Associate Professor Olin Silander staff profile picture

Contact details +6492136618

Associate Professor Olin Silander PhD

Associate Professor in Molecular Cell Biology

School of Natural Sciences

I work on microbial genomics, microbial evolution, and rapid pathogen diagnostics.


Contact details

  • Ph: +64 (0)9 414 0800 ext. 43618
    Location: Building 20
    Campus: Albany


  • Doctor of Philosophy - University of California (2005)

Research Expertise

Research Interests

I am interested in using high throughput DNA sequencing methods to understand microbial evolution and genomics as well as implement novel pathogen diagnostics.

Area of Expertise

Field of research codes
Biological Adaptation (060303): Biological Sciences (060000): Epigenetics (incl. Genome Methylation and Epigenomics) (060404): Evolutionary Biology (060300): Genetics (060400): Genomics (060408): Infectious Agents (060502): Microbial Ecology (060504): Microbial Genetics (060503): Microbiology (060500): Molecular Evolution (060409): Phylogeny and Comparative Analysis (060309): Population, Ecological and Evolutionary Genetics (060411)





DNA Sequencing

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 3 5

Current Projects

Project Title: The Stuff Memories are Made of: How Bacteria Remember and Learn from Environmental Signals

Date Range: 2018 - 2022

Funding Body: Royal Society of New Zealand

Project Team:

Completed Projects

Project Title: Rapid diagnosis and genome sequencing to follow Cov-2019 outbreak

Date Range: 2020 - 2020

Funding Body: Health Research Council of New Zealand

Project Team:

Research Outputs


Sulit, AK., Wilson, K., Pearson, J., Silander, OK., Sampurno, S., Michael, M., . . . Purcell, RV. (2023). Human gene and microbial analyses in rectal cancer complete responses to radiotherapy. BJS Open. 7(3)
[Journal article]Authored by: Silander, O.
Steinberg, AP., Silander, OK., & Kussell, E. (2023). Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools. Proceedings of the National Academy of Sciences of the United States of America. 120(5)
[Journal article]Authored by: Silander, O.
Breckell, GL., & Silander, OK. (2023). Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli. G3: Genes, Genomes, Genetics. 13(2)
[Journal article]Authored by: Silander, O.
Sun, J., Silander, O., Rutherfurd-Markwick, K., Wen, D., Davy, TPP., & Mutukumira, AN. (2022). Phenotypic and genotypic characterisation of Lactobacillus and yeast isolates from a traditional New Zealand Māori potato starter culture. Current Research in Food Science. 5, 1287-1294
[Journal article]Authored by: Mutukumira, A., Rutherfurd, K., Silander, O.
Vlková, M., & Silander, OK. (2022). Gene regulation in Escherichia coli is commonly selected for both high plasticity and low noise. Nature Ecology and Evolution. 6(8), 1165-1179
[Journal article]Authored by: Silander, O.
Pearman, WS., Wells, SJ., Dale, J., Silander, OK., & Freed, NE. (2022). Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod. Royal Society Open Science. 9(1)
[Journal article]Authored by: Dale, J., Silander, O.
Vlková, M., Morampalli, BR., & Silander, OK. (2021). Efficiency of the synthetic self-splicing RiboJ ribozyme is robust to cis- and trans-changes in genetic background. MicrobiologyOpen. 10(4)
[Journal article]Authored by: Silander, O.
O'Toole, Á., Kraemer, MUG., Hill, V., Pybus, OG., Watts, A., Bogoch, II., . . . Rambaut, A. (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Research. 6
[Journal article]Authored by: Silander, O.
Geoghegan, JL., Douglas, J., Ren, X., Storey, M., Hadfield, J., Silander, OK., . . . de Ligt, J. (2021). Use of genomics to track coronavirus disease outbreaks, New Zealand. Emerging Infectious Diseases. 27(5), 1317-1322
[Journal article]Authored by: French, N., Silander, O.
Pearman, WS., Wells, SJ., Silander, OK., Freed, NE., & Dale, J. (2020). Concordant geographic and genetic structure revealed by genotyping-by-sequencing in a New Zealand marine isopod. Ecology and Evolution. 10(24), 13624-13639
[Journal article]Authored by: Dale, J., Silander, O.
Freed, NE., Vlková, M., Faisal, MB., & Silander, OK. (2020). Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding. Biology Methods and Protocols. 5(1), Retrieved from
[Journal article]Authored by: Silander, O.
Breckell, G., & Silander, OK. (2020). Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli. Microbiology Resource Announcements. 9(38), Retrieved from
[Journal article]Authored by: Silander, O.
Pearman, WS., Freed, NE., & Silander, OK. (2020). Testing the advantages and disadvantages of short- And long- read eukaryotic metagenomics using simulated reads. BMC Bioinformatics. 21(1)
[Journal article]Authored by: Silander, O.
Davies, CG., Wojtus, JK., Gilligan, CER., Latu, SF., Manning, TJ., Meyer, CE., . . . Hendrickson, HL. (2019). Complete genome sequences of nine mycobacteriophages from New Zealand, Beatrix, Carthage, Daegal, Dulcie, fancypants, Fenn, Inca, Naira, and Robyn. Microbiology Resource Announcements. 8(20)
[Journal article]Authored by: Silander, O.
Kaiser, M., Jug, F., Julou, T., Deshpande, S., Pfohl, T., Silander, OK., . . . Van Nimwegen, E. (2018). Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software. Nature Communications. 9(1)
[Journal article]Authored by: Silander, O.
Butela, KA., Gurney, SMR., Hendrickson, HL., LeBlanc-Straceski, JM., Zimmerman, AM., Conant, SB., . . . Kagey, JD. (2017). Complete genome sequences of cluster a mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih. Genome Announcements. 5(43)
[Journal article]Authored by: Silander, O.
Freed, NE., Bumann, D., & Silander, OK. (2016). Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. BMC Microbiology. 16(203)
[Journal article]Authored by: Silander, O.
Wolf, L., Silander, OK., & van Nimwegen, E. (2015). Expression noise facilitates the evolution of gene regulation. eLife. 4(JUNE)
[Journal article]Authored by: Silander, O.
Blank, D., Wolf, L., Ackermann, M., & Silander, OK. (2014). The predictability of molecular evolution during functional innovation. Proceedings of the National Academy of Sciences of the United States of America. 111(8), 3044-3049
[Journal article]Authored by: Silander, O.
Bertels, F., Silander, OK., Pachkov, M., Rainey, PB., & Van Nimwegen, E. (2014). Automated reconstruction of whole-genome phylogenies from short-sequence reads. Molecular Biology and Evolution. 31(5), 1077-1088
[Journal article]Authored by: Silander, O.
Hofsteenge, N., Van Nimwegen, E., & Silander, OK. (2013). Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC Microbiology. 13(1)
[Journal article]Authored by: Silander, O.
Silander, OK., Nikolic, N., Zaslaver, A., Bren, A., Kikoin, I., Alon, U., . . . Ackermann, M. (2012). A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLoS Genetics. 8(1)
[Journal article]Authored by: Silander, O.
Bergmiller, T., Ackermann, M., & Silander, OK. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6)
[Journal article]Authored by: Silander, O.
Seddik, R., Jungblut, SP., Silander, OK., Rajalu, M., Fritzius, T., Besseyrias, V., . . . Bettler, B. (2012). Opposite effects of KCTD subunit domains on GABA<inf>B</inf> receptor-mediated desensitization. Journal of Biological Chemistry. 287(47), 39869-39877
[Journal article]Authored by: Silander, O.
O'Keefe, KJ., Silander, OK., McCreery, H., Weinreich, DM., Wright, KM., Chao, L., . . . Turner, PE. (2010). Geographic differences in sexual reassortment in RNA phage. Evolution. 64(10), 3010-3023
[Journal article]Authored by: Silander, O.
Silander, OK., & Ackermann, M. (2009). The constancy of gene conservation across divergent bacterial orders. BMC Research Notes. 2
[Journal article]Authored by: Silander, O.
Hendricks, M., Mathuru, AS., Wang, H., Silander, O., Kee, MZL., & Jesuthasan, S. (2008). Disruption of Esrom and Ryk identifies the roof plate boundary as an intermediate target for commissure formation. Molecular and Cellular Neuroscience. 37(2), 271-283
[Journal article]Authored by: Silander, O.
Freed, NE., Silander, OK., Stecher, B., Böhm, A., Hardt, WD., & Ackermann, M. (2008). A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genetics. 4(12)
[Journal article]Authored by: Silander, O.
Silander, OK., Tenaillon, O., & Chao, L. (2007). Understanding the evolutionary fate of finite populations: the dynamics of mutational effects.. PLoS biology. 5(4)
[Journal article]Authored by: Silander, O.
Tenaillon, O., Silander, OK., Uzan, JP., & Chao, L. (2007). Quantifying organismal complexity using a population genetic approach. PLoS ONE. 2(2)
[Journal article]Authored by: Silander, O.
Kouyos, RD., Silander, OK., & Bonhoeffer, S. (2007). Epistasis between deleterious mutations and the evolution of recombination. Trends in Ecology and Evolution. 22(6), 308-315
[Journal article]Authored by: Silander, O.
Silander, OK., Tenaillon, O., & Chao, L. (2007). Understanding the evolutionary fate of finite populations: The dynamics of mutational effects. PLoS Biology. 5(4), 922-931
[Journal article]Authored by: Silander, O.
Silander, OK., Weinreich, DM., Wright, KM., O'Keefe, KJ., Rang, CU., Turner, PE., . . . Chao, L. (2005). Widespread genetic exchange among terrestrial bacteriophages. Proceedings of the National Academy of Sciences of the United States of America. 102(52), 19009-19014
[Journal article]Authored by: Silander, O.
Morra, M., Simarro-Grande, M., Martin, M., Chen, ASI., Lanyi, A., Silander, O., . . . Terhorst, C. (2001). Characterization of SH2D1A Missense Mutations Identified in X-linked Lymphoproliferative Disease Patients. Journal of Biological Chemistry. 276(39), 36809-36816
[Journal article]Authored by: Silander, O.
Morra, M., Silander, O., Calpe, S., Choi, M., Oettgen, H., Myers, L., . . . Terhorst, C. (2001). Alterations of the X-linked lymphoproliferative disease gene SH2D1A in common variable immunodeficiency syndrome. Blood. 98(5), 1321-1325
[Journal article]Authored by: Silander, O.


Sajuthi, A., White, J., Ferguson, G., Freed, N., & Silander, OK. (2020). Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment.. : BioRXiv
[Internet publication]Authored by: Silander, O.

Teaching and Supervision

Teaching Statement

Genetics and Evolution 203.210 (Co-ordinator)

Genome Science 203.311 (Co-ordinator)

DNA Technology 203.310

Graduate Supervision Statement

I haed a very cross-disciplinary lab, and have had collaborations outside the Molecular and Cell Biology group, inluding faculty working in Ecology and Evolution, Food Tech, and Statistics.

Summary of Doctoral Supervision

Position Current Completed
Main Supervisor 2 3
Co-supervisor 4 2

Current Doctoral Supervision

Main Supervisor of:

  • Tyler Kolisnik - Doctor of Philosophy
    Genomic and Microbial Biomarker Discovery in Colorectal Cancer using Random Forests

Co-supervisor of:

  • Dennis Van Hulten - Doctor of Philosophy
    The ecology and genetic diversity of monostand forming coral populations in shallow and mesophotic habitats
  • Melissa Nehmens - Doctor of Philosophy
    Eco-evolutionary responses of urchin species to climate change in Aotearoa New Zealand
  • Jia Sun - Doctor of Philosophy
    A study to optimise the fermentation and production of Parāroa Rēwena: a traditional Māori bread
  • Kelly Hong - Doctor of Philosophy
    Quantifying the predictability of the emergence of antibiotic resistance in a model strain and environmental isolates of Escherichia coli.

Completed Doctoral Supervision

Main Supervisor of:

  • 2023 - Georgia Breckell - Doctor of Philosophy
    Characterisation of epigenomic variation in natural isolates of E. coli
  • 2022 - Arielle Kae Sulit - Doctor of Philosophy
    Microbiome and Host Immune Responses in Colorectal Cancer Development and Radiotherapy Response
  • 2021 - Marketa Vlkova - Doctor of Philosophy
    Natural variation in bacterial gene regulation

Co-supervisor of:

  • 2019 - Paul Richard Yulo - Doctor of Philosophy
    Evolution of the Spherical Cell Shape in Bacteria
  • 2018 - Elena Denisenko - Doctor of Philosophy
    Transcriptional regulation in mouse macrophages: the role of enhancers in macrophage activation and infection

Media and Links


  • 31 Aug 2020 - Online
    Re-emergence of community transmission in Aotearoa
    Description of August 2020 COVID19 outbreak
  • 28 Jan 2018 - Newspaper
    Bug memories' could help fight looming crisis
    Article in NZ Herlad highlighting research
  • 27 Dec 2020 - Newspaper
    Big Read: The scientists who helped NZ crush Covid
    Description of researchers who played a role in the NZ response to COVID19
  • 23 Jul 2020 - Online
    Massey researchers use new rapid method to sequenc
    Highlight of our work on COVID genome sequencing
  • 23 Jul 2020 - Online
    International eyes turn to progress of COVID-19 ge
    Press release on our research to genome sequence SARS-CoV-2
  • 22 Jul 2020 - Radio
    RNZ Nights interview with Brian Crump
  • 20 Aug 2020 - Online
    New method used to sequence COVID-19 genomes in Au
    Artcile on the role we played in solving the August 2020 COVID outbreak
  • 16 Feb 2022 - Online
    Genome sequencing assays for infectious disease su
    Discussion of methods for SARS-CoV-2 genome sequencing
  • 14 Jul 2021 - Online
    NGS During the COVID-19 Pandemic and Beyond
    Description of our collaborative work with the multinational DNA sequencing and synthesis company IDT
  • 13 Aug 2021 - Online
    SARS-CoV-2: Massey Univ. Profs Develop Method To Q
    Description of our work to quickly sequence the SARS-CoV-2 genome

Other Links