PART IV: SYSTEMS BIOLOGY Expanding Developmental Biology to Medicine, Ecology, and Evolution

Where possible, references have been linked to PubMed, the National Center for Biotechnology Information’s online database of journal article citations. Citations that do not include links to PubMed are either referring to papers that are too old to be included in PubMed, or to books, which are not listed on PubMed.

Anonymous, 1989. “Recursive Subroutine” in MIT Humor Magazine 70(1): 13.
Link

Bard, J. 2011. A systems biology representation of developmental anatomy. J. Anat. 218: 591–599.
PubMed Link

Bertalanffy, L. v. 1928. Kritische Theorie der Formbildung. In J. Schaxel, ed., Abhandlungen zur theoretischen Biologie. Gebrüder Borntraeger, Berlin.

Bertalanffy, L. v. 1932. Theoretische Biologie: Band 1: Allgemeine Theorie, Physikochemie, Aufbau und Entwicklung des Organismus. Gebrüder Borntraeger, Berlin.

Brauckmann, S. 2000. Eine Theorie für Lebendes? Die synthetische Antwort Ludwig von Bertalanffys. Ph.D. thesis, University of Munster.

Callebaut, W. and D. Rasskin-Gutman (eds.). 2009. Modularity: Understanding the Development and Evolution of Complex Natural Systems. MIT Press, Cambridge, MA.

Collier, J. 1985. Entropy in evolution. Biol. Phil. 1: 5–24.

Davidson, E. H. 2006 The Regulatory Genome. Academic Press, San Diego.

Davidson, E. H. and D. H. Erwin. 2009. An integrated view of precambrian eumetazoan evolution. Cold Spring Harbor Symp. Quant. Biol. 74: 65­–80.
PubMed Link

Davidson, E. H., D. R. McClay and L. Hood. 2003. Regulatory gene networks and the properties of the developmental process. Proc. Natl. Acad. Sci. USA 100: 1475–1480.
PubMed Link

De Backer, P., D. De Waele and L. Van Speybroeck. 2010. Ins and outs of systems biology vis-à-vis molecular biology: Continuation or clear cut? Acta Biotheor. 58: 15–49.
PubMed Link

Drack, M., W. Apfalter and D. Pouvreau. 2007. On the making of a system theory of life: Paul A Weiss and Ludwig von Bertalanffy's conceptual connection. Q. Rev. Biol. 82: 349–373.
PubMed Link

Dyke, C. 1988. The Evolutionary Dynamics of Complex Systems: A Study in Biosocial Complexity. Oxford University Press, New York.

Edelman, L. B., S. Chandrasekaran and N. D. Price. 2010. Systems biology of embryogenesis. Reprod. Fertil. Dev. 22: 98–105.
PubMed Link

Erwin, D. H. and E. H. Davidson. 2009. The evolution of hierarchical gene regulatory networks. Nature Rev. Genet. 10: 141–148.
PubMed Link

Gell-Mann, M. 1964. Nonleptonic weak decays and the eightfold way. Phys. Rev. Lett. 12: 155–156.

Gilbert, S. F. and S. Sarkar. 2000. Embryo complexity: Organicism for the twenty-first century. Dev. Dyn. 219: 1–9.

Guenther, C., L. Pantalena-Filho and D. M. Kingsley. 2008. Shaping skeletal growth by modular regulatory elements in the Bmp5 gene. PLoS Genet. 4(12): e1000308.
PubMed Link

Hamburger, V. 1988. The Heritage of Experimental Embryology: Hans Spemann and the Organizer. Oxford University Press, Oxford.

Haraway, D. 2003. The Companion Species Manifesto: Dogs, People, and Significant Otherness. Prickly Paradigm Press of the University of Chicago Press, Chicago.

Haraway, D. J. 1976. Crystals, Fabrics and Fields: Metaphors of Organicism in Twentieth-Century Biology. Yale University Press, New Haven.

Haraway, D. J. 2008. When Species Meet. University of Minnesota Press, Minneapolis.

Hertwig, O. 1894. ‘The biological probem of today: Preformation or epigenesis?’’ P. C. Mitchell (trans.) Macmillan Co., New York.

Horb, M. E., C. N. Shen, D. Tosh and J. M. Slack. 2003. Experimental conversion of liver to pancreas. Curr. Biol. 13: 105–115.
PubMed Link

Huang, A. C., L. Hu, S. A. Kauffman, W. Zhang and I. Shmulevich. 2009a. Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst. Biol. 3: 20.
PubMed Link

Huang, S. 2009a. Non-genetic heterogeneity of cells in development: More than just noise. Development 136: 3853–3862.
PubMed Link

Huang, S. 2009b. Reprogramming cell fates: Reconciling rarity with robustness. Bioessays 31: 546–560.
PubMed Link

Huang, S., G. Eichler, Y. Bar-Yam and D. E. Ingber. 2005. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys. Rev. Lett. 94: 128701.
PubMed Link

Huang, S., I. Ernberg and S. A. Kauffman. 2009b. Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective. Semin. Cell Dev. Biol. 20: 869–876.
PubMed Link

Kauffman, S. A. 1969. Homeostasis and differentiation in random genetic control networks. Nature 224: 177–178.
PubMed Link

Kauffman, S. A. 1987. Developmental logic and its evolution. BioEssays 6: 82–87.
PubMed Link

Kauffman, S. A. 1993. The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, New York.

Kitano, H. 2004. Biological robustness. Nature Rev. Genet. 5: 826–837.
PubMed Link

Koelzer, S. and T. Klein. 2006. Regulation of expression of Vg and establishment of the dorsoventral compartment boundary in the wing imaginal disc by Suppressor of Hairless. Dev. Biol. 289: 77–90.
PubMed Link

Lander, A. D. 2011. Pattern, growth, and control. Cell 144: 955–969.
PubMed Link

Lander, A. D. 2013. How cells know where they are. Science 339: 923–927.
PubMed Link

Madar, A., A. Greenfield, H. Ostrer, E. Vanden-Eijnden and R. Bonneau. 2009. The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models. Conf. Proc. IEEE Eng. Med. Biol. Soc. 1: 5448–5451.
PubMed Link

Moss, L. 2003. What Genes Can’t Do. MIT Press, Cambridge, MA.

Needham, J. 1943. Time: The Refreshing River. Allen and Unwin, London.

Noble, D. 2006. The Music of Life: Biology Beyond Genes. Oxford University Press, New York, p. 21.

O'Malley, M. A. and J. Dupré. 2005. Fundamental issues in systems biology. Bioessays 27: 1270–1276.
PubMed Link

Raff, R. A. 1996. The Shape of Life. University of Chicago Press, Chicago.

Schlosser, G. and G. P. Wagner (eds.). 2004. Modularity in Development and Evolution. University of Chicago Press, Chicago.

Soto, A. M., B. S. Rubin and C. Sonnenschein. 2009. Interpreting endocrine disruption from an integrative biology perspective. Mol. Cell. Endocrinol. 304: 3–7.
PubMed Link

Soto, A. M., C. Sonnenschein and P. A. Miquel. 2008. On physicalism and downward causation in developmental and cancer biology. Acta Biotheor. 56: 257–274.
PubMed Link

Spemann, H. 1927. Neue Arbeiten über Oranisatoren in der tierischen Entwicklung. Naturwissen. 15: 946–951.

Tauber, A. I. and S. Sarkar. 1992. The human genome project: Has blind reductionism gone too far? Perspect. Biol. Med. 35: 220–235.
PubMed Link

Van Speybroeck, L., P. De Backer, J. Van Poucke and D. De Waele. 2005. The conceptual challenge of systems biology. Bioessays 27: 1305–1307.
PubMed Link

von Dassow, G. and E. Munro. 1999. Modularity in animal development and evolution: Elements of a conceptual framework for EvoDevo. J. Exp. Zool. B Mol. Dev. Evol. 285: 307–325.
PubMed Link

von Dassow, G., E. Meir, E. M. Munro and G. M. Odell. 2000. The segment polarity network is a robust developmental module. Nature 406: 188–192.
PubMed Link

Waddington, C. H. 1957. The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology. George Allen and Unwin, London.

Waddington, C. H. 1969. The practical consequences of metaphysical beliefs on a biologist’s work. In Waddington, C. H. (ed.), Towards a Theoretical Biology, Vol. 2. Transaction Publishers. Piscataway, NJ, pp. 72–81.

Waddington, C. H. 1975. Evoluton of an Evolutionist. Cornell University Press.

Wang, Y., P. N. J. Schnegelsberg, J. Dausman and R. Jaenisch. 1996. Functional redundancy of the muscle-specific transcription factors Myf5 and myogenin. Nature 379: 823–826.
PubMed Link

Weiss, P. A. 1926. Morphodynamik: Ein Einblick in die Gesetzte der organischen Gestaltung an Hand von experimentellen Ergebnissen. In J. Schaxel (ed.), Abhandlungen zur theoretischen Biologie. Gebrüder Borntraeger, Berlin.

Whitehead, A. N. 1929. Process and Reality. Free Press, NY.

Wimsatt, W. C. 1995. The ontology of complex systems: Levels of organization, perspectives, and causal thickets. Can. J. Philos. 20: 207–274.

Zhou, Q., J. Brown, A. Kanarek, J. Rajagopal and D. A. Melton. 2008. In vivo reprogramming of adult pancreatic exocrine cells to b-cells. Nature 455: 627–632.
PubMed Link

 

Citation for the BioWeb Conference Links
Barresi, M. J., and Lee, K. 2005–2010. Biology Web Conferences. Smith College, Northampton, MA.

© All the material on this website is protected by copyright. It may not be reproduced in any form without permission from the copyright holder.
Home Link