writing

2017-02-02 - Practicing Machine Learning with Optimism, part of an InfoQ series on machine learning
2014-04-10 - The rOpenSci Unconference , my reflections on participating in ROpenSci's first hackathon

Polyester: simulating RNA-seq datasets with differential transcript expression (Bioinformatics, 2015). There's also code to reproduce results in the paper and software.
Ballgown bridges the gap between transcriptome assembly and expression analysis (Nature Biotechnology, 2015). Again there's code to reproduce results in the paper and software. The paper itself isn't open-access, but there's a free preprint.
DER Finder, or more formally, "Differential expression analysis of RNA-seq data at single-base resolution" (Biostatistics, 2014). There's code that would reproduce the paper several years ago. We also wrote a new and improved version of DER Finder in Nucleic Acids Research in 2016.
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets (BMC Bioinformatics, 2011). An updated version is coming out in 2017 in Nature Biotechnology!

You can't have it all, but you can have cake, by Delia Ephron (New York Times opinion piece, September 2013)
The Night Watch, by James Mickens (Usenix magazine, November 2013). I would highly recommend reading everything James Mickens has written if you're the type of person that enjoys extremely funny writing about computers.
How do I get okay with being bad at stuff?, by S. Bear Bergman (October 2015)
Love After Love, by Derek Walcott (poem, 1986)
Now That We’re in Our 30s, My Friends Are Abandoning Me!, by Heather Havrilesky (Ask Polly, April 2017)
How to blog about code and give zero fucks, by Garann Means (published on her blog in September 2013)
What if the secret to success is failure?, by Paul Tough (New York Times Magazine, September 2011)
Some excellent advice, by the person known only (to me, at least) as the Bad Advisor (posted on her blog in March 2014)