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Putting epigenome comparison into practice

Comparative analysis of epigenomes offers new opportunities to understand cellular differentiation, mutation effects and disease processes. But the scale and heterogeneity of epigenetic data present numerous computational challenges.

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Figure 1: A proposed cyberinfrastructure for epigenome analysis and comparison.

References

  1. Birney, E. et al. Nature 447, 799–816 (2007).

    Article  CAS  Google Scholar 

  2. Barski, A. et al. Cell 129, 823–837 (2007).

    Article  CAS  Google Scholar 

  3. Heintzman, N.D. et al. Nat. Genet. 39, 311–318 (2007).

    Article  CAS  Google Scholar 

  4. Mikkelsen, T.S. et al. Nature 448, 553–560 (2007).

    Article  CAS  Google Scholar 

  5. Ernst, J. & Kellis, M. Nat. Biotechnol. 28, 817–825 (2010).

    Article  CAS  Google Scholar 

  6. Bernstein, B.E. et al. Nat. Biotechnol. 28, 1045–1048 (2010).

    Article  CAS  Google Scholar 

  7. Harris, R.A. et al. Nat. Biotechnol. 28, 1097–1105 (2010)

    Article  CAS  Google Scholar 

  8. Kouzarides, T. Cell 128, 693–705 (2007).

    Article  CAS  Google Scholar 

  9. Levenson, J.M. et al. J. Biol. Chem. 281, 15763–15773 (2006).

    Article  CAS  Google Scholar 

  10. Reik, W. Nature 447, 425–432 (2007).

    Article  CAS  Google Scholar 

  11. Rakyan, V.K. et al. Genome Res. 20, 434–439 (2010).

    Article  CAS  Google Scholar 

  12. Bernstein, B.E. et al. Cell 120, 169–181 (2005).

    Article  CAS  Google Scholar 

  13. Lamb, J. et al. Science 313, 1929–1935 (2006).

    Article  CAS  Google Scholar 

  14. Slack, J.M. Nat. Rev. Genet 3, 889–895 (2002).

    Article  CAS  Google Scholar 

  15. Waddington, C.H. The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology (Allen & Unwin, London, 1957).

    Google Scholar 

  16. Bernstein, B.E. et al. Cell 128, 669–681 (2007).

    Article  CAS  Google Scholar 

  17. van Arensbergen, J. et al. Genome Res. 20, 722–732 (2010).

    Article  CAS  Google Scholar 

  18. Ridley, M. Evolution and Classification: the Reformation of Cladism (Longman, London UK, 1989).

    Google Scholar 

  19. Hennig, W. Phylogenetic Systematics (University of Illinois Press, Urbana, Illinois, 1966).

    Google Scholar 

  20. Meaburn, E.L. et al. Epigenetics 5, 578–582 (2010).

    Article  CAS  Google Scholar 

  21. Schalkwyk, L.C. et al. Am. J. Hum. Genet. 86, 196–212 (2010).

    Article  CAS  Google Scholar 

  22. Tycko, B. Am. J. Hum. Genet. 86, 109–112 (2010).

    Article  CAS  Google Scholar 

  23. Cahan, P. et al. Nat. Genet. 41, 430–437 (2009).

    Article  CAS  Google Scholar 

  24. Tony Hey, S.T. & Tolle, K. (eds). The Fourth Paradigm: Data-Intensive Scientific Discovery (Microsoft Research, Seattle, 2009).

    Google Scholar 

  25. Wang, X. et al. Nat. Biotechnol. 23, 1099–1103 (2005).

    Article  CAS  Google Scholar 

  26. Mesirov, J.P. Science 327, 415–416 (2010).

    Article  CAS  Google Scholar 

  27. McKenna, A. et al. Genome Res. 20, 1297–1303 (2010).

    Article  CAS  Google Scholar 

  28. Xi, Y. & Li, W. BMC Bioinformatics 10, 232 (2009).

    Article  Google Scholar 

  29. Rosenbloom, K.R. et al. Nucleic Acids Res. 38, D620–D625 (2010).

    Article  CAS  Google Scholar 

  30. Goecks, J. et al. Genome Biol. 11, R86 (2010).

    Article  Google Scholar 

  31. Bock, C. et al. Methods Mol. Biol. 628, 275–296 (2010).

    Article  CAS  Google Scholar 

Download references

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Correspondence to Aleksandar Milosavljevic.

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The author is the founder of and owns shares in IP Genesis, Inc., a company that commercializes academically developed software for genomic and epigenomic research.

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Milosavljevic, A. Putting epigenome comparison into practice. Nat Biotechnol 28, 1053–1056 (2010). https://doi.org/10.1038/nbt1010-1053

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