Publications
See all publications on Google Scholar
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/s41586-024-08419-4
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
Puumala E, Sychantha D, Lach E, Reeves S, Nabeela S, Fogal M, Nigram A, Johnson JW, Whitesell L, Robbins N, Aspuru-Guzik A, Shapiro RS, Uppuluri P, Kalyaanamoorthy S, Magolan J, Wright GD, and Cowen LE. Allosteric inhibition of tRNA synthetase Gln4 by N-pyrimidinyl-β-Thiophenylacrylamides exerts highly selective antifungal activity. Cell Chemical Biology (2024) 31(4):760-775.e17 https://doi.org/10.1016/j.chembiol.2024.01.010
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
Iyer KR, Li SC, Revie NM, Lou JW, Duncan D, Sanchez H, Skulska I, Ušaj MM, Larsen B, Wong C, Aman A, Kiyota T, Yoshimura M, Kimura H, Hirano H, Yoshida M, Osada H, Gingras A-C, Andes DR, Shapiro RS, Robbins N, Mazhab-Jafari MT, Whitesell L, Yashiroda Y, Boone C, and Cowen LE. Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity. Cell Chemical Biology (2023) https://doi.org/10.1016/j.chembiol.2023.06.005
Rathie B, Theelen B, Laurence M, and Shapiro RS. Antimicrobial susceptibility testing for three Malassezia species. Microbiology Spectrum (2023) https://doi.org/10.1128/spectrum.05076-22
Puumala E, Zaslaver O, Chen A, Duncan D, Fogal M, Shapiro RS, Mazhab-Jafari MT, Whitesell L, Montenegro-Burke JR, Robbins N, and Cowen LE. The tri-substituted isoxazole MMV688766 exerts broad-spectrum activity against drug-resistant fungal pathogens through inhibition of lipid homeostasis. mBio (2022) https://doi.org/10.1128/mbio.02730-22
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
Cochrane RR, Shrestha A, Severo de Almeida MM, Agyare-Tabbi M, Van Belois K, Brumwell SL, Hamadache S, Meaney J, Nucifora D, Sharma J, Soltysiak M, Tong C, Walker E, Lachance M-A, Edgell DR, Shapiro RS, and Karas BJ.
Superior conjugative plasmids delivered by bacteria to diverse fungi.
BioDesign Research (2022) https://doi.org/10.34133/2022/9802168
Case NT, Berman J, Blehert DS, Cramer RA, Cuomo CA, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, and Cowen LE.
The future of fungi: threats and opportunities.
G3 (2022) https://doi.org/10.1093/g3journal/jkac224.
Revie NM, Iyer KR, Maxson ME, Zhang J, Yan S, Fernandes CM, Meyer KJ, Chen X, Skulska I, Fogal M, Sanchez H, Hossain S, Li S, Yashiroda Y, Hirano H, Yoshida M, Osada H, Boone C, Shapiro RS, Andes DR, Wright GD, Nodwell JR, Del Poeta M, Burke MD, Whitesell L, Robbins N, and Cowen LE.
Targeting fungal membrane homeostasis with imidazopyrazoindoles impairs azole resistance and biofilm formation.
Nature Communications (2022) 13: 3634
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
Uthayakumar D*, Sharma J*, Wensing L*, and Shapiro RS.
CRISPR-based genetic manipulation of Candida species: historical perspective and modern advances.
Frontiers in Genome Editing (2021) doi.org/10.3389/fgeed.2020.606281
Halder V, McDonnell B, Uthayakumar D, Usher J, and Shapiro RS.
Genetic interaction analysis in microbial pathogens: unravelling networks of pathogenesis, antimicrobial susceptibility, and host interactions. FEMS Microbiology Reviews (2020)
Kim G, Rosiana S, Kirienko NV, and Shapiro RS.
A simple nematode infection model for studying Candida albicans pathogenesis.
Current Protocols in Microbiology (2020)
Horianopoulos LC*, Gluck-Thaler E*, Benoit Gelber I, Cowen LE, Geddes-McAlister J, Landry CR, Schwartz IS, Scott JA, Sellam A, Sheppard DC, Spribille T, Subramaniam R, Walker AK, Harris SD^, Shapiro RS^, and Gerstein AC^.
The Canadian Fungal Research Network: current challenges and future opportunities.
Canadian Journal of Microbiology (2020)
Mei Y, Jian T, Zhou J, Li J, Tan J, Wei L, Li J, Dai H, Peng Y, Wang H, Zhang L, Lopez-Ribot J, Shapiro RS, Chen C, Liu N-N, and Wang H.
FDA approved drug library screening identifies robenidine as a repositionable antifungal.
Frontiers in Microbiology (2020) doi.org/10.3389/fmicb.2020.00996
Thomson GJ, Hernon C, Austriaco N, Shapiro RS, Belenky P, and Bennett RJ.
Metabolism-induced oxidative stress and DNA damage selectively trigger genome instability in polyploid fungal cells.
The EMBO Journal (2019) 38:e101597
Shapiro RS.
Evolutionary strategies to sensitize drug-resistant pathogens.
mSphere (2019) 4:e00313-19
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). 14:955–975
Sharma J, Rosiana S, Razzaq I, and Shapiro RS.
Linking cellular morphogenesis with antifungal treatment and susceptibility in Candida pathogens.
Journal of Fungi (2019) 5:17.
Polvi EJ, Veri AO, Liu Z, Hossain S, Hyde S, Kim SH, Tebbji F, Sellam A, Todd RT, Xie JL, Lin ZY, Wong CJ, Shapiro RS, Whiteway M, Robbins N, Gingras A-C, Selmecki A, and Cowen LE.
Functional divergence of a global regulatory complex governing fungal filamentation
PLOS Genetics (2019). doi.org/10.1371/journal.pgen.1007901
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
Veri AO, Miao X, Shapiro RS, Tebbji F, O’Meara TR, Kim SH, Colazo J, Tan K, Whiteway M, Robbins N, Wong KH, and Cowen LE
Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space
PLOS Genetics (2018) 14(3):e1007270
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
PNAS (2018) doi.org/10.1073
Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, and Collins JJ. (2017)
A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans
Nature Microbiology (2017) 3:73-82
Cohen NR, Ross C, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, and Collins JJ
A role for the bacterial GATC methylome 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
Gambaro K, Quinn MCJ, Cáceres-Gorriti, KY, Shapiro RS, Provencher D, Rahimi K, Mes-Masson A-M, and Tonin PN
Low levels of IGFBP7 expression in high-grade serous ovarian carcinoma is associated with patient outcome
BMC Cancer (2015) 15(1):1138
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, Ryan O, Boone C, and Cowen LE
Regulatory circuitry governing morphogenesis in Saccharomyces cerevisiae and Candida albicans
Cell Cycle (2012) 11(23): 4294-4295
Shapiro RS and Cowen LE
Thermal control of microbial development and virulence: molecular mechanisms of microbial temperature sensing
mBio (2012) 3(5):e00238
Shapiro RS, Zaas AK, Betancourt-Quiroz M, Perfect JR, and Cowen LE
The Hsp90 co-chaperone Sgt1 governs Candida albicans morphogenesis and drug resistance
PLOS ONE (2012) 7(9):e44734
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 and Cowen LE
Uncovering cellular circuitry controlling temperature-dependent fungal morphogenesis
Virulence (2012) 3(4):400-404
Senn HE, Shapiro RS and Cowen LE
Cdc28 provides a molecular link between Hsp90, morphogenesis, and cell cycle progression in Candida albicans
Molecular Biology of the Cell (2012) 23(2):268-283
Diezmann S, Michaut M, Shapiro RS, Bader GD, and Cowen LE
Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitry
PLOS Genetics (2012) 8(3):e1002562
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 and Cowen LE
Coupling temperature sensing and development: Hsp90 regulates morphogenetic signalling in Candida albicans
Virulence (2010) 1(1):45-48
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
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/s41586-024-08419-4
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
Puumala E, Sychantha D, Lach E, Reeves S, Nabeela S, Fogal M, Nigram A, Johnson JW, Whitesell L, Robbins N, Aspuru-Guzik A, Shapiro RS, Uppuluri P, Kalyaanamoorthy S, Magolan J, Wright GD, and Cowen LE. Allosteric inhibition of tRNA synthetase Gln4 by N-pyrimidinyl-β-Thiophenylacrylamides exerts highly selective antifungal activity. Cell Chemical Biology (2024) 31(4):760-775.e17 https://doi.org/10.1016/j.chembiol.2024.01.010
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
Iyer KR, Li SC, Revie NM, Lou JW, Duncan D, Sanchez H, Skulska I, Ušaj MM, Larsen B, Wong C, Aman A, Kiyota T, Yoshimura M, Kimura H, Hirano H, Yoshida M, Osada H, Gingras A-C, Andes DR, Shapiro RS, Robbins N, Mazhab-Jafari MT, Whitesell L, Yashiroda Y, Boone C, and Cowen LE. Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity. Cell Chemical Biology (2023) https://doi.org/10.1016/j.chembiol.2023.06.005
Rathie B, Theelen B, Laurence M, and Shapiro RS. Antimicrobial susceptibility testing for three Malassezia species. Microbiology Spectrum (2023) https://doi.org/10.1128/spectrum.05076-22
Puumala E, Zaslaver O, Chen A, Duncan D, Fogal M, Shapiro RS, Mazhab-Jafari MT, Whitesell L, Montenegro-Burke JR, Robbins N, and Cowen LE. The tri-substituted isoxazole MMV688766 exerts broad-spectrum activity against drug-resistant fungal pathogens through inhibition of lipid homeostasis. mBio (2022) https://doi.org/10.1128/mbio.02730-22
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
Cochrane RR, Shrestha A, Severo de Almeida MM, Agyare-Tabbi M, Van Belois K, Brumwell SL, Hamadache S, Meaney J, Nucifora D, Sharma J, Soltysiak M, Tong C, Walker E, Lachance M-A, Edgell DR, Shapiro RS, and Karas BJ.
Superior conjugative plasmids delivered by bacteria to diverse fungi.
BioDesign Research (2022) https://doi.org/10.34133/2022/9802168
Case NT, Berman J, Blehert DS, Cramer RA, Cuomo CA, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, and Cowen LE.
The future of fungi: threats and opportunities.
G3 (2022) https://doi.org/10.1093/g3journal/jkac224.
Revie NM, Iyer KR, Maxson ME, Zhang J, Yan S, Fernandes CM, Meyer KJ, Chen X, Skulska I, Fogal M, Sanchez H, Hossain S, Li S, Yashiroda Y, Hirano H, Yoshida M, Osada H, Boone C, Shapiro RS, Andes DR, Wright GD, Nodwell JR, Del Poeta M, Burke MD, Whitesell L, Robbins N, and Cowen LE.
Targeting fungal membrane homeostasis with imidazopyrazoindoles impairs azole resistance and biofilm formation.
Nature Communications (2022) 13: 3634
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
Uthayakumar D*, Sharma J*, Wensing L*, and Shapiro RS.
CRISPR-based genetic manipulation of Candida species: historical perspective and modern advances.
Frontiers in Genome Editing (2021) doi.org/10.3389/fgeed.2020.606281
Halder V, McDonnell B, Uthayakumar D, Usher J, and Shapiro RS.
Genetic interaction analysis in microbial pathogens: unravelling networks of pathogenesis, antimicrobial susceptibility, and host interactions. FEMS Microbiology Reviews (2020)
Kim G, Rosiana S, Kirienko NV, and Shapiro RS.
A simple nematode infection model for studying Candida albicans pathogenesis.
Current Protocols in Microbiology (2020)
Horianopoulos LC*, Gluck-Thaler E*, Benoit Gelber I, Cowen LE, Geddes-McAlister J, Landry CR, Schwartz IS, Scott JA, Sellam A, Sheppard DC, Spribille T, Subramaniam R, Walker AK, Harris SD^, Shapiro RS^, and Gerstein AC^.
The Canadian Fungal Research Network: current challenges and future opportunities.
Canadian Journal of Microbiology (2020)
Mei Y, Jian T, Zhou J, Li J, Tan J, Wei L, Li J, Dai H, Peng Y, Wang H, Zhang L, Lopez-Ribot J, Shapiro RS, Chen C, Liu N-N, and Wang H.
FDA approved drug library screening identifies robenidine as a repositionable antifungal.
Frontiers in Microbiology (2020) doi.org/10.3389/fmicb.2020.00996
Thomson GJ, Hernon C, Austriaco N, Shapiro RS, Belenky P, and Bennett RJ.
Metabolism-induced oxidative stress and DNA damage selectively trigger genome instability in polyploid fungal cells.
The EMBO Journal (2019) 38:e101597
Shapiro RS.
Evolutionary strategies to sensitize drug-resistant pathogens.
mSphere (2019) 4:e00313-19
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). 14:955–975
Sharma J, Rosiana S, Razzaq I, and Shapiro RS.
Linking cellular morphogenesis with antifungal treatment and susceptibility in Candida pathogens.
Journal of Fungi (2019) 5:17.
Polvi EJ, Veri AO, Liu Z, Hossain S, Hyde S, Kim SH, Tebbji F, Sellam A, Todd RT, Xie JL, Lin ZY, Wong CJ, Shapiro RS, Whiteway M, Robbins N, Gingras A-C, Selmecki A, and Cowen LE.
Functional divergence of a global regulatory complex governing fungal filamentation
PLOS Genetics (2019). doi.org/10.1371/journal.pgen.1007901
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
Veri AO, Miao X, Shapiro RS, Tebbji F, O’Meara TR, Kim SH, Colazo J, Tan K, Whiteway M, Robbins N, Wong KH, and Cowen LE
Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space
PLOS Genetics (2018) 14(3):e1007270
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
PNAS (2018) doi.org/10.1073
Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, and Collins JJ. (2017)
A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans
Nature Microbiology (2017) 3:73-82
Cohen NR, Ross C, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, and Collins JJ
A role for the bacterial GATC methylome 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
Gambaro K, Quinn MCJ, Cáceres-Gorriti, KY, Shapiro RS, Provencher D, Rahimi K, Mes-Masson A-M, and Tonin PN
Low levels of IGFBP7 expression in high-grade serous ovarian carcinoma is associated with patient outcome
BMC Cancer (2015) 15(1):1138
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, Ryan O, Boone C, and Cowen LE
Regulatory circuitry governing morphogenesis in Saccharomyces cerevisiae and Candida albicans
Cell Cycle (2012) 11(23): 4294-4295
Shapiro RS and Cowen LE
Thermal control of microbial development and virulence: molecular mechanisms of microbial temperature sensing
mBio (2012) 3(5):e00238
Shapiro RS, Zaas AK, Betancourt-Quiroz M, Perfect JR, and Cowen LE
The Hsp90 co-chaperone Sgt1 governs Candida albicans morphogenesis and drug resistance
PLOS ONE (2012) 7(9):e44734
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 and Cowen LE
Uncovering cellular circuitry controlling temperature-dependent fungal morphogenesis
Virulence (2012) 3(4):400-404
Senn HE, Shapiro RS and Cowen LE
Cdc28 provides a molecular link between Hsp90, morphogenesis, and cell cycle progression in Candida albicans
Molecular Biology of the Cell (2012) 23(2):268-283
Diezmann S, Michaut M, Shapiro RS, Bader GD, and Cowen LE
Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitry
PLOS Genetics (2012) 8(3):e1002562
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 and Cowen LE
Coupling temperature sensing and development: Hsp90 regulates morphogenetic signalling in Candida albicans
Virulence (2010) 1(1):45-48
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