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Kim M, Rai N, Zorraquino V, et al. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nat Commun. 2016;7:13090doi: 10.1038/ncomms13090.
Kim, M., Rai, N., Zorraquino, V., & Tagkopoulos, I. (2016). Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nature communications, 713090. https://doi.org/10.1038/ncomms13090
Kim, Minseung, et al. "Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli." Nature communications vol. 7 (2016): 13090. doi: https://doi.org/10.1038/ncomms13090
Kim M, Rai N, Zorraquino V, Tagkopoulos I. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nat Commun. 2016 Oct 07;7:13090. doi: 10.1038/ncomms13090. PMID: 27713404; PMCID: PMC5059772.
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Nat Commun. 2016 Oct 07;7:13090. doi: 10.1038/ncomms13090.

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli.

Nature communications

Minseung Kim, Navneet Rai, Violeta Zorraquino, Ilias Tagkopoulos

Affiliations

  1. Department of Computer Science, University of California, Davis, California 95616, USA.
  2. Genome Center, University of California, Davis, California 95616, USA.

PMID: 27713404 PMCID: PMC5059772 DOI: 10.1038/ncomms13090

Abstract

A significant obstacle in training predictive cell models is the lack of integrated data sources. We develop semi-supervised normalization pipelines and perform experimental characterization (growth, transcriptional, proteome) to create Ecomics, a consistent, quality-controlled multi-omics compendium for Escherichia coli with cohesive meta-data information. We then use this resource to train a multi-scale model that integrates four omics layers to predict genome-wide concentrations and growth dynamics. The genetic and environmental ontology reconstructed from the omics data is substantially different and complementary to the genetic and chemical ontologies. The integration of different layers confers an incremental increase in the prediction performance, as does the information about the known gene regulatory and protein-protein interactions. The predictive performance of the model ranges from 0.54 to 0.87 for the various omics layers, which far exceeds various baselines. This work provides an integrative framework of omics-driven predictive modelling that is broadly applicable to guide biological discovery.

References

  1. Phys Rev Lett. 1987 Nov 9;59(19):2229-2232 - PubMed
  2. Bioinformatics. 1999 Jan;15(1):72-84 - PubMed
  3. Yeast. 2000 Apr;17(1):48-55 - PubMed
  4. Microbiology. 2001 Mar;147(Pt 3):709-15 - PubMed
  5. Environ Microbiol. 2001 Sep;3(9):588-99 - PubMed
  6. Nat Genet. 2002 Dec;32 Suppl:496-501 - PubMed
  7. Nucleic Acids Res. 2003 Feb 15;31(4):e15 - PubMed
  8. J Gen Microbiol. 1958 Dec;19(3):592-606 - PubMed
  9. Trends Genet. 2003 Oct;19(10):551-60 - PubMed
  10. Genome Res. 2003 Nov;13(11):2435-43 - PubMed
  11. Bioinformatics. 2004 Feb 12;20(3):307-15 - PubMed
  12. Genetics. 2004 Feb;166(2):669-80 - PubMed
  13. J Proteome Res. 2004 Nov-Dec;3(6):1234-42 - PubMed
  14. Appl Environ Microbiol. 2005 Sep;71(9):5182-91 - PubMed
  15. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D659-63 - PubMed
  16. Microbiology. 2006 Aug;152(Pt 8):2421-31 - PubMed
  17. Nat Biotechnol. 2006 Sep;24(9):1151-61 - PubMed
  18. Nat Biotechnol. 2007 Jan;25(1):117-24 - PubMed
  19. PLoS Biol. 2007 Jan;5(1):e8 - PubMed
  20. Science. 2007 Apr 27;316(5824):593-7 - PubMed
  21. J Biol Chem. 2007 Jul 20;282(29):21259-67 - PubMed
  22. Bioinformatics. 2007 Oct 15;23(20):2700-7 - PubMed
  23. Cell. 2007 Dec 28;131(7):1354-65 - PubMed
  24. PLoS Comput Biol. 2008 Mar 28;4(3):e1000044 - PubMed
  25. Nat Biotechnol. 2008 Dec;26(12):1367-72 - PubMed
  26. PLoS Comput Biol. 2009 Jan;5(1):e1000257 - PubMed
  27. Bioinformatics. 2009 May 1;25(9):1105-11 - PubMed
  28. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33 - PubMed
  29. Nat Chem Biol. 2009 Aug;5(8):593-9 - PubMed
  30. Nucleic Acids Res. 2010 Jan;38(Database issue):D750-3 - PubMed
  31. Microbiology. 2010 Feb;156(Pt 2):287-301 - PubMed
  32. Cell. 2009 Dec 24;139(7):1366-75 - PubMed
  33. Appl Environ Microbiol. 2010 Mar;76(6):1935-45 - PubMed
  34. BMC Bioinformatics. 2010 Apr 29;11:213 - PubMed
  35. Science. 2010 Jul 30;329(5991):533-8 - PubMed
  36. Nat Biotechnol. 2010 Aug;28(8):827-38 - PubMed
  37. Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17845-50 - PubMed
  38. Nat Chem Biol. 2010 Nov;6(11):787-9 - PubMed
  39. Nature. 2011 May 19;473(7347):337-42 - PubMed
  40. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5589-93 - PubMed
  41. PLoS Comput Biol. 2012 Jan;8(1):e1002296 - PubMed
  42. Front Genet. 2012 Jan 06;2:105 - PubMed
  43. Nat Rev Genet. 2012 Mar 13;13(4):227-32 - PubMed
  44. Cell Host Microbe. 2012 Jun 14;11(6):563-75 - PubMed
  45. Nat Commun. 2012 Jul 03;3:929 - PubMed
  46. Cell. 2012 Jul 20;150(2):389-401 - PubMed
  47. Brief Bioinform. 2013 Jul;14(4):469-90 - PubMed
  48. Cell. 2012 Oct 26;151(3):476-82 - PubMed
  49. Nucleic Acids Res. 2013 Jan;41(Database issue):D801-7 - PubMed
  50. Nat Biotechnol. 2013 Jan;31(1):38-45 - PubMed
  51. Mol Syst Biol. 2013 Oct 01;9:693 - PubMed
  52. Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8 - PubMed
  53. Bioinformatics. 2014 May 1;30(9):1316-8 - PubMed
  54. Curr Opin Biotechnol. 2014 Aug;28:111-5 - PubMed
  55. Bioinformatics. 2014 Aug 1;30(15):2114-20 - PubMed
  56. Nat Biotechnol. 2014 Mar;32(3):223-6 - PubMed
  57. OMICS. 2014 Jun;18(6):335-43 - PubMed
  58. Mol Syst Biol. 2014 Jul 01;10:735 - PubMed
  59. Bioinformatics. 2015 Jan 15;31(2):166-9 - PubMed
  60. Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56 - PubMed
  61. Nature. 2015 May 28;521(7553):436-44 - PubMed
  62. Nat Prod Rep. 2015 Aug;32(8):1163-4 - PubMed
  63. EcoSal Plus. 2014 May;6(1):null - PubMed
  64. Nucleic Acids Res. 2016 Jan 4;44(D1):D133-43 - PubMed
  65. Nucleic Acids Res. 2016 Jan 4;44(D1):D620-3 - PubMed
  66. PeerJ. 2016 Jan 21;4:e1621 - PubMed

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