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O. Silander · SciRah

Researcher profile · Semantic Scholar

O. Silander

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O. Silander — researcher profile on SciRah

h-index: 23
Works: 77
Citations: 2,820

Most-cited papers

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads
Frederic Bertels, O. Silander, M. Pachkov, P. Rainey +1 more
2014Molecular biology and evolution452 citations Open access
Semantic Scholar
Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding
Nikki E. Freed, M. Vlková, Muhammad B. Faisal, O. Silander
2020bioRxiv257 citations Open access
Semantic Scholar
Understanding the Evolutionary Fate of Finite Populations: The Dynamics of Mutational Effects
O. Silander, O. Tenaillon, L. Chao
2007PLoS Biology210 citations Open access
Semantic Scholar
A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli
O. Silander, Nela Nikolic, Alon Zaslaver, A. Bren +3 more
2012PLoS Genetics182 citations Open access
Semantic Scholar
Epistasis between deleterious mutations and the evolution of recombination.
R. Kouyos, O. Silander, S. Bonhoeffer
2007Trends in Ecology & Evolution165 citations
Semantic Scholar
Alterations of the X-linked lymphoproliferative disease gene SH2D1A in common variable immunodeficiency syndrome.
M. Morra, O. Silander, S. Calpe, M. Choi +5 more
2001Blood128 citations
Semantic Scholar
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
Á. O'Toole, V. Hill, O. Pybus, A. Watts +85 more
2021Wellcome Open Research127 citations Open access
Semantic Scholar
Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software
Matthias Kaiser, Florian Jug, Thomas Julou, S. Deshpande +4 more
2018Nature Communications120 citations Open access
Semantic Scholar
Characterization of SH2D1A Missense Mutations Identified in X-linked Lymphoproliferative Disease Patients*
M. Morra, María Simarro-Grande, Margarita Martín, Alice Chen +10 more
2001Journal of Biological Chemistry95 citations Open access
Semantic Scholar
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads
William S. Pearman, Nikki E. Freed, O. Silander
2019BMC Bioinformatics93 citations Open access
Semantic Scholar
A Simple Screen to Identify Promoters Conferring High Levels of Phenotypic Noise
Nikki E. Freed, O. Silander, B. Stecher, Alexander A. Böhm +2 more
2008PLoS Genetics89 citations Open access
Semantic Scholar
Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability
T. Bergmiller, M. Ackermann, O. Silander
2012PLoS Genetics86 citations Open access
Semantic Scholar
Quantifying Organismal Complexity using a Population Genetic Approach
O. Tenaillon, O. Silander, J. Uzan, L. Chao
2007PLoS ONE83 citations Open access
Semantic Scholar
The predictability of molecular evolution during functional innovation
Diana Blank, Luise Wolf, M. Ackermann, O. Silander
2014Proceedings of the National Academy of Sciences of the United States of America76 citations Open access
Semantic Scholar
Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli
Niels Hofsteenge, E. van Nimwegen, O. Silander
2013BMC Microbiology76 citations Open access
Semantic Scholar
Widespread genetic exchange among terrestrial bacteriophages.
O. Silander, D. Weinreich, K. Wright, K. J. O'Keefe +3 more
2005Proceedings of the National Academy of Sciences of the United States of America68 citations Open access
Semantic Scholar
Correction: A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli
O. Silander, Nela Nikolic, Alon Zaslaver, A. Bren +3 more
2012PLoS Genetics55 citations Open access
Semantic Scholar
Opposite Effects of KCTD Subunit Domains on GABAB Receptor-mediated Desensitization*
Riad Seddik, Stefan P. Jungblut, O. Silander, M. Rajalu +6 more
2012Journal of Biological Chemistry53 citations Open access
Semantic Scholar
Expression noise facilitates the evolution of gene regulation
L. Wolf, O. Silander, E. van Nimwegen
2014bioRxiv51 citations Open access
Semantic Scholar
Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment
A. Sulit, M. Daigneault, E. Allen-Vercoe, O. Silander +6 more
2022bioRxiv44 citations Open access
Semantic Scholar
SARS-CoV2 genome sequencing protocol (1200bp amplicon "midnight" primer set, using Nanopore Rapid kit) v5
Nikki E. Freed, O. Silander
202130 citations Open access
Semantic Scholar
Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand
J. Geoghegan, J. Douglas, Xiao-Yun Ren, M. Storey +17 more
2021Emerging Infectious Diseases28 citations Open access
Semantic Scholar
Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality
Nikki E. Freed, D. Bumann, O. Silander
2016BMC Microbiology27 citations Open access
Semantic Scholar
Disruption of Esrom and Ryk identifies the roof plate boundary as an intermediate target for commissure formation.
M. Hendricks, A. Mathuru, Hui Wang, O. Silander +2 more
2008Molecular and cellular neurosciences23 citations
Semantic Scholar
Identifying important microbial and genomic biomarkers for differentiating right- versus left-sided colorectal cancer using random forest models
Tyler Kolisnik, A. Sulit, S. Schmeier, F. Frizelle +3 more
2023BMC Cancer22 citations Open access
Semantic Scholar
GEOGRAPHIC DIFFERENCES IN SEXUAL REASSORTMENT IN RNA PHAGE
K. J. O'Keefe, O. Silander, H. McCreery, D. Weinreich +5 more
2010Evolution; international journal of organic evolution20 citations
Semantic Scholar
The constancy of gene conservation across divergent bacterial orders
O. Silander, M. Ackermann
2009BMC Research Notes20 citations Open access
Semantic Scholar
Gene regulation in Escherichiacoli is commonly selected for both high plasticity and low noise
M. Vlková, O. Silander
2022Nature Ecology & Evolution14 citations Open access
Semantic Scholar
Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools
Asher Preska Steinberg, O. Silander, E. Kussell
2022bioRxiv13 citations Open access
Semantic Scholar
The advantages and disadvantages of short- and long-read metagenomics to infer bacterial and eukaryotic community composition
William S. Pearman, Nikki E. Freed, O. Silander
2019bioRxiv10 citations Open access
Semantic Scholar
Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli
Niels Hofsteenge, E. van Nimwegen, O. Silander
2013BMC Microbiology10 citations Open access
Semantic Scholar
Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli
Georgia L Breckell, O. Silander
2022bioRxiv9 citations Open access
Semantic Scholar
Efficiency of the synthetic self‐splicing RiboJ ribozyme is robust to cis‐ and trans‐changes in genetic background
M. Vlková, Bhargava Reddy Morampalli, O. Silander
2021bioRxiv9 citations Open access
Semantic Scholar
Beyond single references: pangenome graphs and the future of genomic medicine
D. Nyaga, R. Zaied, O. Silander, Michael A. Black +1 more
2025Frontiers in Genetics8 citations Open access
Semantic Scholar
pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R
Tyler Kolisnik, Faeze Keshavarz-Rahaghi, R. Purcell, Adam N. H. Smith +1 more
2024bioRxiv8 citations Open access
Semantic Scholar
Human gene and microbial analyses in rectal cancer complete responses to radiotherapy
A. Sulit, K. Wilson, J. Pearson, O. Silander +6 more
2023BJS Open6 citations Open access
Semantic Scholar
Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli
Georgia L Breckell, O. Silander
2020Microbiology Resource Announcements6 citations Open access
Semantic Scholar
Concordant geographic and genetic structure revealed by genotyping‐by‐sequencing in a New Zealand marine isopod
William S. Pearman, S. Wells, O. Silander, Nikki E. Freed +1 more
2020Ecology and Evolution6 citations Open access
Semantic Scholar
DNA quantification using the Qubit fluorometer v1
Nikki E. Freed, O. Silander
2020protocols.io5 citations Open access
Semantic Scholar
New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet
William S. Pearman, Adam N. H. Smith, Georgia L Breckell, J. Dale +2 more
2018bioRxiv5 citations Open access
Semantic Scholar
Do You Want to Build a Genome? Benchmarking Hybrid Bacterial Genome Assembly Methods
Georgia L Breckell, O. Silander
2021bioRxiv4 citations Open access
Semantic Scholar
Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod
William S. Pearman, S. Wells, J. Dale, O. Silander +1 more
2021bioRxiv4 citations Open access
Semantic Scholar
Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment
Andrea Sajuthi, Julia White, G. Ferguson, Nikki E. Freed +1 more
2020bioRxiv4 citations Open access
Semantic Scholar
Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih
K. Butela, Susan M. R. Gurney, H. Hendrickson, J. Leblanc-Straceski +48 more
2017Genome Announcements4 citations Open access
Semantic Scholar
Tracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup
Matthias Kaiser, Florian Jug, O. Silander, S. Deshpande +4 more
2016bioRxiv4 citations Open access
Semantic Scholar
A high-quality Oxford Nanopore assembly of the hourglass dolphin (Lagenorhynchus cruciger) genome
Nick McGrath, Jamie le Roux, Annabel Whibley, A. Alexander +4 more
2024bioRxiv3 citations Open access
Semantic Scholar
SARS-CoV2 genome sequencing protocol (1200bp amplicon "midnight" primer set, using Nanopore Rapid kit) v2
Nikki E. Freed, O. Silander
2021protocols.io3 citations Open access
Semantic Scholar
The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand
J. Geoghegan, J. Douglas, Xiao-Yun Ren, M. Storey +17 more
20203 citations Open access
Semantic Scholar
nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon) v4
Nikki E. Freed, O. Silander
2020protocols.io3 citations Open access
Semantic Scholar
Correction: A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli
O. Silander, Nela Nikolic, Alon Zaslaver, A. Bren +3 more
2012PLoS Genetics2 citations Open access
Semantic Scholar

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Nikki E. Freed×17
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M. Ackermann×7
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E. van Nimwegen×6
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