Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. - Yonatan H. Grad; Frederick P. Roth; Marc S. Halfon; George M. Church (Bioinform., 2004)

REDfly: a Regulatory Element Database for Drosophila. - Steven M. Gallo; Long Li; Zihua Hu; Marc S. Halfon (Bioinform., 2006)

ORegAnno: an open-access community-driven resource for regulatory annotation. - Obi L. Griffith; Stephen B. Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica C. Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M. Gallo; et al. (Nucleic Acids Res., 2008)

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. - Marc S. Halfon; Steven M. Gallo; Casey M. Bergman (Nucleic Acids Res., 2008)

Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. - Qianqian Zhu; Jeffrey C. Miecznikowski; Marc S. Halfon (BMC Bioinform., 2010)

A wholly defined Agilent microarray spike-in dataset. - Qianqian Zhu; Jeffrey C. Miecznikowski; Marc S. Halfon (Bioinform., 2011)

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. - Steven M. Gallo; Dave T. Gerrard; David Miner; Michael Simich; Benjamin Des Soye; Casey M. Bergman; Marc S. Halfon (Nucleic Acids Res., 2011)

REDfly: the transcriptional regulatory element database for Drosophila. - John Rivera; Soile V. E. Keränen; Steven M. Gallo; Marc S. Halfon (Nucleic Acids Res., 2019)

Computational enhancer prediction: evaluation and improvements. - Hasiba Asma; Marc S. Halfon (BMC Bioinform., 2019)

PeakMatcher: Matching Peaks Across Genome Assemblies. - Ronald J. Nowling; Christopher R. Beal; Scott J. Emrich; Susanta K. Behura; Marc S. Halfon; Molly Duman-Scheel (BCB, 2020)