lncRNAdb: a reference database for long noncoding RNAs. - Paulo P. Amaral; Michael B. Clark; Dennis K. Gascoigne; Marcel E. Dinger; John S. Mattick (Nucleic Acids Res., 2011)

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. - Dennis K. Gascoigne; Seth W. Cheetham; Pierre B. Cattenoz; Michael B. Clark; Paulo P. Amaral; Ryan J. Taft; Dagmar Wilhelm; Marcel E. Dinger; John S. Mattick (Bioinform., 2012)