Cell type specific analysis of human transcriptome data. - Xiaoxiao Xu; Arye Nehorai; Joseph D. Dougherty (GENSiPS, 2012)

utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation. - Yating Liu; Joseph D. Dougherty (Bioinform., 2021)

Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data. - Juanru Guo; Wenjin Zhang; Xuhua Chen; Allen Yen; Lucy Chen; Christian A. Shively; Daofeng Li; Ting Wang; Joseph D. Dougherty; Robi D. Mitra (Bioinform., 2024)