Lab members are in bold, corresponding authors noted by an asterisk* 

1. NE Freed*, ANH Smith, G Breckell, J Dale, OK Silander*. New tools for diet analyses: nanopore sequencing of metagenomic DNA from stomach contents to quantify diet in an invasive population of rats. New Zealand Journal of Ecology (2023).

2. AK Sulit, J Pearson, W Liu, OK Silander, K Wilson, A Heriot, F Frizelle, and R Purcell* (2022) Human Gene and Microbial Analyses Suggest Immunotherapy-like Mechanisms in Complete Response to Radiotherapy in Rectal Cancer. medRxiv doi: 10.1101/2022.07.07.22277387.

3. AK Sulit, M Daigneault, E Allen-Vercoe, OK Silander, B Hock et al. (2022) Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment. bioRxiv doi: 10.1101/2022.04.26.489473.

4. GL Breckell and OK Silander. (2022) Growth Condition Dependent Differences in Methylation Implies Transiently Differentiated DNA Methylation States in E. coli. bioRxiv doi: 10.1101/2022.03.24.485589.

5. M Vlková* and OK Silander. (2022) Transcriptional control of the lacZ promoter is under directional and diversifying selection. bioRxiv doi: 10.1101/2022.03.17.484780v1. In revision for Molecular Biology and Evolution

6. GL Breckell and OK Silander*. (2022) Do you want to build a genome: Benchmarking Hybrid Bacterial Genome Assembly Methods. bioRxiv doi: 10.1101/2021.11.07.467652v1.

7. J Sun, OK Silander, K Rutherford, T Poi-poi Davy, AN Mutukumira*. (2022) Phenotypic And Genotypic Characterisation of Lactobacillus and Yeast Isolates from a Traditional New Zealand Māori Sourdough. In press, Current Research in Food Science.

8. M Vlková and OK Silander*. (2022) Gene regulation is commonly selected for both high plasticity and low noise. Nature Ecol & Evol. doi.org/10.1038/s41559-022-01783-2. 

9. W Pearman*, SJ Wells, J Dale, OK Silander, NE Freed. Long read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod. bioRxiv https://www.biorxiv.org/content/10.1101/2021.09.27.462060v1 (2021)

10. M Vlkova, B Morampalli, OK Silander*. Efficiency of the synthetic self-splicing RiboJ ribozyme is robust to​ cis​-and trans​-changes in genetic background. MicrobiologyOpen 10: e1232. (2021)

11. A O’Toole et al. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Research. (2021)

12. JL Geoghegan, J Douglas, X Ren, M Storey, J Hadfield, OK Silander, NE Freed, et al. The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand. Emerging and Infectious Diseases doi.org/10.1101/2020.10.28.20221853 (2021)

13. A Sajuthi, J White, G Ferguson, NE Freed*, OK Silander*. Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment. bioRxiv doi.org/10.1101/2020.09.30.320226 (2020)

14. G Breckell* and OK Silander. Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli. Microbiology Res. Announcements doi.org/10.1128/MRA.00222-20 (2020)

15. W Pearman*, SJ Wells, OK Silander, NE Freed, J Dale. Concordant geographic and genetic structure revealed by genotyping‐by‐sequencing in a New Zealand marine isopod. Ecology and Evolution 10: 13624 (2020)

16. NE Freed*, M Vlková, MB Faisal, OK Silander*. Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding bioRxiv (2020) Biology Methods and Protocols: doi.org/10.1093/biomethods/bpaa014 (2020)

17. W Pearman*, NE Freed, OK Silander*. Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads. BMC Bioinformatics 21: 220 (2020)

18. Davies CG et al. Complete Genome Sequences of Nine Mycobacteriophages from New Zealand, Beatrix, Carthage, Daegal, Dulcie, Fancypants, Fenn, Inca, Naira, and Robyn. Microbiology Res. Announcements 8: e00395-19 (2019)

19. Kaiser M, Jug F, Julou T, Deshpande S, Pfohl T, Silander OK*, Myers G*, van Nimwegen E*. Tracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup. Nature Communications 9: 212 (2018).

20. Kristen A Butela et al. Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih. Genome announcements 5: e01182-17 (2017). 

21. Freed NE, Bumann D, Silander OK*. 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 (2016).

22. Wolf L, Silander OK*, van Nimwegen E*. Expression noise facilitates the evolution of gene regulation. eLife 4: e05856 (2015).

23. Bertels F*, Silander OK, Pachkov M, Rainey P, van Nimwegen E. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution 31: 1077-1088 (2014)  Highlighted in the News Section Molecular Biology and Evolution 31: 1328 (2014).

24. Blank D, Wolf L, Ackermann M, Silander OK*. The predictability of molecular evolution during functional innovation. Proceedings of the National Academy of Sciences 111: 3044-3049 (2014). Highlighted in Evolutionary Applications 7, 337-338 (2014). 

25. Hofsteenge N, van Nimwegen E, Silander OK*. Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC Microbiology 13: 25 (2013). 

26. Seddik R, Jungblut SP, Silander OK, Rajalu M, Fritzius T, Besseyrias V, Jacquier V, Fakler B, Gassmann M*, Bettler B*. Opposite effects of KCTD subunit domains on GABAB receptor-mediated desensitization. Journal of Biological Chemistry 287: 39869 (2012).

27. Bergmiller T*, Ackermann M, Silander OK*. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLOS Genetics 8: e1002803 (2012).

28. Silander OK*, Nikolic N, Zaslaver A, Bren A, Kokoin I, Alon U, Ackermann M. A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLOS Genetics 8: e1002443 (2012)

29. O’Keefe KJ, Silander OK, McCreery H, Weinreich DM, Wright KM, Chao L, Edwards SV, Remold SK, Turner PE*. Geographic differences in sexual reassortment in RNA phage. Evolution 64: 3010-3023 (2010). 

30. Silander OK*, Ackermann M. The constancy of gene conservation across divergent bacterial orders. BMC Research Notes 2:2 (2009). 

31. Freed NE, Silander OK, Stecher B, Boehm A, Hardt WD, Ackermann M*. A simple screen to identify promoters conferring high levels of phenotypic variation. PLOS Genetics 4: e1000307 (2008).

32. Hendricks M, Mathru AS, Hui W, Silander OK, Kee MZL, Jesuthasan S*. Disruption of Esrom and Ryk identifies the roof plate boundary as an intermediate target for commisure formation. Molecular and Cellular Neuroscience 37: 271-283 (2008).

33. Kouyos R, Silander OK, Bonhoeffer S*. Epistasis between deleterious mutations and the evolution of recombination. Trends in Ecology and Evolution 22: 308-315 (2007).

34. Silander OK*, Tenaillon O, Chao L. Understanding the evolutionary fate of finite size populations: surviving deleterious mutations. PLOS Biology 5: e94 (2007). Highlighted in Heredity 99, 359–360 (2007).

35. Tenaillon O*, Silander OK, Uzan J-P, Chao L. Quantifying organismal complexity using a population genetics approach. PLOS One 2: e217 (2007).

36. Silander OK*, Weinreich DM, Wright KM, O’Keefe KJ, Rang CU, Turner PE, Chao L. Widespread genetic exchange among terrestrial bacteriophages. Proceedings of the National Academy of Sciences 102: 19009-14 (2005).

37. Morra M, Silander O, Calpe S, Choi M, Oettgen H, Myers L, Etzioni A, Buckley R, Terhorst C*. Alterations of the X-linked lymphoproliferative disease gene SH2D1A in common variable immunodeficiency syndrome. Blood 98: 1321-25 (2001) 

38. Morra M, Simarro-Grande M, Martin M, Chen ASI, Lanyi A, Silander O, Calpe S, Davis J, Pawson T, Eck MJ, Sumegi J, Engel P, Li SC, Terhorst C*. Characterization of SH2D1A missense mutations identified in X-linked lymphoproliferative disease patients. Journal of Biological Chemistry 276: 36809-16 (2001)