Publications

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

  1. 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)

  2. M Vlkova and OK Silander*. Gene regulation is commonly selected for high plasticity and low noise. bioRxiv doi.org/10.1101/2021.07.18.452581 (2021)

  3. 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)

  4. 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)

  5. 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)

  6. 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)

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. W Pearman, ANH Smith, G Breckell, J Dale, NE Freed*, OK Silander*. New tools for diet analyses: nanopore sequencing of metagenomic DNA from stomach contents to quantify diet in an invasive population of rats. bioRxiv 363622 (2018)

  13. 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).

  14. 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).

  15. 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).

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

  17. 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).

  18. 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).

  19. 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).

  20. 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).

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

  22. 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)

  23. 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).

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

  25. 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).

  26. 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).

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

  28. 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).

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

  30. 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).

  31. 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)

  32. 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)