Dissecting complex transcriptional responses using pathway-level scores based on prior information. - Harmen J. Bussemaker; Lucas D. Ward; André Boorsma (BMC Bioinform., 2007)

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. - Lucas D. Ward; Harmen J. Bussemaker (ISMB, 2008)

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. - Lucas D. Ward; Manolis Kellis (Nucleic Acids Res., 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)

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. - Lucas D. Ward; Manolis Kellis (Nucleic Acids Res., 2016)