References

You can find our publication about STARE and its implementation :

Hecker, D., Behjati Ardakani, F., Karollus, A., Gagneur, J., & Schulz, M. H. (2023). The adapted Activity-By-Contact model for enhancer–gene assignment and its application to single-cell data. Bioinformatics, 39(2), btad062. https://doi.org/10.1093/bioinformatics/btad062

The results of our analyses are available via Zenodo.

Note that STARE is a combination and adaptation based on:

• Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES & Engreitz JM. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nat. Genet. 51, 1664–1669 (2019). (https://www.nature.com/articles/s41588-019-0538-0)

  • https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

• Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction Schmidt et al., Nucleic Acids Research 2016; doi: 10.1093/nar/gkw1061

  • https://github.com/schulzlab/tepic

• Roider, H. G., A. Kanhere, T. Manke, and M. Vingron. “Predicting Transcription Factor Affinities to DNA from a Biophysical Model.” Bioinformatics 23, no. 2 (January 15, 2007): 134–41. https://doi.org/10.1093/bioinformatics/btl565.