guest appearances on other blogs
- 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!
some of my favorite writing by other people
- 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)