Software

• Universal Protein Binding Microarray (PBM) Analysis Suite
  Berger MF, ML Bulyk
  Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature Protocols. (2009) 4(3):393-411

• MultiFinder
  BR Huber and ML Bulyk
  BMC Bioinformatics (2006) 7(1):229 Additional file associated with MultiFinder Software

• PhylCRM
  *Warner JB, *Philippakis AA, *Jaeger SA, He FS, Lin J, Bulyk ML.
  Systematic identification of mammalian regulatory motifs' target genes and functions. Nature Methods. 2008 Apr; 5(4):347-53. Epub 2008 Mar 2 (10.1038/nmeth.1188) (* co-1st authors)

• Lever
  *Warner JB, *Philippakis AA, *Jaeger SA, He FS, Lin J, Bulyk ML.
  Systematic identification of mammalian regulatory motifs' target genes and functions. Nature Methods. 2008 Apr; 5(4):347-53. Epub 2008 Mar 2 (10.1038/nmeth.1188) (* co-1st authors)

• Lever + LOESS correction
  Aboukhalil A, Bulyk ML.
  LOESS correction for length variation in gene set-based genomic sequence analysis. Bioinformatics. (2012) Epub Apr 5, 2012. doi: 10.1093/bioinformatics/bts1555D

Legacy Software




The following has been superceded by newer software. A reference is provided here to support part of the Supplementary Material associated with a previous publication.

• ModuleFinder
  AA Philippakis, FS He and ML Bulyk (2005) PSB p.519-530
  *Superceded by PhylCRM