My new blog/newsletter ("Paired Ends") is now at blog.stephenturner.us. I'll be posting semi-regular updates and literature highlights in bioinformatics, computational biology, and data science, along with the occasional post on programming.
A while back I wrote this post about how I stay current in bioinformatics & genomics. That was nearly five years ago . A lot has changed since then. A few links are dead.
I recently stumbled across this collection of computational biology primers in Nature Biotechnology. Many of these are old, but they're still great resources to get a fundamental understanding of the topic. Here they are in no particular order.
Current Opinion in Microbiology recently published a special issue in genomics. In an excellent editorial overview, “Genomics: The era of genomically-enabled microbiology”, Neil Hall and Jay Hinton give an overview of the state of the field in microbial genomics, summarize recent contributions, and give a great synopsis of each of the reviews in this issue.
Two years ago David Searls published an article in PLoS Comp Bio describing a series of online courses in bioinformatics. Yesterday, the same author published an updated version, "A New Online Computational Biology Curriculum," (PLoS Comput Biol 10(6): e1003662.
A few weeks ago the 2014 AMIA Translational Bioinformatics Meeting (TBI) was held in beautiful San Francisco. This meeting is full of great science that spans the divide between molecular and clinical research, but a true highlight of this meeting is the closing keynote, traditionally given by Russ Altman.
Jeff Leek, biostats professor at Johns Hopkins and instructor of the Coursera Data Analysis course, recently posted on Simly Statistics this list of awesome things other people accomplished in 2013 in genomics, statistics, and data science. At risk of sounding too meta , I'll say that this list itself is one of the awesome things that was put together in 2013.
One of the clearest advantages RNA-seq has over array-based technology for studying gene expression is not needing a reference genome or a pre-existing oligo array. De novo transcriptome assembly allows you to study non-model organisms, cancer cells, or environmental metatranscriptomes.
A handful of good metagenomics papers have come out over the last few months. Below I've linked to and copied my evaluation of each of these articles from F1000. ... 1. Willner, Dana, and Philip Hugenholtz. "From deep sequencing to viral tagging: Recent advances in viral metagenomics." BioEssays (2013). My evaluation: This review lays out some of the challenges and recent advances in viral metagenomic sequencing.
A couple of weeks ago I, with the help of others here at UVA, organized a Software Carpentry bootcamp, instructed by Steve Crouch, Carlos Anderson, and Ben Morris. The day before the course started, Charlottesville was racked by nearly a foot of snow, widespread power outages, and many cancelled incoming flights. Luckily our instructors arrived just in time, and power was (mostly) restored shortly before the boot camp started.