Modeling protein-DNA binding via high-throughput in vitro technologies

Yaron Orenstein, Ron Shamir

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Protein-DNA binding plays a central role in gene regulation and by that in all processes in the living cell. Novel experimental and computational approaches facilitate better understanding of protein-DNA binding preferences via high-throughput measurement of protein binding to a large number of DNA sequences and inference of binding models from them. Here we review the state of the art in measuring protein-DNA binding in vitro, emphasizing the advantages and limitations of different technologies. In addition, we describe models for representing protein-DNA binding preferences and key computational approaches to learn those from high-throughput data. Using large experimental data sets, we test the performance of different models based on different measuring techniques. We conclude with pertinent open problems.

Original languageEnglish
Pages (from-to)171-180
Number of pages10
JournalBriefings in Functional Genomics
Issue number3
StatePublished - 1 May 2017


  • high-throughput SELEX
  • motif finding
  • protein-binding microarrays
  • protein–DNA binding


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