Weekly Roundup - December 4, 2015

Every week, members of the Wilson Sayres’ lab scour journals for interesting and relevant (to lab research) articles. Here’s what we found the week of December 4, 2015:

Sex Chromosomes

QTL mapping of sex determination loci supports an ancient pathway in ants and honey bees Miyakawa and Mikheyev (2015) in PLoS Genetics

Intergenomic interacations between mitochondrial and Y-linked genes shape male mating patterns and fertility in Drosophila melanogaster Yee et al. (2015) in Evolution


Genomics of cancer and a new era for cancer research Brennan and Wild (2015) in PLoS Genetics

Cattle sex-specific recombination and genetic control from a large pedigree analysis Ma et al. (2015) in PLoS Genetics

Convergent evolution during local adaptation to patchy landscapes Ralph and Coop (2015) in PLoS Genetics

Enhancer runaway and the evolution of diploid gene expression Fyon et al. (2015) in PLoS Genetics

Adaptations to high ethanol reveals complex evolutionary pathways Voordeckers et al. (2015) in PLoS Genetics

The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefontal cortex and reveals an underlying role of early growth response 1 Duclot and Kabbaj (2015) in Genome Biology

Genome-wide analysis of evolutionary markers of human influenza A(H1N1)pdm09 and A(H3N2) may guide selection of vaccine strain candidates Belanov et al. (2015) in Genome Biology and Evolution

Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type Isrie et al. (2015) in American Journal of Human Genetics

Mutations preventing regulated exon skipping in MET cause osteofibrous dysplasia Gray et al. (2015) in American Journal of Human Genetics

The epigenomic landscape of African rainforest hunter-gatherers and farmers Fagny et al. (2015) in Nature Communications


Calibrating the human mutation rate via ancestral recombination density in diploid genomes Lipson et al. (2015) in PLoS Genetics

Computing workflows for biologists: a roadmap Shade and Teal (2015) in PLoS Biology


Ernst Rüdin's unpublished 1922-1925 study "Inheritance of manic-depressive insanity": genetic research findings subordinated to eugenic ideology Kösters et al. (2015) in PLoS Genetics

Sex differences in parental care: gametic investment, sexual selection, and social environment Liker et al. (2015) in Evolution

Democratizing education? Examining access and usage patterns in massive open online courses Hansen and Reich (2015) in Science

Protected areas and global conservation of migratory birds Runge et al. (2015) in Science

Codecademy intro to command line

One of the challenges of learning (or teaching) the command line is that different operating systems  have default access to a command line terminal, whereas others will not (e.g., Windows versus Mac versus Linux). In a classroom session, this is especially frustrating, because time must be spent bringing all computers to the same starting position. Browser emulator Codecademy offers a fantastic alternative to this challenge because it has a terminal emulator directly in the browser, so you can practice and execute all the commands in the emulator, regardless of what operating system you have.


In practice Another feature of codecademy command line interface that I like is that tutorials have students first implement a command, then afterwards there is an explanation of what the command does. This allows students to practice first, observe what happens, and then read through a detailed explanation.

So far, students in the lab have liked this tutorial. We start with Codecademy, then work on installing local terminal/Linux-like environments (e.g., cygwin for people with Windows machines).

Intro to Python: Check out Codecademy

An undergraduate in the lab with no prior programming experience has tried out a couple tutorials for "Intro to Python." The student said that this introduction, from CodeAcademy has been the most accessible: https://www.codecademy.com/learn/python


Nov 6 update: One great feature of the codecademy is that it has a terminal emulator, so you can run all of your commands in the browser, and don't need to be concerned about what operating system you have.

Hello, world!

Welcome to the official blog of the Wilson Sayres Lab!  This blog will primarily serve as a repository for links to scientific articles of interest to the lab and its members.  However, we'll also occasionally post in-depth discussions of articles, tutorials, links to resources, and other material relevant to genomics, bioinformatics, evolution, and programming.  Stay tuned, we should post our first round of articles later this week! -Tim