Molecular signatures database (MSigDB) 3.0. - Arthur Liberzon; Aravind Subramanian; Reid Pinchback; Helga Thorvaldsdóttir; Pablo Tamayo; Jill P. Mesirov (Bioinform., 2011)

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. - Helga Thorvaldsdóttir; James T. Robinson; Jill P. Mesirov (Briefings Bioinform., 2013)

Quantitative visualization of alternative exon expression from RNA-seq data. - Yarden Katz; Eric T. Wang; Jacob Silterra; Schraga Schwartz; Bang Wong; Helga Thorvaldsdóttir; James T. Robinson; Jill P. Mesirov; Edoardo M. Airoldi; Christopher B. Burge (Bioinform., 2015)

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. - Daniel E. Carlin; Kassi Kosnicki; Sara Garamszegi; Trey Ideker; Helga Thorvaldsdóttir; Michael Reich; Jill P. Mesirov (F1000Research, 2017)

igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). - James T. Robinson; Helga Thorvaldsdóttir; Douglass Turner; Jill P. Mesirov (Bioinform., 2023)