Evaluation of methods for modeling transcription factor sequence specificity

@article{Weirauch2013EvaluationOM,
  title={Evaluation of methods for modeling transcription factor sequence specificity},
  author={Matthew T. Weirauch and Atina G. Cote and Raquel Norel and Matti Annala and Yue Zhao and Todd Robert Riley and Julio S{\'a}ez-Rodr{\'i}guez and Thomas Cokelaer and Anastasia Vedenko and Shaheynoor Talukder and Harmen J. Bussemaker and Quaid D Morris and Martha L. Bulyk and Gustavo Stolovitzky and Timothy R. Hughes},
  journal={Nature Biotechnology},
  year={2013},
  volume={31},
  pages={126-134}
}
Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein's DNA-binding specificity, but these methods have not been systematically compared. Here we applied 26 such approaches to in vitro protein binding microarray data for 66 mouse TFs belonging to various families. For nine TFs, we also scored the resulting motif models on in… CONTINUE READING
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Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

R Nutiu
  • Nat. Biotechnol
  • 2011