blog posts

I wrote several blog posts while I was in grad school, and I've kept them around for posterity! I don't write much publicly anymore, though I tell myself that could change at any moment.

guest appearances on other blogs

published papers

  • 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