2025) https://doi.org/10.1093/genetics/iyaf154
• Bédard C, Pageau A, Fijarczyk A, Mendoza-Salido D, Alcaniz AJ, Després P, Durand R, Plante S, Alexander EMM, Rouleau F, Giguère M, Bernier M, Sharma J, Maroc L, Gervais NC, Menon A, Jay A, Gagnon-Arsenault I, Bakker S, Rhodes J, Dufresne PJ, Bharat A, Sellam A, De Luca DG, Gerstein AC, Shapiro RS, Quijada NM, and Landry CR. FungAMR: A comprehensive portrait of antimicrobial resistance mutations in fungi. Nature Microbiology (2025) https://doi.org/10.1038/s41564-025-02084-7
• Case N, Gurr S, Fisher M, Blehert D, Boone C, Casadevall A, Chowdhary A, Cuomo C, Currie C, Denning D, Ene I, Fritz-Laylin L, Gerstein AC, Gow C, Gusa A, Iliev I, James T, Jin H, Kahmann R, Klein B, Kronstad J, Ost K, Peay K, Shapiro RS, Sheppard D, Shlezinger N, Stajich J, Stukenbock E, Taylor J, Wright G, and Cowen LE. Fungal impacts on Earth’s ecosystems. Nature (2025) 638: 49–57 https://www.nature.com/articles/s41586-024-08419-
• Agyare-Tabbi MR, Uthayakumar D, Francis D, Maroc L, Grant C, McQueen P, Westmacott G, Shaker H, Skulska I, Gagnon-Asenault I, Boisvert J, Landry CR, and Shapiro RS. The putative error-prone polymerase REV1 mediates DNA damage and drug resistance in Candida albicans. npj Antimicrobials and Resistance (2024) In Press
• Gervais NC and Shapiro RS. Discovering the hidden function in fungal genomes. Nature Communications (2024) 15: 8219 https://www.nature.com/articles/s41467-024-52568-z
• Bédard C, Gagnon-Arsenault I, Boisvert J, Plante S, Dubé AK, Pageau A, Sharma J, Maroc L, Shapiro RS and Landry CR. Most azole antifungal resistance mutations in the drug target provide cross-resistance and carry no intrinsic fitness cost. Nature Microbiology (2024) https://www.nature.com/articles/s41564-024-01819-2
• Després PC, Shapiro RS, and Cuomo C. New approaches to tackle a rising problem: large-scale methods to study antifungal resistance. PLoS Pathogens (2024) 20(9):e1012478. https://doi: 10.1371/journal.ppat.1012478
• Maroc L, Shaker H, and, Shapiro RS. Functional genetic characterization of stress tolerance and biofilm formation in Nakaseomyces (Candida) glabrata via a novel CRISPR activation system. mSphere (2024) doi.org/10.1128/msphere.00761-23
• Librais GMN, Jiang Y, Razzaq I, Brandl CJ, Shapiro RS, and Lajoie P. Evolutionary diversity of the control of the azole response by Tra1 across yeast species. G3 (2023) https://doi.org/10.1093/g3journal/jkad250
• La Bella AA, Andersen MJ, Gervais NC, Molina JJ, Molesan A, Stuckey PV Wensing L, Shapiro RS, Santiago-Tirado FH*, and Flores-Mireles AL*.
  Catheterized bladder environment induces Candida albicans hyphal formation and promotes colonization and persistence through Als1.
  Science Advances (2023) https://doi.org/10.1126/sciadv.ade7689
• Gervais NC, La Bella AA, Wensing LF, Sharma J, Acquaviva V, Best M, López ROC, Fogal M, Uthayakumar D, Chavez A, Santiago-Tirado F, Flores-Mireles A, and Shapiro RS.
  Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans.
  G3 (2022) https://doi.org/10.1093/g3journal/jkac301
• Bock C, Datlinger P, Chardon F, Coelho M, Dong M, Lawson K, Lu T, Maroc L, Norman T, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman J, and Zhuang X.
  High-content CRISPR screening.
  Nature Reviews Methods Primer (2022). 2: 1-23 https://doi.org/10.1038/s43586-021-00093-4
• Gervais NC, Halder V, and Shapiro RS.
  A data library of Candida albicans functional genomic screens
  FEMS Yeast Research (2021). https://doi.org/10.1093/femsyr/foab060
• Razzaq I*, Berg MD*, Jiang Y, Genereaux J, Uthayakumar D, Kim GH, Agyare-Tabbi M, Halder V, Brandl CJ, Lajoie P^, and Shapiro RS^.
  The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis.
  Genetics (2021), https://doi.org/10.1093/genetics/iyab131
• Rosiana S, Zhang L, Kim GH, Revtovich AV, Uthayakumar D, Sukumaran A, Geddes-McAlister J, Kirienko NV, and Shapiro RS. Comprehensive genetic analysis of adhesin proteins and their role in virulence of Candida albicans.
  Genetics (2021) doi.org/10.1093/genetics/iyab003
• Wensing L*, Sharma J*, Uthayakumar D, Proteau Y, Chavez A, and Shapiro RS. A CRISPR interference system for efficient genetic repression in Candida albicans. mSphere (2019). 4:e00002-19
• Halder V, Porter CBM, Chavez A, and Shapiro RS. Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nature Protocols (2019). doi:10.1038/s41596-018-0122-6
• Geddes-McAlister J and Shapiro RS. New pathogens, new tricks: emerging, drug-resistant fungal pathogens and future prospects for antifungal therapeutics. Annals of the New York Academy of Sciences (2018). doi:0.1111/nyas.13739
• Shapiro RS, Chavez A, and Collins JJ. CRISPR-based genomic tools for the manipulation of genetically-intractable microorganisms. Nature Reviews Microbiology (2018) 16:333-339
• Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ, and Church GM. Precise Cas9 targeting enables genomic mutation prevention. Proceedings of the National Academy of Sciences of the United States of America (2018) 115:3669-3673
• Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ. (2017) A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology (2018) DOI: 10.1038/s41564-017-0043-0
• Cohen NR, Ross C, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, and Collins JJ. A role for the bacterial epigenome in antibiotic stress survival. Nature Genetics (2016) 48(5): 581-586
• Shapiro RS. Antimicrobial-induced DNA damage and genomic instability in microbial pathogens. PLOS Pathogens (2015) 11(3):e1004678
• Ryan O*, Shapiro RS*, Kurat C, Mayhew D, Baryshnikova A, Chin B, Costanzo M, Lin Z-Y, Cox M, Vizeacoumar F, Cheung D, Tsui K, Istel F, Tebbji F, Sellam A, Schwarzmuller T, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras A-C, Mitra RD, Johnston M, Andrews B, Fink GR, Cowen LE, and Boone C. Global gene deletion analysis exploring yeast filamentous growth. Science (2012) 337(6100):1353-1356 *These authors contributed equally to this work
• Shapiro RS, Sellam A, Tebbji F, Whiteway M, Nantel A and Cowen LE. Pho85, Pcl1 and Hms1 signaling governs Candida albicans morphogenesis induced by high temperature or Hsp90 compromise. Current Biology (2012) 22(6):461-470
• Shapiro RS, Robbins N and Cowen LE. Regulatory circuitry governing fungal development, drug resistance, and disease. Microbiology and Molecular Biology Reviews (2011) 75(2):213-267
• Shapiro RS, Uppuluri P, Zaas AK, Collins C, Senn H, Perfect JR, Heitman J, and Cowen LE. Hsp90 orchestrates temperature-dependent Candida albicans morphogenesis via Ras1-PKA signaling. Current Biology (2009) 19(8):621-629