MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. - Shane J. Neph; Martin Tompa (Nucleic Acids Res., 2006)

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes. - Zizhen Yao; Jeffrey E. Barrick; Zasha Weinberg; Shane J. Neph; Ronald R. Breaker; Martin Tompa; Walter L. Ruzzo (PLoS Comput. Biol., 2007)

BEDOPS: high-performance genomic feature operations. - Shane J. Neph; Scott Kuehn; Alex P. Reynolds; Eric Haugen; Robert E. Thurman; Audra K. Johnson; Eric Rynes; Matthew T. Maurano; Jeff Vierstra; Sean Thomas; Richard S. Sandstrom; Richard Humbert; et al. (Bioinform., 2012)

Integrative analysis of 111 reference human epigenomes Open. - Roadmap Epigenomics Consortium; Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi Moussavi; Pouya Kheradpour; ZhiZhuo Zhang; Jianrong Wang; Michael J. Ziller; Viren Amin; et al. (Nat., 2015)

Operating on Genomic Ranges Using BEDOPS. - Shane J. Neph; Alex P. Reynolds; Scott Kuehn; John A. Stamatoyannopoulos (Statistical Genomics, 2016)

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data. - Charles E. Breeze; Alex P. Reynolds; Jenny van Dongen; Ian Dunham; John Lazar; Shane J. Neph; Jeff Vierstra; Guillaume Bourque; Andrew E. Teschendorff; John A. Stamatoyannopoulos; Stephan Beck 002 (Bioinform., 2019)