GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data. - Timothy Danford; P. Alexander Rolfe; David K. Gifford (Pacific Symposium on Biocomputing, 2008)

Dissecting the spatial structure of overlapping transcription in budding yeast. - Timothy Danford (2010)

Discovering Regulatory Overlapping RNA Transcripts. - Timothy Danford; Robin D. Dowell; Sudeep Agarwala; Paula Grisafi; Gerald Fink; David K. Gifford (J. Comput. Biol., 2011)

Rethinking Data-Intensive Science Using Scalable Analytics Systems. - Frank Austin Nothaft; Matt Massie; Timothy Danford; Zhao Zhang 007; Uri Laserson; Carl Yeksigian; Jey Kottalam; Arun Ahuja; Jeff Hammerbacher; Michael D. Linderman; Michael J. Franklin; Anthony D. Joseph; et al. (SIGMOD Conference, 2015)