GeneTrack - a genomic data processing and visualization framework. - István Albert; Shinichiro Wachi; Cizhong Jiang; B. Franklin Pugh (Bioinform., 2008)

Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data. - Eric Samorodnitsky; B. Franklin Pugh (PLoS Comput. Biol., 2010)

Characterizing protein-DNA binding event subtypes in ChIP-exo data. - Naomi Yamada; William K. M. Lai; Nina Farrell; B. Franklin Pugh; Shaun Mahony (Bioinform., 2019)

PEGR: a management platform for ChIP-based next generation sequencing pipelines. - Danying Shao; Gretta Kellogg; Shaun Mahony; William K. M. Lai; B. Franklin Pugh (PEARC, 2020)

ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes. - Naomi Yamada; Prashant Kumar Kuntala; B. Franklin Pugh; Shaun Mahony (J. Comput. Biol., 2020)

ScriptManager: an interactive platform for reducing barriers to genomics analysis. - Olivia W. Lang; B. Franklin Pugh; William K. M. Lai (PEARC, 2022)

STENCIL: A web templating engine for visualizing and sharing life science datasets. - Qi Sun; Ali Nematbakhsh; Prashant Kumar Kuntala; Gretta Kellogg; B. Franklin Pugh; William K. M. Lai (PLoS Comput. Biol., 2022)