Dense subgraph computation via stochastic search: application to detect transcriptional modules. - Logan Everett; Li-San Wang; Sridhar Hannenhalli (ISMB (Supplement of Bioinformatics), 2006)

PTM-Switchboard - a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. - Logan Everett; Antony Vo; Sridhar Hannenhalli (Nucleic Acids Res., 2009)

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. - Matthew Hansen; Logan Everett; Larry N. Singh; Sridhar Hannenhalli (Algorithms Mol. Biol., 2010)