Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. - Xiangying Sun; Zhezhen Wang; Johnathon M. Hall; Carlos Perez-Cervantes; Alexander J. Ruthenburg; Ivan P. Moskowitz; Michael Gribskov; Xinan Holly Yang (PLoS Comput. Biol., 2020)

Merging short and stranded long reads improves transcript assembly. - Amoldeep S. Kainth; Gabriela A. Haddad; Johnathon M. Hall; Alexander J. Ruthenburg (PLoS Comput. Biol., 2023)