Virtual Tissues and Developmental Systems Biology

Comprehensive Toxicology, Second Edition

Volumn 12, Issue , 2010, Pages 347-358

  Knudsen, T B ^a   Daston, G P ^b  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b PROCTER AND GAMBLE COMPANY   (United States)

Author keywords

Bioinformatics; Computational toxicology; Developmental toxicity; Gene networks; Genomics; High throughput screening; Multicellular models; Redictive models; Systems biology; Systems modeling; Teratogenesis; Toxicity pathways; Virtual tissues

Indexed keywords

EID: 85012830288     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-08-046884-6.01532-3     Document Type: Chapter

References (62)

1. Bauer-Mehren A., Furlong L.I., Sanz F. Mol. Syst. Biol. 2009, 5:290.
2. Bénazet J.-D., Bischofberger M., Tiecke E., Gonalves A., Martin J.F., Zuniga A., Naef F., Zeller R. Science 2009, 323:1050-1053.
3. Ben-Zvi D., Shilo B.Z., Fainsod A., Barkai N. Nature 2008, 453:1205-1211.
4. Burgoon L.D., Boutros P.C., Dere E., Zacharewski T.R. Toxicol. Sci. 2006, 90:558-568.
5. Cavalieri D., De Filippo C. Drug Discov. Today 2005, 10:727-734.
6. Charlap J.C., Donahue R.J., Knudsen T.B. Birth Defects Res. A Clin. Mol. Teratol. 2003, 67:8-115.
7. Chernoff N.A., Rogers E.A., Gage M.I., Francis B.M. Reprod. Toxicol. 2008, 25:192-202.
8. Cickovski T.M., Huang C., Chaturvedi R., Glimm T., Hentschel H.G.E., Alber M.S., Glazier J.A., Newman S.A., Izaguirre J.A. IEEE/ACM Trans. Comput. Biol. Bioinform 2005, 2:1-15.
9. Collins F.S., Gray G.M., Bucher J.R. Science 2008, 319:906-907.
10. Correa-Villaseñor A., Cragan J., Kucik J., O'Leary L., Siffel C., Williams L. Birth Defects Res. A Clin. Mol. Teratol. 2003, 67:617-624.
11. Corvi R., Ahr H.-J., Albertini S., Blakey D.H., Clerici L., Coecke S., Douglas G.R., Gribaldo L., Groten J.P., Haase B., et al. Environ. Health Perspect. 2006, 114:420-429.
12. Daston G.P. Birth Defects Res. A Clin. Mol. Teratol. 2007, 79:1-7.
13. Davidson E.H. The Regulatory Genome. Gene Regulatory Networks in Development and Evolution 2006, 289. Academic Press, London.
14. Davidson E.H., Erwin D.H. Science 2006, 311:796-800.
15. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., Minokawa T., Amore G., Hinman V., Arenas-Mena C., et al. Science 2002, 295:1669-1678.
16. D'haeseleer P., Liang S., Somogyi R. Bioinformatics 2000, 16:707-726.
17. Dix D.J., Houck K.A., Martin M.T., Richard A.M., Setzer R.W., Kavlock R.J. Toxicol. Sci. 2007, 95:5-12.
18. Ema, M.; Ise, R.; Kato, H.; Oneda, S.; Hirose, A.; Hirata-Koizumi, M.; Singh, A.V.; Knudsen, T.B.; Ihara, T. Reprod. Toxicol. 2009, in press. 10.1016/j.reprotox.2009.09.003.
19. Engler A.J., Humbert P.O., Wehrle-Haller B., Weaver V.M. Science 2009, 324:208-212.
20. Ganter B., Zidek N., Hewitt P.R., Müller D., Vladimirova A. Pharmacogenomics 2008, 9:35-54.
21. Gohlke M., Griffith W.C., Faustman E.M. Toxicol. Sci. 2005, 86:470-484.
22. Goldbeter A., Pourquie O. J. Theor. Biol. 2008, 256:574-585.
23. Graner F., Glazier J.A. Phys. Rev. Lett. 1992, 69:2013-2016.
24. Green M.L., Zhang Y., Singh A.V., Zhang Y., Nemeth K.A., Sulik K.K., Knudsen T.B. Dev. Dyn. 2007, 236:613-631.
25. Gregor T., Tank D.W., Wieschaus E.F., Bialek W. Cell 2007, 130:153-164.
26. Hartung T. Nature 2009, 460:208-212.
27. Huang S., Eichler G., Bar-Yam Y., Ingber D.E. Phys. Rev. Lett. 2005, 94. 128701-1 (4 pages).
28. Hurtt M.E., Cappon G.D., Browning A. Food Chem. Toxicol. 2003, 41:611-619.
29. Ideker T., Lauffenburger D. Trends Biotechnol. 2003, 21:255-262.
30. Izaguirre J.A., Chaturvedi R., Huang C., Cickovski T., Coffland J., Thomas G., Forgacs G., Alber M., Hentschel G., Newman S.A., Glazier J.A. Bioinformatics 2004, 20:1129-1137.
31. Judson, R.S.; Houck, K.A.; Kavlock, R.J.; Knudsen, T.B.; Martin, M.T.; Mortensen, H.M.; Reif, D.M.; Richard, A.M.; Rotroff, D.M.; Shah, I.; Dix, D.J. Environ. Hlth. Persp. 2010, (in press).
32. Julien E., Willhite C.C., Richard A.M., DeSesso J.M. Birth Defects Res. A Clin. Mol. Teratol. 2004, 70:902-911.
33. Kavlock R.J., Setzer R.W. Environ. Health Perspect. 1996, 104(Suppl. 1):107-121.
34. Keller P.J., Schmidt A.D., Wittbrodt J., Stelzer E.H.K. Science 2008, 322:1065-1069.
35. Kercel S.W. Systems Biology. Principles, Methods, and Concepts 2007, 139-178. CRC Press, Taylor & Francis Group, LLC, Boca Raton, FL. A.K. Konopka (Ed.).
36. Kimmel C.A., Generoso W.M., Thomas R.D., Bakshi K.S. Toxicol. Appl. Pharmacol. 1993, 119:159-165.
37. Kitano H. Science 2002, 295:1662-1664.
38. Knudsen T.B., Kavlock R.J. Developmental Toxicology 2008, Vol. 3:311-360. Taylor and Francis, New York. B. Abbott, D. Hansen (Eds.).
39. Knudsen T.B., Martin M.T., Kavlock R.J., Judson R.S., Dix D.J., Singh A.V. Reprod. Toxicol. 2009, 28:209-219.
40. Kriete A., Sokhansanj B.A., Coppock D.L., West G.B. Ageing Res. Rev. 2006, 5:434-448.
41. Kriete A., Eils R. Computational System Biology 2006, 409. Elsevier Academic Press, London.
42. Lamb J., Crawford E.D., Peck D., Modell J.W., Blat I.C., Wrobel M.J., Lerner J., Brunet J.-P., Subramanian A., Ross K.N., et al. Science 2006, 313:1929-1935.
43. Lewis J. Science 2008, 322:399-403.
44. Martin M.T., Judson R.S., Reif D.M., Kavlock R.J., Dix D.J. Environ. Health Perspect. 2009, 117:392-399.
45. Martin M.T., Mendez E., Corum D.G., Judson R.S., Kavlock R.J., Rotroff D.M., Dix D.J. Toxicol. Sci. 2009, 110:181-190.
46. Masamizu Y., Ohtsuka T., Takashima Y., Nagahara H., Takenaka Y., Yoshikawa K., Okamura H., Kageyama R. Proc. Natl. Acad. Sci. USA 2006, 103:1313-1318.
47. Matthews E.J., Kruhlak N.L., Benz R.D., Contrera J.F. Regul. Toxicol. Pharmacol. 2007, 47:115-135.
48. Megason S.G., Fraser S.E. Mech. Dev. 2003, 120:1407-1420.
49. Naciff J.M., Hess K.A., Overmann G.J., Torontali S.M., Carr G.J., Tiesman J.P., Foertsch L.M., Richardson B.D., Martinez J.E., Daston G.P. Toxicol. Sci. 2005, 86:396-416.
50. Scientific Frontiers in Developmental Toxicology and Risk Assessment 2000, National Research Council, National Academy Press, Washington, DC. http://www.nap.edu/books/0309070864/html/.
51. Toxicity Testing in the 21st Century: A Vision and a Strategy 2007, 196. National Research Council, The National Academies Press, Washington, DC.
52. Nikitina N., Sauka-Spengler T., Bronner-Fraser M. Proc. Natl. Acad. Sci. USA 2008, 105:20083-20088.
53. Oates A.C., Gorfinkiel N., González-Gaitán M., Heisenberg C.-P. Nat. Rev. Genet. 2009, 10:517-530.
54. O'Hara M.F., Nibbio B.J., Craig R.C., Nemeth K.R., Nemeth K.R., Charlap J.H., Knudsen T.B. Reprod. Toxicol. 2003, 17:365-375.
55. Olson E.N. Science 2006, 313:1922-1927.
56. O'Malley M.A., Dupré J. Bioessays 2005, 27:1270-1276.
57. Robertson S.H., Smith C.K., Langhans A.L., McLinden S.E., Oberhardt M.A., Jakab K.R., Dzamba B., DeSimone D.W., Papin J.A., Peirce S.M. BMC Systems Biology 2007, 22:1-46.
58. Scheuerle A., Tilson H. Pharmacoepidemiol. Drug Safety 2002, 11(1):465-475.
59. Shmulevich I., Dougherty E.R., Kim S., Zhang W. Bioinformatics 2002, 18:261-274.
60. Wilson J.G. Handbook of Teratology 1977, Vol. 1:47-74. Plenum Press, New York. J.G. Wilson, F.C. Fraser (Eds.).
61. Wuensche A. Discrete Dynamics Lab (DD Lab) 1996, http://www.ddlab.com.
62. Yu X., Griffith W.C., Hanspers K., Dillman J.F., Ong H., Vredevoogd M.A., Faustman E.M. Toxicol. Sci. 2006, 92:560-577.