Software
Concordance Workbench (Bottomly et al 2010 NAR): Approach to combine ChIP-seq results from different peak-finding algorithms in order to assess concordance among the approaches and identify high-confidence peaks.
SNPMask (Walter et al 2007 Nature Methods): Computational mask to filter out SNPs that impact hybridization-based techniques when non-reference samples are being examined on standard manufacturer arrays.
Consense (Laderas and McWeeney 2007, OMICS): A consensus framework for exploring functional genomics data using multiple clustering methods
Tandtraq (Laderas et al 2007, Bioinformatics): An open-source tool for integrated protein identification and quantitation.