SVMtm: Support vector machines to predict transmembrane segments. - Zheng Yuan; John S. Mattick; Rohan D. Teasdale (J. Comput. Chem., 2004)

There's more to a model than code: understanding and formalizing in silico modeling experience. - Janet Wiles; Nicholas Geard; James E. M. Watson; Kai Willadsen; John S. Mattick; Daniel R. Bradley; Jennifer Hallinan (GECCO Workshops, 2005)

RNAdb - a comprehensive mammalian noncoding RNA database. - Ken C. Pang; Stuart Stephen; Pär G. Engström; Khairina Tajul-Arifin; Weisan Chen; Claes Wahlestedt; Boris Lenhard; Yoshihide Hayashizaki; John S. Mattick (Nucleic Acids Res., 2005)

Inherent size constraints on prokaryote gene networks due to "accelerating" growth. - Michael J. Gagen; John S. Mattick (Theory Biosci., 2005)

Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks. - Jennifer Hallinan; Daniel R. Bradley; John S. Mattick; Janet Wiles (IEEE Congress on Evolutionary Computation, 2006)

GONOME: measuring correlations between GO terms and genomic positions. - Stefan M. Stanley; Timothy L. Bailey; John S. Mattick (BMC Bioinform., 2006)

RNAdb 2.0 - an expanded database of mammalian non-coding RNAs. - Ken C. Pang; Stuart Stephen; Marcel E. Dinger; Pär G. Engström; Boris Lenhard; John S. Mattick (Nucleic Acids Res., 2007)

Delineating Slowly and Rapidly Evolving Fractions of the Drosophila Genome. - Jonathan M. Keith; Peter Adams 001; Stuart Stephen; John S. Mattick (J. Comput. Biol., 2008)

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities. - Marcel E. Dinger; Ken C. Pang; Tim R. Mercer; John S. Mattick (PLoS Comput. Biol., 2008)

NRED: a database of long noncoding RNA expression. - Marcel E. Dinger; Ken C. Pang; Tim R. Mercer; Mark L. Crowe; Sean M. Grimmond; John S. Mattick (Nucleic Acids Res., 2009)

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)

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci. - Fabian A. Buske; Denis C. Bauer; John S. Mattick; Timothy L. Bailey (Bioinform., 2013)

Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver. - Tung T. Nguyen; John S. A. Mattick; Qian Yang; Mehmet A. Orman; Marianthi G. Ierapetritou; Francois Berthiaume; Ioannis P. Androulakis (BMC Bioinform., 2014)