2014 was the second full year of Haldane’s Sieve, which we started in 2012 to bring attention to preprints in population and evolutionary genetics. This year we had over 100,000 visitors from across the globe; the most viewed posts were:
- Author post: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome. Adam Siepel writes about the motivation for his group’s preprint. The preprint contained a comparison of the authors’ new method to CADD. The CADD authors disagreed with some aspects of this comparison and posted their detailed comments as Thoughts on: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome.
- Our paper: Sashimi plots: Quantitative visualization of RNA sequencing read alignments. This post by Yarden Katz from 2013 describes a method for visualizing RNA sequencing data.
- Author post: Genome Sequencing Highlights the Dynamic Early History of Dogs. Ilan Gronau describes some of the computational details of a preprint on dog domestication. This paper was published in PLOS Genetics.
- LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies. Bulik-Sullivan et al. describe a new method to correct for population stratification in genome-wide association studies.
- Our Paper: Genome-wide inference of ancestral recombination graphs. This post was the most viewed post last year, and the paper was published this year in PLOS Genetics.
- The Landscape of Human STR Variation. Willems et al. discuss a survey of microsatellite variation in humans; Karl Broman posted a review of the paper in the comments. The paper was published in Genome Research.
- Author post: Inferring human population size and separation history from multiple genome sequences. Stephan Schiffels describes his preprint on extensions of the PSMC model. The paper was published in Nature Genetics.
- Author post: qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Stephen Turner describes his preprint on visualization methods for genome-wide association studies.
- The existence and abundance of ghost ancestors in biparental populations. Gravel and Steel explore the differences between genealogical and genetic ancestry.
- Author post: Long non-coding RNAs as a source of new peptides. Mar Alba discusses her group’s preprint on the evolution of gene content. This paper was published in eLife.