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)

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. - Xiu Cheng Quek; Daniel W. Thomson; Jesper L. V. Maag; Nenad Bartonicek; Bethany Signal; Michael B. Clark; Brian S. Gloss; Marcel E. Dinger (Nucleic Acids Res., 2015)

NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing. - Yupei You; Michael B. Clark; Heejung Shim (Bioinform., 2022)