Publications
bold: MicroStats lab members, *equal contribution
2024
Y. Syvolos, O.E. Salama, A.C. Gerstein. Constraint on boric acid resistance and tolerance evolvability in Candida albicans.
Canadian Journal of Microbiology. In press (2024).
2023
J. San Juan Galán, V. Poliquin & A.C. Gerstein. Insights and advances in recurrent vulvovaginal candidiasis. PloS Pathogens Pearls.
19: e1011684. (2023)
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. Frontiers in Systems Biology. 1:1248065. (2023)
R. Shapiro*, A.C. Gerstein*. Powering up antifungal treatment: Using small molecules to unlock the potential of existing therapies. mBio.14:e0107323 (2023) Invited commentary.
S. Prentice, J. Protudjer, A. Nijdam-Jones, S. Shaw, L. Kelly, A.C. Gerstein. Please Help Us: Canadian Childcare Providers’ Calls for Aid During the COVID-19 Pandemic. Journal of Early Childhood Research. 21:498-509. (2023) https://doi.org/10.1177/1476718X231186620
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, A. Selmecki. Antifungal drug concentration impacts the spectrum of
adaptive mutations in Candida albicans. Molecular Biology and Evolution. 40: msad009. (2023) (link)
2022
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
2021
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)
Pre-2020 fungal pathogens
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
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)
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)
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)
Pre-2020 Saccharomcyes cerevisiae (and other)
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
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 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*, 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
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)
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 SocietyTransaction. 34, 519-522. (2006)
(pdf)
Pre-printed
I. A.-R. Adamu Bukari, R. Kukurudz, A. de Graaf*, D. Habon*, B. Manyaz*, Y. Syvolos, A. Sumanarathne,
V. Poliquin, A.C. Gerstein. Genotypic and phenotypic homogeneity of vaginal and rectal yeast isolates from
recurrent vulvovaginal candidiasis. BioRxiv: https://doi.org/10.1101/2023.07.19.549743
SOFTWARE (*Creator)
PloidyPeaks: identification of ploidy variation in flow cytometry data. (2023)
Author(s): M. Henry*, C. Kostna, A. C. Gerstein
https://github.com/margothenry/PloidyPeaks
diskImageR: an R package to analyze drug resistance and tolerance from photographs of disk diffusion assays. (updated 2023)
Author(s): AC Gerstein*, S. Friesen, N. Tahmasebi; Contributor(s): Inbal Hecht
https://github.com/acgerstein/diskImageR
dgconstraint: an R package to measure genetic constrain (2014)
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
2024
Y. Syvolos, O.E. Salama, A.C. Gerstein. Constraint on boric acid resistance and tolerance evolvability in Candida albicans.
Canadian Journal of Microbiology. In press (2024).
2023
J. San Juan Galán, V. Poliquin & A.C. Gerstein. Insights and advances in recurrent vulvovaginal candidiasis. PloS Pathogens Pearls.
19: e1011684. (2023)
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. Frontiers in Systems Biology. 1:1248065. (2023)
R. Shapiro*, A.C. Gerstein*. Powering up antifungal treatment: Using small molecules to unlock the potential of existing therapies. mBio.14:e0107323 (2023) Invited commentary.
S. Prentice, J. Protudjer, A. Nijdam-Jones, S. Shaw, L. Kelly, A.C. Gerstein. Please Help Us: Canadian Childcare Providers’ Calls for Aid During the COVID-19 Pandemic. Journal of Early Childhood Research. 21:498-509. (2023) https://doi.org/10.1177/1476718X231186620
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, A. Selmecki. Antifungal drug concentration impacts the spectrum of
adaptive mutations in Candida albicans. Molecular Biology and Evolution. 40: msad009. (2023) (link)
2022
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
2021
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)
Pre-2020 fungal pathogens
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
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)
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)
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)
Pre-2020 Saccharomcyes cerevisiae (and other)
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
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 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*, 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
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)
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 SocietyTransaction. 34, 519-522. (2006)
(pdf)
Pre-printed
I. A.-R. Adamu Bukari, R. Kukurudz, A. de Graaf*, D. Habon*, B. Manyaz*, Y. Syvolos, A. Sumanarathne,
V. Poliquin, A.C. Gerstein. Genotypic and phenotypic homogeneity of vaginal and rectal yeast isolates from
recurrent vulvovaginal candidiasis. BioRxiv: https://doi.org/10.1101/2023.07.19.549743
SOFTWARE (*Creator)
PloidyPeaks: identification of ploidy variation in flow cytometry data. (2023)
Author(s): M. Henry*, C. Kostna, A. C. Gerstein
https://github.com/margothenry/PloidyPeaks
diskImageR: an R package to analyze drug resistance and tolerance from photographs of disk diffusion assays. (updated 2023)
Author(s): AC Gerstein*, S. Friesen, N. Tahmasebi; Contributor(s): Inbal Hecht
https://github.com/acgerstein/diskImageR
dgconstraint: an R package to measure genetic constrain (2014)
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