Below are publications I have contributed to, either minorly, majorly, or solely.
Major Contributions
Recovering data from summary statistics: Sample Parameter Reconstruction via Iterative TEchniques (SPRITE) PeerJ Preprints
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.
Statistical infarction: A postmortem of the Cornell Food and Brand Lab pizza publications PeerJ Preprints
I analyzed the data release for the pizza papers.
Statistical heartburn: An attempt to digest four pizza publications from the Cornell Food and Brand Lab PeerJ Preprints
I noticed some errors in publications from a famous lab. I then sent out a bat signal to my squad and we performed a thorough investigation of the papers. This included writing code, reading up on various statistical tests and packages, contacting the lab to try and understand what happened, and writing the preprint.
OncoRank: A pan-cancer method of combining survival correlations and its application to mRNAs, miRNAs, and lncRNAs PeerJ Preprints
Everything, including coming up with the idea, writing all code, writing the publication.
The GRIMMER test: A method for testing the validity of reported measures of variability PeerJ Preprints
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.
Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets BMC Biology
I came up with the idea to use PAR-CLIP data and CLASH data to see if tRFs may function like miRNAs, and downloaded the data and performed the analyses myself, which required custom algorithms and scripts and the use of a computing cluster. I also discovered the data sets for Rhodobacter. I was the primary contributor to the writing of the manuscript.
A Pan-cancer analysis of prognostic genes PeerJ
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.
Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis PLOS Medicine
Along with Reon BJ conceived the project. Along with Reon BJ developed and ran a pipeline for finding novel lncRNAs. Provided Reon BJ with various Python scripts needed for further analysis and consulted on statistical analyses.
OncoLnc: Linking TCGA survival data to lncRNAs, mRNAs, and miRNAs PeerJ Computer Science
Everything, which includes conceiving the project, downloading all TCGA data, writing all code, developing the Django application, and writing the paper.
Guide to TCGA data Biostars
I wrote this guide for users new to TCGA data on Biostars and it has received over 13K views.
PrePubMed: A PubMed for preprints Omnes Res
I wrote an article explaining how PrePubMed works.
Minor Contributions
tRFdb: a database for transfer RNA fragments Nucleic Acids Research
I found the Rhodobacter data set and my analysis of it resulted in it being included in the database. I assisted with preparation of the manuscript.
The lncRNA DRAIC/PCAT29 locus constitutes a tumor-suppressive nexus Molecular Cancer Research
I helped with the ChIP-SEQ analyses present in the paper. I also provided general bioinformatics support for the project which included analyses that did not make it into the paper including microarray and TCGA analyses.