I frequently get asked to recommend workshops or online learning resources for bioinformatics, genomics, statistics, and programming. I compiled a list of both online learning resources and in-person workshops (preferentially highlighting those where workshop materials are freely available online): List of Bioinformatics Workshops and Training Resources I hope to keep the page above as up-to-date as possible.

For over 15 years, members of the computer science, machine learning, and data mining communities have gathered in a beautiful European location each spring to share ideas about biologically-inspired computation.  Stemming from the work of John Holland who pioneered the field of genetic algorithms, multiple approaches have been developed that exploit the dynamics of natural systems to solve computational problems.

Metagenomics is the study of DNA collected from environmental samples (e.g., seawater, soil, acid mine drainage, the human gut, sputum, pus, etc.). While traditional microbial genomics typically means sequencing a pure cultured isolate, metagenomics involves taking a culture-free environmental sample and sequencing a single gene (e.g. the 16S rRNA gene), multiple marker genes, or shotgun sequencing everything in the sample in order to

If you ever write code for scientific computing (chances are you do if you're here), stop what you're doing and spend 8 minutes reading this open-access paper: Wilson et al. Best Practices for Scientific Computing.

Two of the most common questions at the beginning of an RNA-seq experiments are "how many reads do I need?" and "how many replicates do I need?". This paper describes a web application for designing RNA-seq applications that calculates an appropriate sample size and read depth to satisfy user-defined criteria such as cost, maximum number of reads or replicates attainable, etc.

For 18 years now, computational biologists have convened on the beautiful islands of Hawaii to present and discuss research emerging from new areas of biomedicine. PSB Conference Chairs Teri Klein (@teriklein), Keith Dunker, Russ Altman (@Rbaltman) and Larry Hunter (@ProfLHunter) organize innovative sessions and tutorials that are always interactive and thought-provoking.

I've said it before: Twitter makes me a lazy blogger. Lots of stuff came across my radar this week that didn't make it into a full blog post.

Here are links to all of this year's posts (excluding seminar/webinar announcements), with the most visited posts in bold italic . As always, you can follow me on Twitter for more frequent updates. Happy new year!

In case you missed it, a new paper was published in Nature Biotechnology on a method for detecting isoform-level differential expression with RNA-seq Data: Trapnell, Cole, et al. "Differential analysis of gene regulation at transcript resolution with RNA-seq." Nature Biotechnology (2012). THE PROBLEM RNA-seq enables transcript-level resolution of gene expression, but there is no proven methodology for simultaneously accounting for

Many papers have noted the challenges associated with assigning function to non-coding genetic variation, and since the majority of GWAS hits for common traits are non-coding, resources for providing some mechanism for these associations are desperately needed.