Hot Papers!
This is a stream of papers by other groups which come out which we think are interesting and deserve to be shared!
If you have something that you think we’d like, why not comment, send us an email or tweet @killemorganlab!
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Posted on 21 August 2014 by Pete
Genetic Structure of Earthworm Populations at a Regional Scale: Inferences from Mitochondrial and Microsatellite Molecular Markers in Aporrectodea icterica (Savigny 1826) (2014) PLoS ONE (2014) vol. 9 (7) pp. e101597 http://dx.doi.org/10.1371/journal.pone.0101597 Abstract Despite the fundamental role that soil invertebrates (e.g. earthworms) play in soil ecosystems, the magnitude of their spatial genetic variation is still largely
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Posted on 18 August 2014 by Pete
Abstract RNA-based applications requiring high quality, non-degraded RNA are a foundational element of many research studies. As such, it is paramount that the integrity of experimental RNA is validated prior to cDNA synthesis or other downstream applications. In the absence of expensive equipment such as microfluidic electrophoretic devices, and as an alternative to the costly
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Posted on 17 August 2014 by Pete
ABSTRACT We report reference-grade de novo assemblies of four model organisms and the human genome from single-molecule, real-time (SMRT) sequencing. Long-read SMRT sequencing is routinely used to finish microbial genomes, but the available assembly methods have not scaled well to larger genomes. 100mg viagra sale Here we introduce the MinHash Alignment Process (MHAP) for efficient
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Posted on 16 August 2014 by Pete
Aim The latitudinal gradient in species richness is one of the most studied biodiversity patterns. Here we explore a north–south gradient in earthworm diversity, and evaluate the importance of current and historical filters in shaping the distribution of present-day below-ground species richness. Methods Using high resolution data on earthworm distributions across France, we document the
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Posted on 8 January 2014 by Pete
Ever wanted to know the effect of the software you use for trimming your Illumina data – this is a great bench-marking paper spotted by Luis. Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM (2013) An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis. PLoS ONE 8(12): e85024. doi:10.1371/journal.pone.0085024 Next Generation
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Posted on 23 December 2013 by Pete
http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12157/full NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data neestimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. neestimator v2 includes three single-sample estimators (updated versions of
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Posted on 23 December 2013 by Pete
http://www.nature.com/hdy/journal/v112/n1/abs/hdy201342a.html?WT.ec_id=HDY-201401 Quantitative genetic study of the adaptive process The additive genetic variance with respect to absolute fitness, VA(W), divided by mean absolute fitness, sets the rate of ongoing adaptation. Fisher’s key insight yielding this quantitative prediction of adaptive evolution, known as the Fundamental Theorem of Natural Selection, is well appreciated by evolutionists. Nevertheless, extremely scant
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Posted on 23 December 2013 by Pete
http://www.nature.com/hdy/journal/v112/n1/abs/hdy201352a.html?WT.ec_id=HDY-201401 Post-GWAS: where next? More samples, more SNPs or more biology? The power of genome-wide association studies (GWAS) rests on several foundations: (i) there is a significant amount of additive genetic variation, (ii) individual causal polymorphisms often have sizable effects and (iii) they segregate at moderate-to-intermediate frequencies, or will be effectively ‘tagged’ by polymorphisms that
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Posted on 23 December 2013 by Pete
http://bioinformatics.oxfordjournals.org/content/30/1/123.abstract.html?etoc Phylowood: interactive web-based animations of biogeographic and phylogeographic histories Summary: Phylowood is a web service that uses JavaScript to generate in-browser animations of biogeographic and phylogeographic histories from annotated phylogenetic input. The animations are interactive, allowing the user to adjust spatial and temporal resolution, and highlight phylogenetic lineages of interest. Availability and implementation: All
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Posted on 15 December 2013 by Pete
The Hidden Codes That Shape Protein Evolution Robert J. Weatheritt, M. Madan Babu + Author Affiliations MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. E-mail: rweather; madanm Despite redundancy in the genetic code (1), the choice of codons used is highly biased in some proteins, suggesting that additional constraints operate in
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