Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. - Derek Y. Chiang; Patrick O. Brown; Michael B. Eisen (ISMB (Supplement of Bioinformatics), 2001)

Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts. - Derek Y. Chiang; Alan M. Moses; Manolis Kamvysselis; Eric S. Lander; Michael B. Eisen (RECOMB, 2003)

Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures. - Alan M. Moses; Derek Y. Chiang; Michael B. Eisen (Pacific Symposium on Biocomputing, 2004)

A probabilistic framework for aligning paired-end RNA-seq data. - Yin Hu; Kai Wang; Xiaping He; Derek Y. Chiang; Jan F. Prins; Jinze Liu (Bioinform., 2010)

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. - Darshan Singh; Christian F. Orellana; Yin Hu; Corbin D. Jones; Yufeng Liu; Derek Y. Chiang; Jinze Liu; Jan F. Prins (Bioinform., 2011)

A Robust Method for Transcript Quantification with RNA-Seq Data. - Yan Huang 006; Yin Hu; Corbin D. Jones; James N. MacLeod; Derek Y. Chiang; Yufeng Liu; Jan F. Prins; Jinze Liu (J. Comput. Biol., 2013)

PureCN: copy number calling and SNV classification using targeted short read sequencing. - Markus Riester; Angad P. Singh; Angela Rose Brannon; Kun Yu; Catarina D. Campbell; Derek Y. Chiang; Michael P. Morrissey (Source Code Biol. Medicine, 2016)