Systems biology - The broader perspective

Cells

Volumn 2, Issue 2, 2013, Pages 414-431

  Bard, Jonathan ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Developmental biology; Evolution; Graphs; Mathematical; Networks; Phenotypic processes; Physiology; Systems biology concepts

Indexed keywords

CASPASE; FAS ANTIGEN; MITOGEN ACTIVATED PROTEIN KINASE; VASCULOTROPIN;

APOPTOSIS; ARTICLE; CELL PROLIFERATION; DEVELOPMENTAL BIOLOGY; DRUG ACTIVITY; EVOLUTION; GENE MUTATION; HUMAN; MOLECULAR DYNAMICS; MOLECULAR GENETICS; MORPHOGENESIS; NEUROBIOLOGY; PHENOTYPE; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84908456801     PISSN: None     EISSN: 20734409     Source Type: Journal    
DOI: 10.3390/cells2020414     Document Type: Article

References (55)

1. Mendel, G. Experiments in Plant Hybridization. 1865. (Verhandlungen des naturforschenden Vereins Brünn.) Available online: www.mendelweb.org/Mendel.html (accessed on 1 January 2013).
2. Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life; John Murray: London, UK, 1859
3. Guyton, A.C. Determination of cardiac output by equating venous return curves with cardiac output responses. Physiol. Rev. 1955, 35, 123-129.
4. Hodgkin, A.L.; Huxley, A.F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. 1952, 117, 500-544.
5. Turing, A.M. The chemical theory of morphogenesis. Phil. Trans R. Soc. 1952, 237B, 37-72.
6. Gilbert, S. Developmental Biology, 9th ed.; Sinauer Press: Sunderland, MA, USA, 2010.
7. Caestecker, K.W.; Van de Walle, G.R. The role of BRCA1 in DNA double-strand repair: Past and present. Exp. Cell. Res. 2012, 319, 575-587.
8. Boogerd, F., Bruggeman, F.J.S., Hofmeyr, H., Westerhoff, H.V., Eds. Systems Biology, Philosophical Foundations; Elsevier: Amsterdam, Netherlands, 2007.
9. Noble, D. Claude Bernard, the first systems biologist, and the future of physiology. J. Exp. Physiol. 2008, 93, 16-26.
10. Marcum, J.A. The aConceptual Foundations of Systems Biology: An Introduction; Nov Science Publishers: Hauppauge, NY, USA, 2009.
11. Melham, T., Bard, J., Werner, E., Noble, D., Eds. The conceptual foundations of systems biology. Prog. Biophys. Mol. Biol. 2013, 111, 55-150.
12. Bard, J.; Melham, T.; Noble, D. Epilogue: Some conceptual foundations of systems biology. Prog. Biophys. Mol. Biol. 2013, 3, 147-149.
13. Bard, J. A new ontology (structured hierarchy) of human developmental anatomy for the first seven weeks (Carnegie Stages 1-20). J. Anat. 2012, 221, 406-416.
14. Schoenwolf, G.; Bleyl, S.; Brauer, P.; Francis-West, P. Larsen's Human Embryology, 4th ed.; Churchill Livingstone: Philadelphia, PA, USA, 2008.
15. Werner, E.O. In silico multicellular systems biology and minimal genomes. Drug Discovery Today 2003, 8, 1121-1127.
16. Goodwin, B.C. Temporal Organization in Cells; Academic Press: London, UK, 1963
17. Bernard, C. Introduction à l'étude de la Médecine Expérimentale; J.B. Ballière et fils: Paris, France, 1865.
18. Monod, J.; Jacob, F. Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. Symp. Quant Biol. 1961, 26, 389-401.
19. Gilbert, S.; Epel, D. Ecological Developmental Biology; Sinauer Press: Sunderland, MA, USA, 2008.
20. SA Biosciences. Pathways Central. Available online: www.sabiosciences.com/pathwaycentral.php (accessed on 14 June 2013).
21. Wang, D.Y.Q.; Cardelli, L.; Phillips, A.; Piterman, N.; Fisher, J. Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics. BMC Syst. Biol. 2009, 3, 118-135.
22. Noble, D. Biophysics and systems biology. Phil. Trans. R. Soc. 2010, 368A, 1125-1139.
23. Bard, J. Driving developmental and evolutionary change: A systems biology view. Prog. Biophys. Mol. Biol. 2013, 2, 83-91.
24. Dressler, G.R. Advances in early kidney specification, development and patterning. Development 2009, 136, 3863-3874.
25. Milner, R. A Calculus of Communicating Systems; Springer-Verlag: New York, NY, USA, 1980.
26. Condon, A., Harel, D., Kok, J.N., Salomaa, A., Winfree E., Eds. Algorithnmic Bioprocesses Springer: New York, NY, USA, 2009.
27. Karp, P.D.; Paley, S.M.; Krummenacker, M.; Latendresse, M.; Dale, J.M.; Lee, T.J.; Kaipa, P.; Gilham, F.; Spaulding, A.; Popescu, L., et al. Pathway tools version 13.0: Integrated software for pathway/genome informatics and systems biology. Brief. Bioinf. 2010, 11, 40-79.
28. Kwiatkowska, M.; Norman, G.; Parker, D. Probabilistic model checking for systems biology. In Symbolic Systems Biology; Iyenga, M.S., Ed.; Jones and Bartlett: Burlington, MA, USA, 2010; pp. 31-59.
29. Wang, Y.; Christley, S.; Mjolsness, E.; Xie, X. Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. BMC Syst. Biol. 2010, 4, 99-115.
30. Kauffman, S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theoret. Biol. 1969, 22, 437-467.
31. Huang, S.; Ernberg, I.; Kauffman, S. Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective. Sem. Cell Dev. Biol. 2009, 20, 869-876.
32. Emmert-Streib, F.; Dehmer, M. Networks for systems biology: Conceptual connection of data and function. IET Syst. Biol. 2011, 5, 185-207.
33. The Systems Biology Markup Language. Available online: www.sbml.org (accessed on 14 June 2013).
34. Systems Biology Graphical Notation. Available online: www.sbgn.org (accessed on 14 June 2013).
35. Bard, J. A systems biology formulation of developmental anatomy. J. Anat. 2011, 218, 591-599.
36. Resource Description Framework. Available online: semanticweb.org/wiki/RDF (accessed on 14 June 2013).
37. Noble, D. Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations. Nature 1960, 188, 495-497.
38. Physiome Project. Available online: physiomeproject.org (accessed on 14 June 2013).
39. Barabási, A.L.; Gulbahce, N.; Loscalzo, J. Network medicine: A network-based approach to human disease. Nat. Rev. Genet. 2011, 12, 56-68.
40. Ben-Neriah, Y.; Karin, M. Inflammation meets cancer, with NF-κB as the matchmaker. Nat. Imm. 2011, 12, 715-723.
41. Morriss-Kay, G.M.; Wilkie, A.O. Growth of the normal skull vault and its alteration in craniosynostosis: Insights from human genetics and experimental studies. J. Anat. 2005, 207, 637-653.
42. Hopkins, A.L. Network pharmacology: The next paradigm in drug discovery. Nat. Chem. Biol. 2008, 4, 682-690.
43. Cockell, S.J.; Weile, J.; Lord, P.; Wipat, C.; Andriychenko, D.; Pocock, M.; Wilkinson, D.; Young, M.; Wipat, A. An integrated dataset for in silico drug discovery. J. Integr. Bioinform. 2010, 7, 116.
44. Ihekwaba, A.E.; Nguyen, P.T.; Priami C. Elucidation of functional consequences of signaling pathway interactions. BMC Bioinf. 2009, 10, 370.
45. Cinquin, O. Is the somitogenesis clock really cell-autonomous? A coupled-oscillator model of segmentation. J. Theor. Biol. 2003, 224, 459-468.
46. Mayr, E.; Provine, W. The Evolutionary Synthesis; Harvard University Press: Cambridge, MA, USA, 1980.
47. Irwin, D.E.; Bensch, S.; Price, T.D. Speciation in a ring. Nature 2001, 409, 333-337.
48. Waddington, C.H. Genetic assimilation of the bithorax phenotype. Evolution 1953, 10, 1-13.
49. Shapiro, J. Evolution: A View from the 21st Century; FT Press Science: New Jersey, NJ, USA, 2011.
50. The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491, 56-65.
51. Bard, J. A systems view of evolutionary genetics. Bioessays 2010, 32, 559-563.
52. Waddington, C.H. The Strategy of the Genes: a Discussion of Some Aspects of Theoretical Biology; Allen and Unwin: London, UK, 1957.
53. Smith, N.P.; Crampin, E.J. Development of models of active ion transport for whole-cell. Mol. Biol. 2004, 85, 387-405.
54. Sydney Brenner. Available online: elegans.som.vcu.edu/Sydney.html (accessed on 14 June 2013).
55. Rolls, E.; Treve, A. Neural Networks and Brain Function; OUP: Oxford, UK, 1997.