Table of Contents Author Guidelines Submit a Manuscript
Computational and Mathematical Methods in Medicine
Volume 2014, Article ID 293980, 10 pages
http://dx.doi.org/10.1155/2014/293980
Research Article

Modeling and Visualizing Cell Type Switching

1Computer Science Department, Utah State University, Logan, UT 84322, USA
2Biology Department, Utah State University, Logan, UT 84322, USA
3Center for Integrated BioSystems, Utah State University, Logan, UT 84322, USA
4Institute for Systems Biology, Seattle, WA 98109, USA
5Synthetic Biomanufacturing Institute, Logan, UT 84322, USA

Received 30 September 2013; Revised 20 December 2013; Accepted 10 January 2014; Published 14 April 2014

Academic Editor: Marco Villani

Copyright © 2014 Ahmadreza Ghaffarizadeh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. Huang, “Reprogramming cell fates: reconciling rarity with robustness,” BioEssays, vol. 31, no. 5, pp. 546–560, 2009. View at Publisher · View at Google Scholar · View at Scopus
  2. T. Masaki, J. Qu, J. Cholewa-Waclaw, K. Burr, R. Raaum, and A. Rambukkana, “Reprogramming adult Schwann cells to stem cell-like cells by Leprosy Bacilli promotes dissemination of infection,” Cell, vol. 152, no. 1, pp. 51–67, 2013. View at Publisher · View at Google Scholar
  3. J. P. Their, “Epithelial-mesenchymal transitions in tumor progression,” Nature Reviews Cancer, vol. 2, no. 6, pp. 442–454, 2002. View at Google Scholar · View at Scopus
  4. J. Krumsiek, C. Marr, T. Schroeder, and F. J. Theis, “Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network,” PLoS ONE, vol. 6, no. 8, Article ID e22649, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. S. Huang, G. Eichler, Y. Bar-Yam, and D. E. Ingber, “Cell fates as high-dimensional attractor states of a complex gene regulatory network,” Physical Review Letters, vol. 94, no. 12, Article ID 128701, 2005. View at Publisher · View at Google Scholar · View at Scopus
  6. H. H. Chang, M. Hemberg, M. Barahona, D. E. Ingber, and S. Huang, “Transcriptome-wide noise controls lineage choice in mammalian progenitor cells,” Nature, vol. 453, no. 7194, pp. 544–547, 2008. View at Publisher · View at Google Scholar · View at Scopus
  7. D. Orrell and H. Bolouri, “Control of internal and external noise in genetic regulatory networks,” Journal of Theoretical Biology, vol. 230, no. 3, pp. 301–312, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. S. Huang, I. Ernberg, and S. Kauffman, “Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective,” Seminars in Cell and Developmental Biology, vol. 20, no. 7, pp. 869–876, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. L. T. MacNeil and A. J. M. Walhout, “Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression,” Genome Research, vol. 21, no. 5, pp. 645–657, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. Q. Hu, A. M. Friedrich, L. V. Johnson, and D. O. Clegg, “Memory in induced pluripotent stem cells: reprogrammed human retinal-pigmented epithelial cells show tendency for spontaneous redifferentiation,” Stem Cells, vol. 28, no. 11, pp. 1981–1991, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. C. H. Waddington, The Strategy of Genes, George Unwin & Unwin, 1957.
  12. C. Furusawa and K. Kaneko, “A dynamical-systems view of stem cell biology,” Science, vol. 338, no. 6104, pp. 215–217, 2012. View at Publisher · View at Google Scholar
  13. N. Suzuki, C. Furusawa, and K. Kaneko, “Oscillatory protein expression dynamics endows stem cells with robust differentiation potential,” PLoS ONE, vol. 6, no. 11, Article ID e27232, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. J. X. Zhou, M. D. S. Aliyu, E. Aurell, and S. Huang, “Quasi-potential landscape in complex multi-stable systems,” Journal of the Royal Society Interface, vol. 9, no. 77, pp. 3539–3553, 2012. View at Publisher · View at Google Scholar
  15. S. Bhattacharya, Q. Zhang, and M. Andersen, “A deterministic map of Waddington’s epigenetic landscape for cell fate specification,” BMC Systems Biology, vol. 5, article 85, 2011. View at Publisher · View at Google Scholar
  16. I. Shmulevich, E. R. Dougherty, and W. Zhang, “Gene perturbation and intervention in probabilistic Boolean networks,” Bioinformatics, vol. 18, no. 10, pp. 1319–1331, 2002. View at Google Scholar · View at Scopus
  17. S. A. Kauffman, “Metabolic stability and epigenesis in randomly constructed genetic nets,” Journal of Theoretical Biology, vol. 22, no. 3, pp. 437–467, 1969. View at Google Scholar · View at Scopus
  18. Y. Xue, K. Ouyang, J. Huang et al., “Direct conversion of fibroblasts to neurons by reprogramming PTB-regulated MicroRNA circuits,” Cell, vol. 152, pp. 82–96, 2013. View at Publisher · View at Google Scholar
  19. T. Vierbuchen, A. Ostermeier, Z. P. Pang, Y. Kokubu, T. C. Südhof, and M. Wernig, “Direct conversion of fibroblasts to functional neurons by defined factors,” Nature, vol. 463, no. 7284, pp. 1035–1041, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. J. Ellson, E. R. Gansner, E. Koutsofios, S. C. North, and G. Woodhull, “Graphviz and dynagraph—static and dynamic graph drawing tools,” Graph Drawing Software, pp. 127–148, 2003. View at Publisher · View at Google Scholar
  21. R. Albert and H. G. Othmer, “The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster,” Journal of Theoretical Biology, vol. 223, no. 1, pp. 1–18, 2003. View at Publisher · View at Google Scholar · View at Scopus
  22. J. W. Bodnar, “Programming the Drosophila Embryo,” Journal of Theoretical Biology, vol. 188, no. 4, pp. 391–445, 1997. View at Publisher · View at Google Scholar · View at Scopus
  23. A. L. Bauer, T. L. Jackson, Y. Jiang, and T. Rohlf, “Receptor cross-talk in angiogenesis: mapping environmental cues to cell phenotype using a stochastic, Boolean signaling network model,” Journal of Theoretical Biology, vol. 264, no. 3, pp. 838–846, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. I. Shmulevich, S. A. Kauffman, and M. Aldana, “Eukaryotic cells are dynamically ordered or critical but not chaotic,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 38, pp. 13439–13444, 2005. View at Publisher · View at Google Scholar · View at Scopus
  25. S. Kauffman, C. Peterson, B. Samuelssont, and C. Troein, “Random Boolean network models and the yeast transcriptional network,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 25, pp. 14796–14799, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. A. C. Huang, L. Hu, S. A. Kauffman, W. Zhang, and I. Shmulevich, “Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation,” BMC Systems Biology, vol. 3, article 20, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. A. Bar-Even, J. Paulsson, N. Maheshri et al., “Noise in protein expression scales with natural protein abundance,” Nature Genetics, vol. 38, no. 6, pp. 636–643, 2006. View at Publisher · View at Google Scholar · View at Scopus
  28. G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” PLoS ONE, vol. 3, no. 7, Article ID e2774, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. L. Bruno, R. Hoffmann, F. McBlane et al., “Molecular signatures of self-renewal, differentiation, and lineage choice in multipotential hemopoietic progenitor cells in vitro,” Molecular and Cellular Biology, vol. 24, no. 2, pp. 741–756, 2004. View at Publisher · View at Google Scholar · View at Scopus
  30. M. Villani, A. Barbieri, and R. Serra, “A dynamical model of genetic networks for cell differentiation,” PLoS ONE, vol. 6, no. 3, Article ID e17703, 2011. View at Publisher · View at Google Scholar · View at Scopus