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screen-shot-2016-09-27-at-4-11-45-pmTracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup 
Kaiser M, Jug F, Julou T, Deshpande S, Pfohl T, Silander OK*, Myers G*, van Nimwegen E* (2017)
bioRxiv (accepted at Nature Communicationspdf 


Screen Shot 2017-12-11 at 10.29.25 AMComplete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih
Butela KA, Gurney SMR, et al. (2017)
Genome Announcements 5: e01182-17



Combining Shigella Tn-seq data with Gold-standard E. coli Gene Deletion Data Suggests Rare Transitions between Essential and Non-essential Gene Functionality
Freed NE, Bumann D, Silander OK* (2016)
bioRxiv pdf


Screen Shot 2014-08-06 at 10.45.01

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



Bertels_editAutomated reconstruction of whole genome phylogenies from short sequence reads
Bertels F*, Silander OK, Pachkov M, Rainey P, van Nimwegen E  (2014)
Mol Biol Evol 31 (5): 1077-1088 pdf (News comment)


growth_editThe predictability of molecular evolution during functional innovation
Blank D, Wolf L, Ackermann M, Silander OK* (2014)
PNAS 111(8): 3044-3049 pdf (Evol. Appl. comment)



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


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


essential_editPatterns of evolutionary conservation of essential genes correlate with their compensability pdf
Bergmiller T, Ackermann M, Silander OK* (2012)
PLOS Genetics 8(6): e1002803


genomewide_editA Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli
Silander OK*, Nikolic N, Zaslaver A, Bren A, Kikoin I, Alon U, Ackermann M (2012)
PLOS Genetics 8(1): e1002443 pdf

*indicates corresponding author


Geographic differences in sexual reassortment in RNA phage
O’Keefe KJ, Silander OK, McCreery H, Weinreich DM, Wright KM, ChaoL, Edwards SV, Remold SK, Turner PE (2010)
Evolution, doi: 10.1111/j.1558-5646.2010.01040.

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

A simple screen to identify promoters conferring high levels of phenotypic variation
Freed NE, Silander OK, Stecher B, Boehm A, Hardt WD, Ackermann M (2008)
PLOS Genetics 4(12): e1000307.

Disruption of Esrom and Ryk identifies the roof plate boundary as an intermediate target for commisure formation
Hendricks M, Mathru AS, Hui W, Silander O, Kee MZL, Jesuthasan S (2008)
Molecular and Cellular Neuroscience. 37(2): 271-283.

Epistasis and the Evolution of Recombination
Kouyos R, Silander OK, Bonhoeffer S (2007)
Trends in Ecology and Evolution 22(6): 308-315.

Understanding the evolutionary fate of finite size populations: Surviving deleterious mutations
Silander OK, Tenaillon O, Chao L (2007)
PLOS Biology 5(4): e94.

Quantifying Organismal Complexity using a Population Genetics Approach
Tenaillon O, Silander OK, Uzan J-P, Chao L (2007)
PLoS One 2(2): e217.

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

Alterations of the X-linked lymphoproliferative disease gene SH2D1A in common variable immunodeficiency syndrome
Morra M, Silander O, Calpe S, Choi M, Oettgen H, Myers L, Etzioni A, Buckley R, Terhorst C (2001)
Blood 98 (5): 1321-25.

Characterization of SH2D1A missense mutations identified in X-linked lymphoproliferative disease patients
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 (2001)
Journal of Biological Chemistry 276 (39): 36809-16.


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