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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
Updated January  2022
  • HOME
  • PEOPLE
  • RESEARCH
  • PUBLICATIONS
  • PROTOCOLS & SCRIPTS
    • diskImageR
  • COURSES
    • CSM_Repro
    • MBIO4030-SciComm
    • MBIO7040: Data analysis and visualization for microbiologists
    • R Resources
    • STAT7350
  • VALUES
  • LINKS