Publications
bold: MicroStats lab members, *equal contribution
A.C. Gerstein. mSphere of Influence: Deterministic and stochastic processes drive microbial evolution.
mSphere, 7:e0002223. (2023) (link)
R.T. Todd, N. Soisangwan, S. Peters, B. Kemp, T. Crooks, A.C. Gerstein, Anna Selmecki. Antifungal drug
concentration impacts the spectrum of adaptive mutations in Candida albicans. Molecular
Biology and Evolution. 40: msad009. (2023) (link)
A.C. Gerstein, P. Sethi. Experimental evolution of drug resistance in human fungal pathogens.
Current Opinion in Genetics & Development. 76:101965. (2022) (link)
R.J. Kukurudz, M. Chapel*, Q. Wonitowy*, A-R Adamu Bukari, B Sidney, R Sierhuis, A.C. Gerstein.
Acquisition of cross-azole tolerance and aneuploidy in Candida albicans strains evolved to posaconazole.
G3: Genes|Genomes|Genetics. 12: jkac156. (2022) (link)
R code on GitHub
OE Salama, AC Gerstein. Differential response of Candida species morphologies and isolates to fluconazole
and boric acid. Antimicrobial Agents and Chemotherapy. 66: e02406-21 (2022) (link)
R code on GitHub
N. Case, […], A.C. Gerstein^, […], J. Heitman, L. Cowen. The Future of Fungi: Threats and Opportunities.
G3: Genes|Genomes|Genetics 12: jkac224. (2022) (link)
^Gerstein is one of 31 authors that contributed equally. Meeting report: CIFAR-BWF Future of Mycology Workshop
OE Salama, AC Gerstein. High throughput computational analysis of biofilm formation from time-lapse microscopy.
Current Protocols. 1, e194. doi: 10.1002/cpz1.194. (2021) (pdf)
R code on GitHub
AC Gerstein* & N Sharp*. The population genetics of ploidy change in unicellular fungi. FEMS Microbiology Reviews.
45: fuab006 (2021) (link)
I Ene, MA Hickman & AC Gerstein. The interplay between neutral and adaptive processes shapes genetic variation during Candida species evolution. Current Clinical Microbiology Reports. (2021) https://doi.org/10.1007/s40588-021-00171-x
R code on GitHub
L Horianopoulos, E Gluck-Thaler, I. Benoit Gelber, LE Cowen, J Geddes-McAlister, CR. Landry, IS Schwartz, JA Scott, A Sellam,
DC Sheppard, T Spribille, R Subramaniam, AK Walker, SD Harris, RS. Shapiro, AC Gerstein. The Canadian Fungal
Research Network: Current Challenges and Future Opportunities. Canadian Journal of Microbiology. 67:13-22. (2021) (pdf)
AC Gerstein, J Berman. Candida albicans genetic background influences mean and heterogeneity of drug responses
and genome stability during evolution to fluconazole. mSphere. 5:e00480-20. (2020) (pdf)
Raw data & R code are posted on GitHub
AC Gerstein, KM Jackson, TR McDonald, Y Wang, BD Lueck, KD Smith, A Akampurira, DB Meya, C Xue, DR Boulware,
K Nielsen. Identification of pathogen genomic differences that impact human immune response and disease during
Cryptococcus neoformans infection. mBio. DOI: 10.1128/mBio.01440-19. (2019) (pdf)
Raw data & R code are posted on GitHub
M Mandic, ML Ramon, AC Gerstein, AY Gracey & JG Richards. Variable gene transcription underlies phenotypic
convergence of hypoxia tolerance in sculpins. BMC Evolutionary Biology. 18:163. (2018)
S Yeaman, AC Gerstein, KA Hodgins, MC Whitlock. Quantifying how constraints limit the diversity of viable routes to
adaptation. PLoS Genetics. 14: e1007717 (2018) (link)
Raw data & R code are posted on GitHub
A Forche, G Cromie, AC Gerstein, N Solis, Z Pisithkul, W Srifa, E Jeffery, D Abbey, SG Filler, A Dudley, J Berman. Rapid phenotypic
and genotypic diversification after exposure to the oral host niche in Candida albicans. Genetics. 209: 725-741 (2018) (link)
AC Gerstein, H Lim, J Berman & M Hickman Ploidy tug-of-war: Evolutionary and genetic environments influence the
rate of ploidy drive in a human fungal pathogen. Evolution. 71: 1025-1038 (2017) (link)
Raw data & R code are posted on dryad
AC Gerstein & K Neilsen. It’s not all about us: Evolution and maintenance of Cryptococcus virulence requires selection
outside the human host. Yeast. 34: 143-154 (2017) (link)
J Ono, AC Gerstein & S.P. Otto Widespread genetic incompatibilities between first-step mutations during parallel
adaptation of Saccharomyces cerevisiae to a common environment. PLoS Biology. 15: e1002591 (2017) (pdf)
Raw data & R code are posted on dryad
AC Gerstein, A Rosenberg, I Hecht & J Berman. diskiImageR: quantification of resistance and tolerance to antimicrobial
drugs using disk diffusion assays. Microbiology. 162(7):1059-68. (2016) (link) (R package) (github)
Supporting Information including package vignette and R code walkthrough (pdf)
AC Gerstein*, MS Fu*, L Mukaremera, Z Li, KL Ormerod, JA Fraser, J Berman, & K Nielsen. Polyploid titan cells produce
haploid and aneuploid progeny to promote stress adaptation. mBio. 5: e01340-15 (2015) (pdf)
AC Gerstein & J Berman. Shift and adapt: the costs and benefits of karyotype variations. Current Opinion in
Microbiology. 26:130–136 (2015) (pdf)
AC Gerstein*, J Ono*, DS Lo^, ML Campbell, A Kuzmin, & SP Otto. Too much of a good thing: The unique and repeated paths
toward copper adaptation. Genetics. 199: 555-571 (2015)
Fastq files have been posted to the NCBI SRA (here)
Raw data & R code are posted on dryad
MZ Anderson, AC Gerstein, L Wigen, JA Baller, & J Berman. Silencing is noisy: Population and cell level noise in
telomere-adjacent genes is dependent on telomere position and Sir2. PLoS Genetics. 10: e1004436 (2014) (pdf)
AC Gerstein, A Kuzmin & SP Otto. Loss of heterozygosity facilitates passage through Haldane’s sieve for
Saccharomyces cerevisiae undergoing adaptation. Nature Communications DOI: 10.1038/ncomms4819. (2014) (pdf)
Recommended as exceptional on F1000Prime
Blog post about this paper at SGD (the Saccharomyces Genome Database) (link)
AC Gerstein. Mutational effects depend on ploidy level: All else in not equal. Biology Letters 9: 20120614. (2013) (pdf)
Supporting Information (pdf)
Raw data & R code are posted on dryad
AC Gerstein, D.S. Lo^ & S.P. Otto. Parallel genetic changes and non-parallel gene-environment interactions underlie
nystatin resistance in yeast. Genetics 192: 241-252 (2012) (pdf)
'New and Noteworthy' writeup on SGD (here) Fastq files have been posted to the NCBI SRA (here)
AC Gerstein & SP Otto. Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent
advantage as measured by standard fitness assays. PLoS One. 6, e26599. (2011) (pdf)
The presentation I gave on this work as an invited symposium speaker at CSEE in 2010 (pdf)
AC Gerstein & J-S Moore. Small is the new big: Assessing the population structure of microoganisms. Molecular
Ecology. 20, 4385–4387. (2011) (pdf)
AC Gerstein, MA Mandegar*^, LA Cleathero*^, SP Otto. Haploids adapt faster than diploids across a range of
environments. Journal of Evolutionary Biology. 24, 531-540 (pdf). (2010)
Supporting Information (pdf)
Raw data & R code are posted on dryad (here)
AC Gerstein & SP Otto. Ploidy and The Causes of Evolution. Journal of Heredity. 100, 571-581. (2009) (pdf)
SP Otto & AC Gerstein. Primer: The evolution of haploidy and diploidy. Current Biology 18, R1121-R1124. (2008) (pdf)
AC Gerstein, R McBride, SP Otto. Ploidy reduction in Saccharomyces cerevisiae. Biology Letters, 91-94. (2008) (pdf)
AC Gerstein, HE Chun, A Grant, & SP Otto. Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS
Genetics. 9, e145. (2006) (pdf)
SP Otto & AC Gerstein. Why have sex? The population genetics of sex and recombination. Biochemical Society
Transaction. 34, 519-522. (2006) (pdf)
Pre-printed
I. Tolle, S. Oehm, M.G. Hoesl, C. Treiber-Kleinke, L. Peil, A.-R. Adamu Bukari, T. Semmler, J.Rappsilber,
A.C. Gerstein, N. Budisa. Evolving a mitigation of the stress response pathway to change the basic
chemistry of life. bioRxiv. https://doi.org/10.1101/2021.09.23.461486 (2021)
SOFTWARE (*Creator)
diskImageR: an R package to analyze drug resistance and tolerance from photographs of disk diffusion assays.
Author(s): AC Gerstein*; Contributor(s): Inbal Hecht
https://cran.r-project.org/web/packages/diskImageR/index.html
https://github.com/acgerstein/diskImageR
dgconstraint: an R package to measure genetic constrain
Author(s): S Yeaman*, AC Gerstein; Contributor(s): A Schick, M Henry
https://github.com/samyeaman/dgconstraint
POPULAR SCIENCE, etc.
AC Gerstein. On luck, success, and becoming a professor. Medium. (link)
AC Gerstein & A Gerkin. Pesticide 2.0: Spray-on gene silencers. With Alison Gerkin. Genes to Genomes blog, Genetics Society of America. (link)
AC Gerstein. Knowing what I know now: graduate school. The Molecular Ecologists blog. (link)
THESES
B Sidney, Honours Thesis (2021) - New clade designation revealed from whole genome sequencing of Candida glabrata isolates.
M Chapel, Honours Thesis (2020) - Evolution of posaconazole tolerance in Candida albicans.
AC Gerstein. PhD Thesis (2012) - A Characterization of Adaptive Mutations. The University of British Columbia.
Thesis defense presentation (pdf)
AC Gerstein. MSc Thesis (2006) - Genomic convergence in Saccharomyces cerevisiae: Patterns and mechanisms. The University of British Columbia
bold: MicroStats lab members, *equal contribution
A.C. Gerstein. mSphere of Influence: Deterministic and stochastic processes drive microbial evolution.
mSphere, 7:e0002223. (2023) (link)
R.T. Todd, N. Soisangwan, S. Peters, B. Kemp, T. Crooks, A.C. Gerstein, Anna Selmecki. Antifungal drug
concentration impacts the spectrum of adaptive mutations in Candida albicans. Molecular
Biology and Evolution. 40: msad009. (2023) (link)
A.C. Gerstein, P. Sethi. Experimental evolution of drug resistance in human fungal pathogens.
Current Opinion in Genetics & Development. 76:101965. (2022) (link)
R.J. Kukurudz, M. Chapel*, Q. Wonitowy*, A-R Adamu Bukari, B Sidney, R Sierhuis, A.C. Gerstein.
Acquisition of cross-azole tolerance and aneuploidy in Candida albicans strains evolved to posaconazole.
G3: Genes|Genomes|Genetics. 12: jkac156. (2022) (link)
R code on GitHub
OE Salama, AC Gerstein. Differential response of Candida species morphologies and isolates to fluconazole
and boric acid. Antimicrobial Agents and Chemotherapy. 66: e02406-21 (2022) (link)
R code on GitHub
N. Case, […], A.C. Gerstein^, […], J. Heitman, L. Cowen. The Future of Fungi: Threats and Opportunities.
G3: Genes|Genomes|Genetics 12: jkac224. (2022) (link)
^Gerstein is one of 31 authors that contributed equally. Meeting report: CIFAR-BWF Future of Mycology Workshop
OE Salama, AC Gerstein. High throughput computational analysis of biofilm formation from time-lapse microscopy.
Current Protocols. 1, e194. doi: 10.1002/cpz1.194. (2021) (pdf)
R code on GitHub
AC Gerstein* & N Sharp*. The population genetics of ploidy change in unicellular fungi. FEMS Microbiology Reviews.
45: fuab006 (2021) (link)
I Ene, MA Hickman & AC Gerstein. The interplay between neutral and adaptive processes shapes genetic variation during Candida species evolution. Current Clinical Microbiology Reports. (2021) https://doi.org/10.1007/s40588-021-00171-x
R code on GitHub
L Horianopoulos, E Gluck-Thaler, I. Benoit Gelber, LE Cowen, J Geddes-McAlister, CR. Landry, IS Schwartz, JA Scott, A Sellam,
DC Sheppard, T Spribille, R Subramaniam, AK Walker, SD Harris, RS. Shapiro, AC Gerstein. The Canadian Fungal
Research Network: Current Challenges and Future Opportunities. Canadian Journal of Microbiology. 67:13-22. (2021) (pdf)
AC Gerstein, J Berman. Candida albicans genetic background influences mean and heterogeneity of drug responses
and genome stability during evolution to fluconazole. mSphere. 5:e00480-20. (2020) (pdf)
Raw data & R code are posted on GitHub
AC Gerstein, KM Jackson, TR McDonald, Y Wang, BD Lueck, KD Smith, A Akampurira, DB Meya, C Xue, DR Boulware,
K Nielsen. Identification of pathogen genomic differences that impact human immune response and disease during
Cryptococcus neoformans infection. mBio. DOI: 10.1128/mBio.01440-19. (2019) (pdf)
Raw data & R code are posted on GitHub
M Mandic, ML Ramon, AC Gerstein, AY Gracey & JG Richards. Variable gene transcription underlies phenotypic
convergence of hypoxia tolerance in sculpins. BMC Evolutionary Biology. 18:163. (2018)
S Yeaman, AC Gerstein, KA Hodgins, MC Whitlock. Quantifying how constraints limit the diversity of viable routes to
adaptation. PLoS Genetics. 14: e1007717 (2018) (link)
Raw data & R code are posted on GitHub
A Forche, G Cromie, AC Gerstein, N Solis, Z Pisithkul, W Srifa, E Jeffery, D Abbey, SG Filler, A Dudley, J Berman. Rapid phenotypic
and genotypic diversification after exposure to the oral host niche in Candida albicans. Genetics. 209: 725-741 (2018) (link)
AC Gerstein, H Lim, J Berman & M Hickman Ploidy tug-of-war: Evolutionary and genetic environments influence the
rate of ploidy drive in a human fungal pathogen. Evolution. 71: 1025-1038 (2017) (link)
Raw data & R code are posted on dryad
AC Gerstein & K Neilsen. It’s not all about us: Evolution and maintenance of Cryptococcus virulence requires selection
outside the human host. Yeast. 34: 143-154 (2017) (link)
J Ono, AC Gerstein & S.P. Otto Widespread genetic incompatibilities between first-step mutations during parallel
adaptation of Saccharomyces cerevisiae to a common environment. PLoS Biology. 15: e1002591 (2017) (pdf)
Raw data & R code are posted on dryad
AC Gerstein, A Rosenberg, I Hecht & J Berman. diskiImageR: quantification of resistance and tolerance to antimicrobial
drugs using disk diffusion assays. Microbiology. 162(7):1059-68. (2016) (link) (R package) (github)
Supporting Information including package vignette and R code walkthrough (pdf)
AC Gerstein*, MS Fu*, L Mukaremera, Z Li, KL Ormerod, JA Fraser, J Berman, & K Nielsen. Polyploid titan cells produce
haploid and aneuploid progeny to promote stress adaptation. mBio. 5: e01340-15 (2015) (pdf)
AC Gerstein & J Berman. Shift and adapt: the costs and benefits of karyotype variations. Current Opinion in
Microbiology. 26:130–136 (2015) (pdf)
AC Gerstein*, J Ono*, DS Lo^, ML Campbell, A Kuzmin, & SP Otto. Too much of a good thing: The unique and repeated paths
toward copper adaptation. Genetics. 199: 555-571 (2015)
Fastq files have been posted to the NCBI SRA (here)
Raw data & R code are posted on dryad
MZ Anderson, AC Gerstein, L Wigen, JA Baller, & J Berman. Silencing is noisy: Population and cell level noise in
telomere-adjacent genes is dependent on telomere position and Sir2. PLoS Genetics. 10: e1004436 (2014) (pdf)
AC Gerstein, A Kuzmin & SP Otto. Loss of heterozygosity facilitates passage through Haldane’s sieve for
Saccharomyces cerevisiae undergoing adaptation. Nature Communications DOI: 10.1038/ncomms4819. (2014) (pdf)
Recommended as exceptional on F1000Prime
Blog post about this paper at SGD (the Saccharomyces Genome Database) (link)
AC Gerstein. Mutational effects depend on ploidy level: All else in not equal. Biology Letters 9: 20120614. (2013) (pdf)
Supporting Information (pdf)
Raw data & R code are posted on dryad
AC Gerstein, D.S. Lo^ & S.P. Otto. Parallel genetic changes and non-parallel gene-environment interactions underlie
nystatin resistance in yeast. Genetics 192: 241-252 (2012) (pdf)
'New and Noteworthy' writeup on SGD (here) Fastq files have been posted to the NCBI SRA (here)
AC Gerstein & SP Otto. Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent
advantage as measured by standard fitness assays. PLoS One. 6, e26599. (2011) (pdf)
The presentation I gave on this work as an invited symposium speaker at CSEE in 2010 (pdf)
AC Gerstein & J-S Moore. Small is the new big: Assessing the population structure of microoganisms. Molecular
Ecology. 20, 4385–4387. (2011) (pdf)
AC Gerstein, MA Mandegar*^, LA Cleathero*^, SP Otto. Haploids adapt faster than diploids across a range of
environments. Journal of Evolutionary Biology. 24, 531-540 (pdf). (2010)
Supporting Information (pdf)
Raw data & R code are posted on dryad (here)
AC Gerstein & SP Otto. Ploidy and The Causes of Evolution. Journal of Heredity. 100, 571-581. (2009) (pdf)
SP Otto & AC Gerstein. Primer: The evolution of haploidy and diploidy. Current Biology 18, R1121-R1124. (2008) (pdf)
AC Gerstein, R McBride, SP Otto. Ploidy reduction in Saccharomyces cerevisiae. Biology Letters, 91-94. (2008) (pdf)
AC Gerstein, HE Chun, A Grant, & SP Otto. Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS
Genetics. 9, e145. (2006) (pdf)
SP Otto & AC Gerstein. Why have sex? The population genetics of sex and recombination. Biochemical Society
Transaction. 34, 519-522. (2006) (pdf)
Pre-printed
I. Tolle, S. Oehm, M.G. Hoesl, C. Treiber-Kleinke, L. Peil, A.-R. Adamu Bukari, T. Semmler, J.Rappsilber,
A.C. Gerstein, N. Budisa. Evolving a mitigation of the stress response pathway to change the basic
chemistry of life. bioRxiv. https://doi.org/10.1101/2021.09.23.461486 (2021)
SOFTWARE (*Creator)
diskImageR: an R package to analyze drug resistance and tolerance from photographs of disk diffusion assays.
Author(s): AC Gerstein*; Contributor(s): Inbal Hecht
https://cran.r-project.org/web/packages/diskImageR/index.html
https://github.com/acgerstein/diskImageR
dgconstraint: an R package to measure genetic constrain
Author(s): S Yeaman*, AC Gerstein; Contributor(s): A Schick, M Henry
https://github.com/samyeaman/dgconstraint
POPULAR SCIENCE, etc.
AC Gerstein. On luck, success, and becoming a professor. Medium. (link)
AC Gerstein & A Gerkin. Pesticide 2.0: Spray-on gene silencers. With Alison Gerkin. Genes to Genomes blog, Genetics Society of America. (link)
AC Gerstein. Knowing what I know now: graduate school. The Molecular Ecologists blog. (link)
THESES
B Sidney, Honours Thesis (2021) - New clade designation revealed from whole genome sequencing of Candida glabrata isolates.
M Chapel, Honours Thesis (2020) - Evolution of posaconazole tolerance in Candida albicans.
AC Gerstein. PhD Thesis (2012) - A Characterization of Adaptive Mutations. The University of British Columbia.
Thesis defense presentation (pdf)
AC Gerstein. MSc Thesis (2006) - Genomic convergence in Saccharomyces cerevisiae: Patterns and mechanisms. The University of British Columbia