- Manatakis, Raghu, Benos (2018) Bioinformatics (Proc ECCB 2018), 34:i848–i856 (pdf)
- Simulated network data
- Running example (for testing the code)
- 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