Below are publications I have contributed to, either minorly, majorly, or solely.
Recovering data from summary statistics: Sample Parameter Reconstruction via Iterative TEchniques (SPRITE)
James Heathers called me and asked that I help with turning his SPRITE blog posts into a publication. Nick Brown and I independently made our own implementations of SPRITE, with Nick making an optimization which considerably improved performance. Nick and I also made web versions of our implementations, with mine available at PrePubMed. I performed the analyses in the paper, which were sometimes reproductions of analyses James had already performed in his blog posts. My code for the analyses and figures is available at my GitHub. I also contributed to the writing of the manuscript and used my LaTeX skills to make the manuscript so beautiful people think it is a journal article.
The GRIMMER test: A method for testing the validity of reported measures of variability
After a discussion with Nicholas Brown about the GRIM test and possibly extending it to other statistics, I looked into developing a GRIM test for standard deviations. I stumbled upon a statistical phenomenon which may have never been reported before, and developed the GRIMMER test, created a user friendly web application, and wrote a paper.
A structural role for the PHP domain in E. coli DNA polymerase III
BMC Structural Biology
This project was my honors thesis. I designed and ordered the primers and made mutations in the PHP domain with site directed mutagenesis. I expressed all the mutant proteins and purified them. I crystallized the proteins, harvested the crystals, shot them at ALS, and solved the structures with molecular replacement. I came up with the idea to use fluorescence anisotropy to measure exonuclease activity and performed the measurements myself. Further studies on the effect of the mutations on stability and activity were performed after I left the lab.
A Pan-cancer analysis of prognostic genes
I came up with this project, downloaded all data, and wrote all code. Chen W was consulted on Cox regression analyses and he provided code for inverse normalization. Bekiranov S was consulted on data normalization and provided the function for sigmoidal normalization. I wrote the entire publication, submitted the paper to the journal, and responded to reviewers' comments.
Guide to TCGA data
I wrote this guide for users new to TCGA data on Biostars and it has received over 13K views.
A site by Jordan Anaya