Journal
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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 https://academic.oup.com/biomethods/article/5/1/bpaa014/5873518
[Journal article]Authored by: Silander, O.Read Online:
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Breckell, G., & Silander, OK. (2020). Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli.
Microbiology Resource Announcements. 9(38), Retrieved from https://journals.asm.org/doi/full/10.1128/MRA.00222-20
[Journal article]Authored by: Silander, O.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read article at Massey Research Online:
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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.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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Silander, OK., & Ackermann, M. (2009). The constancy of gene conservation across divergent bacterial orders.
BMC Research Notes. 2
[Journal article]Authored by: Silander, O.Read Online:
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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.Read Online:
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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.Read article at Massey Research Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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
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