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Monthly Archives: September 2013
What we're reading: GWAS hits lost in translation, the mutational load of range expansions, and killing the comments section to save science
In the journals Carlson, C. S., Matise, T. C., North, K. E., Haiman, C. a., Fesinmeyer, M. D., Buyske, S., … Kooperberg, C. L. (2013). Generalization and dilution of association results from European GWAS in populations of non-European ancestry: The … Continue reading
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Scientific computing doesn't have to hurt
Amy Brown handles communication and scheduling for Software Carpentry. The post title alludes to the goals of Software Carpentry, a volunteer organization whose members teach basic software skills to researchers in science, engineering, and medicine. It’s a great organization, and … Continue reading
What we're reading: The tiger genome, pooled sequencing for population genomics, and more fretting about academic careers
In the journals Cho YS et al. 2013. The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Communications 4:2433. doi: 10.1038/ncomms3433. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular … Continue reading
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For viruses, ecology shapes the speed of evolutionary change
Molecular ecologists are interested in understanding what patterns in genetic variation across and among populations can tell us about the ecology of the living things we study. But a paper published in the latest issue of The American Naturalist demonstrates … Continue reading
What we're reading: Next-generation admixture estimates, mutation rates shaped by epidemiology, and whatever happened to that data?
In the journals Skotte L, TS Korneliussen, and A Albrechtsen. 2013. Estimating individual admixture proportions from next generation sequencing data. Genetics doi: 10.1534/genetics.113.154138. This paper presents a new method for inferring individ- ual’s ancestry that takes the uncertainty introduced in … Continue reading
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Analytical software management for your Mac? Homebrew to the rescue!
Source: http://www.popsci.com/diy/article/2007-08/ultimate-all-one-beer-brewing-machine Much of the big processing tasks in biological research remain the domain of clusters of computer nodes, whether local or an Amazon EC2 instance, running various flavors of Linux. It is perhaps safe to say that this fact will … Continue reading
What we're reading: Compressed genomes, drafting genes, and the third post-publication peer reviewer
In the journals Deorowicz, S., A. Danek, and S. Grabowski. 2013. Genome compression: A novel approach for large collections. Bioinformatics 1–7. doi: 10.1093/bioinformatics/btt460. More precisely, our novel Ziv-Lempel-style compression algorithm squeezes a single human genome to ~400KB. The key to … Continue reading
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Using R to run parallel analyses of population genetic data in STRUCTURE: ParallelStructure
In this guest post, Francois Besnier explains how to use ParallelStructure, his new R package for running STRUCTURE analyses in parallel computing environments. To start with, thanks to The Molecular Ecologist blog team (Tim and Jeremy) for the invitation to … Continue reading
Posted in howto, population genetics, R, software, STRUCTURE
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