Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

ChIPs and regulatory bits

Machine learning reveals combinatorial patterns of transcription factor binding that drive gene expression.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Pipeline for discovery of cis-regulatory modules involved in mesoderm specification.


  1. Davidson, E.H. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic Press, 2006).

    Google Scholar 

  2. Zinzen, R.P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E.E. Nature 462, 65–70 (2009).

    Article  CAS  Google Scholar 

  3. Janssens, H. et al. Nat. Genet. 38, 1159–1165 (2006).

    Article  CAS  Google Scholar 

  4. Segal, E. & Widom, J. Nat. Rev. Genet. 10, 443–456 (2009).

    Article  CAS  PubMed Central  Google Scholar 

  5. Beer, M.A. & Tavazoie, S. Cell 117, 185–198 (2004).

    Article  CAS  Google Scholar 

  6. Arnosti, D.N. & Kulkarni, M.M. J. Cell. Biochem. 94, 890–898 (2005).

    Article  CAS  Google Scholar 

  7. Warner, J.B. et al. Nat. Methods 5, 347–353 (2008).

    Article  CAS  PubMed Central  Google Scholar 

  8. Tomancak, P. et al. Genome Biol. 8, R145 (2007).

    Article  PubMed Central  Google Scholar 

  9. Venter, M. Trends Plant Sci. 12, 118–124 (2007).

    Article  CAS  Google Scholar 

  10. Haseltine, E.L. & Arnold, F.H. Annu. Rev. Biophys. Biomol. Struct. 36, 1–19 (2007).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Xin He or Saurabh Sinha.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

He, X., Sinha, S. ChIPs and regulatory bits. Nat Biotechnol 28, 142–143 (2010).

Download citation

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing