miRconnX image Condition-specific mRNA-microRNA regulatory networks    
    (Looking for mirConnect? Click here)  
ASTRO image Analysis of Short Time-series using Rank Order preservation  
enoLogos image energy normalized LOGOs  
enoLogosC2H2 image energy normalized LOGOs of the C2H2 protein family  
footer image finding mammalian transcription factor binding sites using phylogentic footprinting  
STAMP image Alignment, Similarity, & Database Matching for DNA Motifs  
TRANSFAC ® BIOBASE database and tools (internal access only - pswd required)  


Data Downloads

  • Corcoran, Pandit et al. (2009) PLoS ONE, 4:e5279 (pdf)
    • raw ChIP-chip data
    • training datasets
  • Kadri et al. (2009) APBC/BMC Bioinformatics, 10(Suppl 1):S35 (pdf)
    • miRNA cross-species characteristics
    • HHMMiR algorithm
    • Training and testing datasets
  • Mahony et al. (2007) Genome Biol 8: R84 (pdf)
    • README file (text - description fo the dataset files)
    • Datasets (protein coding, microRNA, tRNA and developmental gene datasets)
  • Mahony et al. (2007) ISMB (Proc ISMB) 23: i297-i304 (pdf)
    • README file (text - description fo the dataset files)
    • Dataset (ZIP archive file)
  • Mahony et al. (2007) PLoS Comput Biol 3: e61 (pdf)
    • Supplementary Table (performance of strategies for aligning DNA motifs - complete list)
    • PSSM models with the corresponding family of each transcription factor
  • Mahony et al. (2006) Neural Networks 19: 950-962 (pdf)
    • Supplementary Table (Comparing motif-finders in 77 yeast datasets)
  • Corcoran et al. (2005) Nucl Acids Res 33(Web Server issue): W442-W446 (pdf)
    • Supplementary Table (Footer predictions)
  • Corcoran et al. (2005) Genome Res 15: 840-847 (pdf)
    • Supplementary Table 1 (Footer predictions)
    • Supplementary Table 2 (comparison with other methods)
    • Promoter regions (test set)
    • DBA alignments
    • PSSM models
  • Benos et al. (2002) J Mol Biol 323: 701-727 (pdf)
    • EGR selection dataset (SAMIE training set)
    • SAMIE EGR model


Software Downloads

STAMP image STAMP version 1.1 (March 2008) ZIP archive
HHMMiR image HHMMiR version v1.2 (April 2009) ZIP archive


University of Pittsburgh Department of Computational Biology