Dr. Rebecca Shapiro

Meet Dr. Rebecca Shapiro


Profile(s): Department of Cellular and Molecular Biology, Research Laboratory Page

Keywords: CRISPR-based technologies, functional genomics, and microbial genomic analysis, microbial fungal pathogens

Current Positions:

  • Assistant Professor – Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Guelph ON

Education and Employment Background:

  • BSc (Biology) – Department of Biology, McGill University (Montreal, QC)
  • PhD (Molecular Genetics) – Department of Molecular Genetics, University of Toronto (Toronto ON)
  • Banting Postdoctoral Fellow (Biological Engineering, Dr. Jim Collins) –MIT/Broad Institute (Cambridge, MA, USA)

Research Themes & Interests:

Dr. Shapiro’s research program focuses on fungal pathogens of humans and plants, which are emerging as a critical threat to human health, especially amongst elderly and immunocompromised individuals. Fungal infections are notoriously difficult to treat, with few antifungal drugs, and high rates of antifungal drug resistance. This research aims to identify new fungal cell factors that may serve as targets for antifungal treatment. We are developing and employing CRISPR-based functional genomic technologies to allow us to better understand the biology and pathogenesis of these organisms.

Recent Research Focuses & Partnerships:

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.

Select Publications:

  • 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 albicansNature 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 albicansNature 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 RSSellam 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
  • Google Scholars Compilation for Dr. Shapiro: Link Out


  • CRISPR in Fungi: An Interview with Rebecca Shapiro’ CRISPR Cuts Synthego Podcast, interview by Minu Prabhune, highlighting research from the Shapiro lab. https://www.synthego.com/blog/crispr-fungi-shapiro (September 2019)
  • Self-destructing mosquitoes and sterilized rodents: the promise of gene drives’, Nature, News Feature, interview highlighting research from the Shapiro lab. https://www.nature.com/articles/d41586-019-02087-5 (July 2019)
  • CRISPR Adapted to Prevent Unwanted Mutations’, Genetic Engineering and Biotechnology News, highlighting research. https://www.genengnews.com/topics/drug-discovery/crispr-adapted-to-prevent-unwanted-mutations/ (March 2018)
  • This Week in CRISPR – Using CRISPR to Avoid Unwanted Mutations & Prevent Antibiotic Resistance’, The Bench blog by Synthego, highlighting research. https://www.synthego.com/blog/twic-crispr-avoids-mutations-antibiotic-resistance (March 2018)
  • A CRISPR/Cas9 mutation prevention system could help prevent and fight disease in the future’, ScienceDaily Press Release, highlighting research https://www.sciencedaily.com/releases/2018/03/180326140219.htm (March 2018)
  • Top 10 CRISPR papers of 2017’, Nature blogs, highlighting research http://blogs.nature.com/ofschemesandmemes/2018/01/16/our-10-most-popular-crispr-papers-of-2017 (January 2018)
  • Driving drug resistance out of fungi’, ScienceDaily Press Release (also phys.org and Infection Control Today), highlighting research (October 2017)
  • ’Driving’ Candida Research’, Nature Microbiology Community Blog, highlighting research https://naturemicrobiologycommunity.nature.com/users/65575-rebecca-shapiro/posts/21410-driving-candida-research (October 2017)
  • Expanding the genetic toolbox for fungi’, Nature Reviews Microbiology Research spotlight, by Andrea Du Toit, highlighting research https://www.nature.com/articles/nrmicro.2017.141 (October 2017)
  • The Bhagirath Singh Early Career Award in Infection and Immunity (2019)


Email: shapiror@uoguelph.ca

Phone: 519.824.4120 ext. 53390

Office: SSC 3248

Department of Molecular and Cellular Biology
Summerlee Science Complex
University of Guelph
Guelph, ON, Canada, N1G 2W1