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Publications

2009

1. Aragon, A.D. Imani, R.A., Blackburn, V.R., Cupit, P.M., Melman, S.D., Goronga, T., Webb, T., Loker, E.S. & Cunningham, C. (2009). Towards an understanding of the mechanism of action of praziquantel. Molecular & Biochemical Parasitology, 164(1): 57-65.

2. Carman, R.L., Old, J.M., Baker, M., Jacques, N.A., & Deane, E.M. Identification and expression of a novel marsupial cathelicidin from the tammar wallaby (Macropus eugenii) (2009). Veterinary Immunology and Immunopathology, 127(3): 269-276.

3. Dahari, H., Shudo, E., Ribeiro, R.M. & Perelson, A.S. (2009). Mathematical modeling of HCV infection and treatment. Methods in molecular biology, 510: 439-453.

4. Dahari, H., Shudo, E., Ribeiro, R. M., and Perelson A. S. (2009) Modeling complex decay profiles of Hepatitis B virus during antiviral therapy. Hepatology, 49(1):32-8.

5. Lennard, R., Hikima, M.L., Wilson, J., Miller, N.W., Cunningham, C. & Warr, G.W. (2009). BOB.1 of the Channel Catfish, Ictalurus punctatus: not a transcriptional coactivator? Molecular Immunology, 46(3):481-91.

6. Moses, M. (2009). Being human: engineering: worldwide ebb. Nature, 457(7230):660-1.

7. Parra, Z.E., Baker, M. L., Lopez, A. M., Trujillo, J., Volpe, J. M. and Miller, R.D. (2009). TCRµ recombination and transcription relative to the conventional TCR during postnatal development in opossums. Journal of Immunology, 182(1):154-63.

8. Roy, S., Lane, T., Werner-Washburne, M., & Martinez, D. (2009) Inference of functional networks of condition-specific response: A case study of quiescence in yeast. Proceedings of the 2009 Pacific Symposium on Biocomputing (PSB). 51-62.

2008

1. Adema, C.M., Lun, C-M. , & Hanelt, B. & Seville, R.S. (2008). Digenean trematode infections of native fresh water snails and invasive Potamopyrgus antipodarum in the Grand Teton National Park/John D Rockefeller Memorial Parkway Area. Journal of Parasitology, In Press, PMID: 18576875.

2. Anderson-Teixeira, K.J., Vitousek, P.M. & Brown, J.H. (2008). Amplified temperature dependence in ecosystems developing on the lava flows of Mauna Loa, Hawai’i. Proceedings of the National Academy of Sciences, 105, 228-233.

3. Aragon, A.D., Imani, R.A., Blackburn, V.R. & Cunningham, C. (2008). Microarray based analysis of temperature and oxidative stress induced messenger RNA in Schistosoma mansoni. Molecular and Biochemical Parasitology, 162(2):134-41.

4. Arora, T., and Moses, M. E. (to appear in 2009). Using ant colony optimization for routing in VLSI chips. Proceedings of the Conference on Bio-Inspired Computational Methods Used for Difficult Problem Solving (BICS 2009), published by the American Institute of Physics.

5. Baker, M. L., Melman, S. D., Huntley, J. and Miller, R.D. (2008). Evolution of the opossum MHC: Evidence for diverse alternative splice patterns and low polymorphism among class I genes. Immunology. DOI:10.1111/j.1365-2567.2008.02994.

6. Beauchemin, C. A. A., McSharry, J. J., Drusano, G. L., Nguyen, J. T., Went, G. T., Ribeiro,R. M. & Perelson, A. S. (2008). Modeling amantadine treatment of influenza A virus in vitro. Journal of Theoretical Biology, 254, 439-451.

7. Bettencourt L. M. A. & Ribeiro R. M. (2008). Real time Bayesian estimation of the epidemic potential of emerging infectious diseases. PLoS One 3: e2185.

8. Coustau, C., Gourbal, B., Mitta, G. & Adema, CM. (2008). Echinostomes and snails: exploring complex interactions. In B. Fried and R. Toledo (Eds) The Biology of Echinostomes, Chapter 2. New York: Springer (in press).

10. Eaton, E., desJardins, M., & Lane, T. (2008). Modeling transfer relationships between learning tasks for improved inductive transfer. Proceedings of the 2007 European Conference on Machine Learning (ECML). doi: 10.1007/978-3-540-87479-9_39.

11. Esponda, F., Ackley, E.S., Helman, P., Jia, H., & Forrest, S. (2008). Protecting data privacy through hard-to-reverse negative databases. International Journal of Information Security 6(6):403-415.

12. Faeder, J.R., Blinov, M. L. & Hlavacek, W.S. Rule-based modeling of biochemical systems with BioNet Gen. Methods Mol. Biol. In I. V. Maly (Ed) Systems Biology Humana Press, Totowa, NJ. (in press).

13. Gerrish, P.J., Colato, A., Perelson, A.S., Sniegowski, P.D. (2008). Complete genetic linkage can subvert natural selection. Proceedings of the National Academy of Sciences USA, 104(15): 6266-6271.

14. Goldstein, B., Coombs, D., Faeder, J. R., & Hlavacek, W. S. (200X). Kinetic proofreading model. In A. B. Sigalov (Ed.) Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization.

15. Hall S.R., Lafferty K.D., Brown, J.H., Cáceres, C.E., Chase, J.M., Dobson, A.P., Holt, R.D., Jones, C.G., Randolph, S.E. & Rohani, P. (2008). Is infectious disease just another type of predator-prey interaction? In: Ostfeld R.S., Keesing F. & Eviner V.T. (Eds.). Infectious Disease Ecology: Effects of Ecosystems on Disease and of Disease on Ecosystems. Princeton, N.J: Princeton University Press.

16.Hanelt B, Lun C-M, & Adema, CM (2008). Comparative ORESTES-sampling of transcriptomes of immune-challenged Biomphalaria glabrata snails. Journal of Invertebrate Pathology, 99(2):192-203.

17. Hou, C, W. Zuo, M. E. Moses, J.H. Brown and G. B. West (2008). Energy uptake and allocation during ontogeny. Science, 322(5902):736-9.

18. Katju, V., LaBeau, E. M., Lipinski, K. J. & Bergthorsson, U. (2008). Sex change by gene conversion in a Caenorhabditis elegans fog-2 mutant. Genetics, 180:669-672.

19. Kaur A., Di Mascio M., Barabasz A., Rosenzweig M., McClure H. M., Perelson A. S., Ribeiro R. M., Johnson R. P. (2008). Dynamics of T- and B-Lymphocyte Turnover in a Natural Host of Simian Immunodeficiency Virus. Journal of Virology, 82:1084-1093.

20. Kim, D. I., Burge, J., Lane, T., Kiehl, K. A., Pearlson, G. D., & Calhoun, V. D. (2008). Hybrid ICA-Bayesian network approach reveals distinct effective connectivity differences in schizophrenia. NeuroImage. Appeared online Jun. doi: 10.1016/j.neuroimage.2008.05.065

22. Lotfy, W.M., Brant, S.V., DeJong, R.J., Le, T.H., Demiaszkiewicz, A., Kinsella, J.M., Rajapakse, R.P.V.J., Perera, B.V.P, Laursen, J.R., Mkoji, G.M., and Loker. E.S. (2008). Phylogenetic relationships among flukes of the Family Fasciolidae Railliet, 1895 with implications regarding their evolutionary biology and biogeography. American Journal of Tropical Medicine and Hygiene, 79, 248-255.

23. Moses, M.E., S. Forrest, A.L. Davis, M. Loder and J.H. Brown (2008). Scaling theory for information networks. Journal of the Royal Society’s Interface, 5(29):1469-80.

24. Moses, M.E., C. Hou, W.H. Woodruff, G.B. West, J.C. Nekola, W. Zuo, and J.H. Brown (2008). Revisiting a model of ontogenetic growth: Estimating model parameters from theory and data. The American Naturalist, 171(5):632.

25. Nemenman, I. , Escola, G. S. , Hlavacek, W. S., Unkefer, P. J., Unkefer, C. J., & Wall, M. E. (2008). Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Annals of the New York Academy of Sciences. 1115:102-15.

26. Pandrea I., Ribeiro R. M. et al. (2008). Viral replication is sustained by short-lived infected cells in SIVagm-infected African green monkeys. Journal of Virology, 82:3713-3724.

27. Parra, Z.E., Baker, M. L., Hathaway, J., Lopez, A. M., Trujillo, J., Sharp, A. and Miller, R.D. (2008). Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics, 9:111.

28. Parra, Z.E., Baker, M. L., Lopez, A. M., Trujillo, J., Volpe, J. M. and Miller, R.D. (2008) TCRµ recombination and transcription relative to the conventional TCR during postnatal development in opossums. Journal of Immunology, 104(23): 9776-9781.

29. Ribeiro R. M. & De Boer R. J. (2008). The contribution of the thymus to the recovery of peripheral naïve T cell numbers during antiretroviral treatment for HIV infection. Journal of AIDS, 49:1-8.

30. Rohani P, HJ Wearing, DA Vasco & Y Huang. Understanding host-multi-pathogen systems: the interaction between ecology and immunology. In Osfeld, Keesing & Eviner (Eds) Ecology of Infectious Diseases, Princeton University Press (2008).


31. Roy, S., Werner-Washburne, M., & Lane, T. (2008). A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics. Appeared online, Apr 8. doi: 10.1093/bioinformatics/btn126.


33. Samaniego, H. and M.E. Moses (2008). Cities as organisms: Allometric scaling of urban road networks in the USA. Journal of Transport and Land Use, 1:1.

34. Stout, B.A., Adema, C.M., Zhang, S.-M., Loker, E.S. (2008). The biology of FREPs: diversified lectins with fibrinogen-related domains from the freshwater snail B. glabrata. In G. Vasta & H. Ahmed (Eds.), Animal Lectins: A Functional View. London: CRC Press Taylor & Francis.

35. Steinauer, M.L., Maina, G., Mwangi, I.N., Kinuthia, J., Matuku, M., Mkoji, G.M., and Loker, E.S. (2008). Interactions between natural populations of human and rodent schistosome parasites in the Lake Victoria region of Kenya: a molecular epidemiological approach. PLOS Neglected Tropical Diseases, 2(4),1-11.

36. Steinauer, M.L., Agola, L.E., Mwangi, I.N., Mkoji, G.M., and Loker, E.S. (2008). Molecular epidemiology of Schistosoma mansoni: a robust, high-throughput method to assess multiple microsatellite markers from individual miracidia. Infection, Genetics and Evolution, 8, 68-73.

37. Steinauer, M.L., Hanelt, B., Mwangi, I.N., Maina, g.M., Agola, L.E., Kinuthia, J.M., Matuka, M.W., Mungai, M.N. Wilson, W.D., Mkoji, G.M., and Loker, E.S. (2008). Introgressive hypbridization of human and rodent schistosome parasites in western Kenya. Molecular Ecology, 17(23):5062-74.

38. Thibault, K.T & Brown, J.H. (2008). Impact of an extreme climatic event on community assembly. Proceedings of the National Academy of Sciences, 105, 3410-3415.

39. Yackley, B., Corona, E., & Lane, T. Function approximation using a metagraph kernel. Advances in Neural Information Processing Systems, 21 (NIPS). (In press)

40. Zhang S.-M., Zeng Y., Loker E. S. (2008). Expression profiling and binding properties of fibrinogen-related proteins (FREPs), plasma lectins from the schistosome snail host Biomphalaria glabrata. Innate Immunity, 14:175-189.

41. Zhang, S-M., Nian, H., Zeng, Y., DeJong R. J. (2008). Fibrinogen-bearing protein genes in the snail Biomphalaria glabrata: Characterization of two novel genes and expression studies during ontogenesis and trematode infection. Developmental and Comparative Immunology, 32:1119-1130.

2007

42. Baker, M.L., Indiviglio, S., Nyberg, A.M., Rosenberg, G.H., Lindblad-Toh, K., Miller, R.D. and Papenfuss, A.T. (2007). Analysis of a set of Australian northern brown bandicoot expressed sequence tags with comparison to the genome sequence of the South American grey short tailed opossum. BMC Genomics, 8, 50.

43. Baker, M.L. and Miller, R.D. (2007). Evolution of mammalian CD1: marsupial CD1 is not orthologous to the eutherian isoforms and is a pseudogene in the opossum Monodelphis domestica. Immunology, 121(1), 113-121.

44. Beauchemin, C., Dixit, N.M. and Perelson, A.S. (2007). Characterizing T cell movement within lymph nodes in the absence of antigen. Journal of Immunology, 178, 5505-5512.

45. Bragg, J.G. and Wagner, A. (2007). Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes. Proceedings of the Royal Society of London, Series B, 274, 1063-1070.

46. Brant, S.V. (2007). The occurrence of the avian schistosome. Folia Parasitologica, 54, 99-104.

47. Cable, J.M., B.J. Enquist and M.E. Moses (2007). The Allometry of host-pathogen interactions. PLoS ONE 2(11): e1130. DOI:10.1371/journal.pone.0001130.

48. Charnov, E.L., R. Warne, and M.E. Moses (2007). Lifetime reproductive effort in mammals and lizards. The American Naturalist, 170: E129-E142. DOI: 10.1086/522840.

49. Ciliberti, S., Martin, O.C. and Wagner, A. (2007). Robustness can evolve gradually in complex regulatory networks with varying topology. PLoS Computational Biology, 3(2), e15.

50. Ciupe, S., Ribeiro, R.M., Nelson, P.W., Dusheiko, G. and Perelson, A.S. (2007). The role of cells refractory to productive infection in acute hepatitis B viral dynamics. Proceedings of the National Academy of Sciences, USA, 104, 5050-5055.

51. Ciupe, S.M., Ribeiro, R.M., Nelson, P.W. and Perelson, A.S. (2007). Modeling the mechanisms of acute hepatitis B virus infection. Journal of Theoretical Biology, 247(1), 23-35.

52. Dahari, H., Lo, A., Ribeiro, R.M. and Perelson, A.S. (2007). Modeling hepatitis C virus dynamics: Liver regeneration and critical drug efficacy. Journal of Theoretical Biology, 247(2), 371-381.

53. Dahari, H., Markatou, M., Zeremski, M., Haller, I., Ribeiro, R., Licholai, T., Perelson, A.S. and Talal, A.H. (2007). Early ribavirin pharmacokinetics, HCV RNA and alanine aminotransferase kinetics in HIV/HCV co-infected patients during treatment with pegylated interferon and ribavirin. Journal of Hepatology, 47(1), 23-30.

54. Dahari, H. and Perelson, A.S. (2007). Hepatitis C virus RNA kinetics: drug efficacy and the rate of HCV-infected cells loss. World Journal of Gastroenterology, 13(21), 3020-3021.

55. Dahari, H., Ribeiro, R.M. and Perelson, A.S. (2007). Triphasic decline of hepatitis C virus RNA during antiviral therapy. Hepatology, 46(1), 16-21.

56. Dahari, H., Ribeiro, R.M., Rice, C.M. and Perelson, A.S. (2007). Mathematical modeling of subgenomic hepatitis C virus replication in Huh-7 cells. Journal of Virology, 81(2), 750-760.

57. Davenport, M.P., Ribeiro, R.M., Zhang, L., Wilson, D.P. and Perelson, A.S. (2007). A quantitative understanding of the mechanisms and limitations of immune control of HIV. Immunological Reviews, 216, 164-175.

58. Davenport, M.P., Ribeiro, R.M., Zhang, L., Wilson, D.P. and Perelson, A.S. (2007). Understanding the mechanisms and limitations of immune control of HIV, Immunological Reviews, 216, 164-175.

59. Decker, E.D., A.J. Kerkhoff and M.E. Moses (2007). Global patterns of city size distributions and their fundamental drivers. PLoS ONE, 2(9):e934. DOI:10.1371/journal.pone.0000934.

60. Enquist, B.J., Allen, A.P., Brown, J.H., Gillooly, J.F., Kerkhoff, A.J., Niklas, K.J., Price, C.A. and West, G.B. (2007). Biological scaling: does the exception prove the rule? Nature, 45(7127), E9-10; discussion E10-1.

61. Forrest, S. and Beauchemin, C. (2007). Computer immunology. Immunology Review, 216, 176-97.

62. Gerrish, P.J., Colato, A., Perelson, A.S. and Sniegowski, P.D. (2007). Complete genetic linkage can subvert natural selection. Proceedings of the National Academy of Sciences, USA, 104, 6266-6671.

63. Goldstein, B., Coombs, D., Faeder, J.R. and Hlavacek, W.S. (2007). Kinetic proofreading model. In A. B. Sigalov (Ed) Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization to Human Disease. Austin, TX: Landes Bioscience.

64. Hamilton, M.J., Milne, B.T., Walker, R.S. and Brown, J.H. (2007). Nonlinear scaling of space use in human hunter-gatherers. Proceedings of the National Academy of Sciences, USA, 104(11), 4765-9.

65. Hamilton, M.J., Milne, B.T., Walker, R.S., Burger, O. and Brown, J.H. (2007). The complex structure of hunter-gatherer social networks. Proceedings, Biological Sciences: The Royal Society, 274, 2195-2202.

66. Herpin, A., Lelong, C., Becker, T., Favrel, P. and Cunningham, C. (2007). A tolloid homologue from the Pacific oyster Crassostrea gigas. Gene Expression Patterns, 7(6), 700-708.

67. Jones, L.E. and Perelson, A.S. (2007). Transient viremia, plasma viral load, and reservoir replenishment in HIV-infected patients on antiretroviral therapy. Journal of Acquired Immune Deficiency Syndromes, 45(5), 483-493.

68. Lee, H.Y. and Perelson, A.S. (2007). Computational models of B cell and T cell receptors. In D. R. Flower and J. Timmis (Eds.), Silico Immunology (pp.65-82). New York,NY: Springer.

69. Markowitz, M. and Perelson, A.S. (2007). HIV-1 viral dynamics studies in the setting of clinical trials - a window of opportunity. Journal of Infectious Diseases, 195, 1087-1088.

70. Mikkelsen, T.S., Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S.M.J., Sharpe, T., Baker, M.L., Batzer, M.A., Benos, P.V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J.E., Fazzari, M.J., Glass J.L., Grabherr, M., Greally, J.M., Gu, W., Hore, T.A., Huttley G.A., Jirtle, R.L., Koina, E., Lee J.T., Mahony, S., Marra, M.A., Miller, R.D., Nicholls, R.D., Oda, M., Papenfuss, A.T., Parra, Z.E., Pollock, D.D., Ray, D.A., Schein, J.E., Speed, T.P., Thompson, K., VandeBerg, J.L., Wade, C.M., Walker, Waters, P.D., J.A., Webber, C., Weidman, J.R., Xie, X., Zody, M.C., Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Marshall Graves, J.A., Ponting, C.P., Breen, M., Samollow, .B., Lander, E.S., and Lindblad-Toh, K.S. (2007). Genome of the marsupial Monodelphis domestica reveals lineage-specific innovation in coding sequences. Nature, 447:167-178.

71. Nekola, J.C. and Brown, J.H. (2007). The wealth of species: ecological communities, complex systems and the legacy of Frank Preston. Ecological Letters, 10(3), 188-196.

72. Parra, Z.E., Baker, M.L., Schwarz, R.S., Deakin, J.E., Lindblad-Toh, K. and Miller, R.D. (2007). A unique T cell receptor discovered in marsupials. Proceedings of the National Academy of Sciences, USA, 104(23), 9776-9781.

73. Perelson, A.S. and Layden, T.J. (2007). Ribavirin: Is it a mutagen for hepatitis C virus? Gastroenterology, 132, 2050-2052.

74. Ribeiro, R.M. (2007). Dynamics of CD4(+) T cells in HIV-1 infection. Immunology and Cell Biology, 5(4), 287-294.

75. Ribeiro, R.M. and Perelson, A.S. (2007). Determining thymic output quantitatively: Using models to interpret experimental T cell receptor excision circle (TREC) data. Immunological Reviews, 216, 21-34.

76. Rong, L., Feng, Z. and Perelson, A.S. (2007). Emergence of HIV-1 drug resistance during antiretroviral treatment. Bulletin of Mathematical Biology, 69(6), 2027-2060.

77. Rong, L., Feng, Z. and Perelson, A.S. (2007). Mathematical analysis of age-structured HIV-1 dynamics with combination therapy. SIAM Journal on Applied Mathematics, 67, 731-756.

78. Rubenstein, R., Gray, P.C., Cleland, T.J., Piltch, M.S., Hlavacek, W.S., Roberts, R.M., J., A. and J.-I., K. (2007). Dynamics of the nucleated polymerization model of prion replication. Biophysical Chemistry, 125, 360-367.

79. Samaniego, H. and M.E. Moses (2007) Cities as organisms: Allometric scaling as an optimization model to assess road networks in the USA. Proceedings of Access to Destinations II, Minneapolis, MN, August 2007.

80. Savage, V.M., Allen, A.P., Brown, J.H., Gillooly, J.F., Herman, A.B., Woodruff, W.H. and West, G.B. (2007). Scaling of number, size, and metabolic rate of cells with body size in mammals. Proceedings of the National Academy of Sciences, USA, 104(11), 4718-23.

81. Schwarz, R.S., Hodes-Villamar, L., Fitzpatrick, K.A., Fain, M.G., Hughes, A.L. and Cadavid, L.F. (2007). A gene family of putative immune recognition molecules in the hydroid Hydractinia. Immunogenetics, 59(3), 233-46.

82. Wagner, A. and Wright, J. (2007). Alternative routes and mutational robustness in complex regulatory networks. BioSystems, 88, 163-172.

83. Xu, Y., Allen, L.J. and Perelson, A.S. (2007). Stochastic model of an influenza epidemic with drug resistance. Journal of Theoretical Biology, 248(1), 179-193.

2006

84. Abbott, R.G., Forrest, S. and Pienta, K.J. (2006). Simulating the hallmarks of cancer. Artificial Life, 12(4). 617-34.

85. Abramson, G., Giuggioli, L., Kenkre, V.M., Dragoo, J.W., Parmenter, R.R., Parmenter, C.A. and Yates, T.L. (2006). Diffusion and home range parameters for rodents: Peromyscus maniculatus in New Mexico. Ecological Complexity, 3, 64-70.

86. Adema, C.M., Luo, M.-Z., Hanelt, B., Hertel, L.A., Marshall, J.J., Zhang, S.M., DeJong, R.J., Kim, H.R., Kudrna, D., Wing, R.A., Soderlund, C., Knight, M., Lewis, F.A., Caldeira, R.L., Jannotti-Passos, L.K., Carvalho Odos, S., and Loker, E.S. (2006). A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni. Memorias do Instituto Oswaldo Cruz, 101(Suppl. I), 167-177.

87. Agola, L., Mburu, D., DeJong, R., Mungai, B., Muluvi, G., Njagi, E., Loker, E. and Mkoji, G. (2006). Microsatellite typing reveals strong genetic structure of Schistosoma mansoni from localities in Kenya. Infection, Genetics and Evolution, 6(6), 484-90.

88. Allen, A.P., Gillooly, J.F., Savage, V.M. and Brown, J.H. (2006). Kinetic effects of temperature on rates of genetic divergence and speciation. Proceedings of the National Academy of Sciences, USA, 103(24), 9130-5.

89. Allen, C., Buttner, S., Aragon, A., Thomas, J., Meirelles, O., Jaetao, J., Benn, D., Ruby, S., Veenhuis, M., Madeo, F. and Werner-Washburne, M. (2006). Isolation of quiescent and nonquiescent cells from yeast stationary-phase cultures. Journal of Cell Biology, 174(1), 89-100.

90. Anderson, K.J., Allen, A.P., Gillooly, J.F. and Brown, J.H. (2006). Temperature-dependence of biomass accumulation rates during secondary succession. Ecology Letters, 9(6), 673-82.

91. Auchtung, T., Takacs-Vesbach, C. and Cavanaugh, C. (2006). 16S rRNA phylogenetic investigation of the candidate division "Korarchaeota". Applications in Environmental Microbiology, 72(7), 5077-82.

92. Aragon, A., Quinones, G., Thomas, E., Roy, S. and Werner-Washburne, M. (2006). Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress, Genome Biology, 7(8), 403.

93. Aragon, A., Quinones, G., Allen, C., Thomas, J., Roy, S., Davidson, G., Wentzell, P., Millier, B., Jaetao, J., Rodriguez, A. and Werner-Washburne, M. (2006). An automated, pressure-driven sampling device for harvesting from liquid cultures for genomic and biochemical analyses. Journal of Microbiological Methods, 65(2), 357-60.

94. Baccam, P., Beauchemin, C., Macken, C.A., Hayden, F.G. and Perelson, A.S. (2006). Kinetics of influenza A virus infection in humans. Journal of Virology, 80(15), 7590-7599.

95. Belov, K., Deakin, J.E., Papenfuss, A.T., Baker, M.L., Melman, S.D., Siddle, H.V., Gouin, N., Goode, D.L., Sargeant, T.J., Robinson, M.D., Wakefield, M.J., Mahony, S., Cross, J.G., Benos, P.V., Samollow, P.B., Speed, T.P., Graves, J.A., and Miller, R.D. (2006). Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biology, 4(3), 317-328.

96. Blinov, M.L., Faeder, J.R., Goldstein, B. and Hlavacek, W.S. (2006). A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. BioSystems, 83, 136-151.

97. Blinov, M.L., Yang, J., Faeder, J.R. and Hlavacek, W.S. (2006). Depicting signaling cascades. Nature Biotechnology, 24, 137-138.

98. Brant, S.V., Morgan, J.A.T., Mkoji, G.M., Snyder, S.D., Rajapakse, R.P.V.J. and Loker, E.S. (2006). An approach to revealing blood fluke life cycles, taxonomy, and diversity: Provision of key reference data including DNA sequence from single life cycle stages. Journal of Parasitology, 92(1), 77-88.

99. Brown, J.H. and Sibly, R.M. (2006). Life-history evolution under a production constraint. Proceedings of the National Academy of Sciences, USA, 103(47), 17595-9.

100. Cunningham, C., Hikima, J., Jenny, M.J., Chapman, R.W., Fang, G.C., Saski, C., Lundqvist, M.L., Wing, R.A., Cupit, P.M., Gross, P.S., Warr, G.W. and Tomkins, J.P. (2006). New resources for marine genomics: Bacterial artificial chromosome libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas). Marine Biotechnology, 8(5), 521-33.

101. Cupit, P.M., Lennard, M.L., Hikima, J., Warr, G.W. and Cunningham, C. (2006). Characterization of two POU transcription factor family members from the urochordate Oikopleura dioica. Gene, 383, 1-11.

102. Dahari, H., Forns, X., Neumann, A.U. and Perelson, A.S. (2006). The extrahepatic contribution to HCV plasma viremia. Journal of Hepatology, 45(4), 626-627.

103. Dahari, H., Ribeiro, R., Rice, C.M. and Perelson, A.S. (2006). Mathematical modeling of subgenomic hepatitis C viral replication in Huh-7 cells. Journal of Hepatology, 44(Suppl. 2), S273-S273.

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2004

221. Ackerman, J.L., Bellwood, D.R. and Brown, J.H. (2004). The contribution of small individuals to density-body size relationships: examination of energetic equivalence in reef fishes. Oecologia, 139, 568-571.

222. Baker, M.L., Harrison, G.A., Wares, J.P. and Miller, R.D. (2004). The relationship of the marsupial families and the mammalian subclasses based on recombination activating gene-1. Journal of Mammalian Evolution, 11: 1-16.

223. Baker, M.L., Wares, J.P., G.A., H. and Miller, R.D. (2004). The relationship of the marsupial families and the mammalian subclasses based on recombination activating gene-1. Journal of Mammalian Evolution. 11, 1-16.

224. Balthrop, J., Forrest, S., Newman, M.E.J. and Williamson, M.M. (2004). Technological networks and the spread of computer viruses. Science, 304(5670), 527-529.

225. Belov, K., Miller, R.D., Ilijeski, A., Hellman, L. and Harrison, G.A. (2004). Isolation of monotreme T-cell receptor alpha and beta chains. Immunogenetics, 56(3), 164-169.

226. Berg, J., Lässig, M. and Wagner, A. (2004). Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplication. BMC Evolutionary Biology, 4, 51.

227. Blinov, M.L., Faeder, J.R., Goldstein, B. and Hlavacek, W.S. (2004). BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics, 20, 3289-3291.

228. Bridgwater, J., Forrest, S. and Parker, D.J. (2004). PEPT for agglomeration? Powder Technology, 140(3), 187-193.

229. Brown, J.H., Bedrick, E.J., Ernest, S.K.M., Cartron, J.-L.E. and Kelly, J.F. (2004). Constraints on negative relationships: mathematical causes and ecological consequences. In M. L. Taper, S. Lele and N. Lewin-Koh (Eds.) The Nature of Scientific Evidence. Baltimore, MD: Johns Hopkins University Press.

230. Brown, J.H., Gillooly, J.F., Allen, A.P., Savage, V.M. and West, G.B. (2004). Response to forum commentary on "toward a metabolic theory of ecology”. Ecology, 85, 1818-1821.

231. Brown, J.H., Gillooly, J.F., Allen, A.P., Savage, V.M. and West, G.B. (2004). Toward a metabolic theory of ecology. Ecology, 85, 1771-1789.

232. Brown, J.H. and Sax, D. (2004). An Essay on some topics concerning invasive species. Austral Ecology, 29, 530-536.

233. Brown, J.H. and Sax, D. (2004). Gradients in species diversity: Why are there so many species in the tropics? In M. V. Lomolino, D.F Sax and J. H. Brown (Eds.) Foundations of Biogeography. Chicago, IL: University Press.

234. Brown, J.H. and West, G.B. (2004). One rate to rule them all. New Scientist, 182: 38-41.

235. Browning, T.L., Belov, K., Miller, R.D. and Eldridge, M.D.B. (2004). Molecular cloning and characterization of the polymorphic MHC class II DBB from the tammar wallaby (Macropus eugenii). Immunogenetics, 55(11): 791-795.

236. Cadavid, L.F. (2004). Self-discrimination in colonial invertebrates: genetic control of allorecognition in the hydroid Hydractinia. Developmental and Comparative Immunology, 28(9), 871-9.

237. Cadavid, L.F., Powell, A.E., Nicotra, M.L., Moreno, M. and Buss, L.W. (2004). An invertebrate histocompatibility complex. Genetics, 167(1), 357-65.

238. Chao, D.L., Davenport, M.P., Forrest, S. and Perelson, A.S. (2004). Modelling the impact of antigen kinetics on T-cell activation and response. Immunology and Cell Biology, 82(1), 55-61.

239. Chao, D.L., Davenport, M.P., Forrest, S. and Perelson, A.S. (2004). A stochastic model of cytotoxic T cell responses. Journal of Theoretical Biology, 228(2), 227-240.

240. Conant, G.C. and Wagner, A. (2004). Duplicate genes and robustness to transient gene knockouts in Caenorhabditis elegans. Proceedings of the Royal Society of London, Series B, 271, 89-96.

241. Conant, G.C. and Wagner, A. (2004). A fast algorithm for determining the longest combination of local alignments to a query sequence. BMC Bioinformatics, 5(62), 17-20.

242. Davenport, M.P., Chao, D.L., Ribeiro, R.M. and Perelson, A.S. (2004). Predicting the impact of a nonsterilizing vaccine against human immunodeficiency virus. Journal of Virology, 78, 11340-11351.

243. Davenport, M.P., Ribeiro, R.M. and Perelson, A.S. (2004). Kinetics of virus specific CD8+ T cells and the control of HIV infection. Journal of Virology, 78, 10096-10103.

244. DeJong, R.J., Emery, A.M. and Adema, C.M. (2004). The mitochondrial genome of Biomphalaria glabrata (Gastropoda : Basommatophora), intermediate host of Schistosoma mansoni. Journal of Parasitology, 90(5), 991-997.

245. Di Mascio, M., Markowitz, M., Ho, D.D. and Perelson, A.S. (2004). Modeling the longterm control of viremia in HIV-1 infected patients treated with antiretroviral therapy. Mathematical Biosciences, 188, 47-62.

246. Di Mascio, M., Markowitz, M., Louie, M., Hurley, A., Hogan, C., Simon, V., Follman, D., Ho, D.D. and Perelson, A.S. (2004). Dynamics of intermittent viremia during highly active antiretroviral therapy in patients who initiate therapy during chronic versus acute and early human immunodeficiency virus type 1 infection. Journal of Virology, 78, 10566-10573.

247. Dixit, N.M., Layden-Almer, J.E., Layden, T.J. and Perelson, A.S. (2004). Modelling how ribavirin improves interferon response rates in hepatitis C virus infection. Nature, 432, 922-924.

248. Dixit, N.M., Markowitz, M., Ho, D.D. and Perelson, A.S. (2004). Estimates of intracellular delay and average drug efficacy from viral load data of HIV infected individuals under antiretroviral therapy. Antiviral Therapy, 9, 237-246.

249. Dixit, N.M. and Perelson, A.S. (2004). Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay. Journal of Theoretical Biology, 226(1), 95-109.

250. Dixit, N.M. and Perelson, A.S. (2004). Multiplicity of human immunodeficiency virus infections in lymphoid tissue. Journal of Virology, 78, 8942-8945.

251. Elson, K., Ribeiro, R.M., Perelson, A.S., Simmons, A. and Speck, P. (2004). The lifespan of satellite cells in murine sensory ganglia estimated by the uptake of bromodeoxyuridine. Experimental Neurology, 186, 99-103.

252. Esponda, F., Forrest, S. and Helman, P. (2004). A formal framework for positive and negative detection. IEEE Transactions on Systems, Man, and Cybernetics, 34(1), 357-373.

253. Evangelisti, A. and Wagner, A. (2004). Molecular evolution in the transcriptional regulation network of yeast. Journal of Experimental Zoology Part B - Molecular and Developmental Evolution, 302B, 392-411.

254. Flores-Ramirez, S., Miller, R.D. and Urban-Ramirez, J. (2004). Major histocompatibility complex I polymorphism in a cetacean: The gray whale (Eschrichtius robustus). Marine Mammal Science. 20(2), 262-273.

255. Gilchrist, M.A., Coombs, D. and Perelson, A.S. (2004). Optimizing within-host viral fitness: Infected cell lifespan and virion production rate. Journal of Theoretical Biology, 229, 281-288.

256. Gilchrist, M.A., Salter, L.A. and Wagner, A. (2004). A statistical framework for combining and interpreting proteomic datasets. Bioinformatics, 20, 689-700.

257. Goldstein, B., Faeder, J.R. and Hlavacek, W.S. (2004). Mathematical and computational models of immune-receptor signalling. Nature Reviews Immunology, 4, 445-456.

258. Hahn, M., Conant, G.C. and Wagner, A. (2004). Evolution in large genetic networks: does connectivity equal importance? Journal of Molecular Evolution, 58, 203-211.

259. Hertel, L.A., Barbosa, C.S., Santos, R.A.A.L. and Loker, E.S. (2004). Molecular identification of symbionts from the pulmonate snail Biomphalaria glabrata in Brazil. Journal of Parasitology, 90(4), 759-763.

260. Jacobson, D.J., Powell, A.J., Dettman, J.R., Saenz, G.S., Barton, M.M., Hiltz, M.D., Dvorachek, W.H., Glass, N.L., Taylor, J.W. and Natvig, D.O. (2004). Neurospora in temperate forests of western North America. Mycologia, 96(1), 66-74.

261. Jetz, W., Carbone, C., Fulford, J. and Brown, J.H. (2004). The scaling of animal space use. Science, 306, 266-268.

262. Levin, S., Ricciardi, L., Diekmann, O. and Perelson, A.S. (2004). Topics in biomathematics and related computational problems – Foreword. Mathematical Biosciences, 188(SI), VII-VIII.

263. Loker, E.S., Adema, C.M., Zhang, S.M. and Kepler, T.B. (2004). Invertebrate immune systems - not homogeneous, not simple, not well understood. Immunological Reviews. 198, 10-24.

264. Lomolino, M.V., Sax, D. and Brown, J.H. (2004). Foundations of Biogeography. Chicago, IL: University of Chicago Press.

265. Lyons, S.K., Smith, F.A. and Brown, J.H. (2004). Of mice, mastodons, and men: human mediated extinctions on four continents. Evolutionary Ecology Research, 6, 339-358.

266. Lyons, S.K., Smith, F.A., Wagner, P.J., White, E.P. and Brown, J.H. (2004). Was a "hyperdisease" responsible for the late Pleistoncene megafaunal extinction? Ecology Letters, 7, 859-868.

267. Maurer, B.A., Brown, J.H., Dayan, T., (2004). Similarities in body size distributions of small-bodied flying vertebrates. Evolutionary Ecology Research, 6, 783-797.

268. Meehan, T.D., Jetz, W. and Brown, J.H. (2004). Energetic determinants of abundance in winter landbird communities. Ecology Letters, 7, 532-537.

269. Miska, K.B., Wright, A.M., Lundgren, R., Sasaki-McClees, R., Osterman, A., Gale, J.M. and Miller, R.D. (2004). Analysis of a marsupial MHC region containing two recently duplicated class I loci. Mammalian Genome, 15(10), 851-864.

270. Nelson, P.W., Gilchrist, M.A., Coombs, D., Hyman, J.M. and Perelson, A.S. (2004). An age-structured model of HIV infection that allows for variations in the production rate of viral particles and the death rate of productively infected cells. Mathematical Biosciences and Engineering, 1, 267-288.

271. Nowak, M.A., Parra, Z.E., Hellman, L. and Miller, R.D. (2004). The complexity of expressed kappa light chains in egg-laying mammals. Immunogenetics, 56(8), 555-563.

272. Nowak, T.S., Woodards, A.C., Jung, Y.H., Adema, C.M. and Loker, E.S. (2004). Identification of transcripts generated during the response of resistant Biomphalaria glabrata to Schistosoma mansoni infection using suppression subtractive hybridization. Journal of Parasitology, 90(5), 1034-1040.

273. Perelson, A.S. and Ribeiro, R.M. (2004). Hepatitis B virus kinetics and mathematical modeling. Seminars in Liver Disease, 24(Suppl1), 11-16.

274. Pimm, S.L. and Brown, J.H. (2004). Domains of diversity. Science, 304, 832-833.

275. Posner, R.G., Paar, J.M., Licht, A., Pecht, I., Conrad, D.H. and Hlavacek, W.S. (2004). Interaction of monoclonal IgE-specific antibody with cell-surface IgE-FceRI: characterization of equilibrium binding and secretory response. Biochemistry, 43, 11352-11360.

276. Ramratnam, B., Ribeiro, R.M., He, T., Chung, C., Simon, V., Vanderhoeven, J., Hurley, A., Zhang, L., Perelson, A.S., Ho, D.D. and Markowitz, M. (2004). Intensification of antiretroviral therapy accelerates the decay of the latent reservoir of HIV-1 and decreases but does not eliminate ongoing virus replication. Journal of Acquired Immune Deficiency Syndromes, 35, 33-37.

277. Ribeiro, R. and Perelson, A.S. (2004). The analysis of HIV dynamics using mathematical models. In G. P. Wormser (Ed.), AIDS and other Manifestations of HIV Infection (pp. 905-912). New York: Academic Press.

278. Savage, V.M., Gillooly, J.F., Brown, J.H., West, G.B. and Charnov, E.L. (2004). Effects of body size and temperature on population growth. American Naturalist, 163, E429-E441.

279. Smith, F.A., Brown, J.H., Haskel, J.P., et al. (2004). Similarity of mammalian body size across the taxonomic hierarchy and across space and time. American Naturalist, 163, 672-691.

280. Talal, A.H., Shata, M.T., Dorante, G., Chadburn, A., Kock, R., Neumann, A.U., Ribeiro, R.M. and Perelson, A.S. (2004). Virus dynamics and immune responses during treatment in patients co-infected with hepatitis C and HIV. Journal of Acquired Immune Deficiency Syndromes, 35:103-113.

281. Tringe, S.G., Wagner, A. and Ruby, S.W. (2004). Enriching for direct regulatory targets in perturbed gene expression profiles. Genome Biology, 5, 109.

282. Wagner, A. (2004). Reconstructing pathways in large genetic networks from genetic perturbations. Journal of Computational Biology, 11, 53-60.

283. Wall, M.E., Hlavacek, W.S. and Savageau, M.A. (2004). Design of gene circuits: lessons from bacteria. Nature Reviews Genetics, 5, 34-42.

284. Warrender, C., Forrest, S. and Segel, L. (2004). Homeostasis of peripheral immune effectors. Bulletin of Mathematical Biology, 66(6), 1493-1514.

285. West, G.B. and Brown, J.H. (2004). Life's universal scaling laws. Physics Today, 57, 36-42.

286. West, G.B., Brown, J.H. and Enquist, B.J. (2004). Growth models based on first principles of phenomenology. Functional Ecology, 18, 188-196.

287. Wiegel, F.W. and Perelson, A.S. (2004). Some scaling principles for the immune system. Immunology and Cell Biology, 82, 127-131.

288. Zhang, L., Ribeiro, R.M., Mascola, J.R., Lewis, M.G., Stiegler, G., Katinger, H., Perelson, A.S. and Davenport, M.P. (2004). Effects of antibody on viral kinetics in SHIV infection: Implications for vaccination. Journal of Virology, 78, 5520-5522.

289. Zhang, S.-M., Adema, C.M., Kepler, T.B. and Loker, E.S. (2004). Diversification of Ig superfamily genes in an invertebrate. Science, 305(5681), 251-254.

290. Zhang, S.-M. and Loker, E.S. (2004). Representation of an immune responsive gene family encoding fibrinogen-related proteins in the freshwater mollusc Biomphalaria glabrata, an intermediate host for Schistosoma mansoni. Gene, 341, 255-266.

2003

291. Coombs, D., Gilchrist, M.A., Percus, J. and Perelson, A.S. (2003). Optimal viral production. Bulletin of Mathematical Biology, 65(6), 1003-1023.

292. De Boer, R.J., Homann, D. and Perelson, A.S. (2003). Different dynamics of CD4+ and CD8+ T cell responses during and after acute lymphocytic choriomeningitis virus infection. Journal of Immunology, 171(8), 3928-3935.

293. DeJong, R.J., Morgan, J.A., Wilson, W.D., et al. (2003). Phylogeography of Biomphalaria glabrata and B. pfeifferi, important intermediate hosts of Schistosoma mansoni in the New and Old World tropics. Molecular Ecology, 12(11), 3041-3056.

294. Di Mascio, M., Markowitz, M., Louie, M., Hogan, C., Hurley, A., Chung, C., Ho, D.D. and Perelson, A.S. (2003). Viral blip dynamics during highly active antiretroviral therapy. Journal of Virology, 77(22), 12165-1272.

295. Ernest, S.K.M., Enquist, B.J., Brown, J.H., Charnov, E.L., Gillooly, J.F., Savage, V.M., White, E.P., Smith, F.A., Hadly, E.A. and Haskell, J.P. (2003). Thermodynamic and metabolic effects on the scaling of production and population energy use. Ecology Letters, 9, 990-995.

296. Esponda, F., Forrest, S. and Helman, P. (2003). The crossover closure and partial match detection. Artificial Immune Systems, Proceedings, 2787, 249-260.

297. Gutierrez, A., Pointier, J.P., Fraga, J., Jobet, E., Modat, S., Perez, R.T., Yong, M., Sanchez, J., Loker, E.S. and Theron, A. (2003). Fasciola hepatica: identification of molecular markers for resistant and susceptible Pseudosuccinea columella snail hosts. Experimental Parasitology, 105(3-4), 211-218.

298. Harrison, G.A., Taylor, C.L., Miller, R.D. and Deane, E.M. (2003). Primary structure and variation of the T-cell receptor delta-chain from a marsupial, Macropus eugenii. Immunology Letters, 88(2), 117-125.

299. Hlavacek, W.S., Faeder, J.R., Blinov, M.L., Perelson, A.S. and Goldstein, B. (2003). The complexity of complexes in signal transduction. Biotechnology and Bioengineering, 84(7), 783-794.

300. Morgan, J.A.T., DeJong, R.J., Kazibwe, F., Mkoji, G.M. and Loker, E.S. (2003). A newly-identified lineage of Schistosoma. International Journal For Parasitology, 33(9), 977-985.

301. Smith, F.A., Lyons, S.K., Ernest, S.K.M., Jones, K.E., Kaufman, D.M., Dayan, T., Marquet, P.A., Brown, J.H. and Haskel, J.P. (2003). Body mass of late quaternary mammals. Ecology, 84, 3403-3403.

302. Thornhill, R., Gangestad, S.W., Miller, R.D., Scheyd, G., McCollough, J. and Franklin, M. (2003). Major Histocompatibility Complex genes, symmetry and body scent attractiveness in men and woman. Behavioral Ecology, 14(5), 668-678.

303. Torriani, F.J., Ribeiro, R.M., Gilbert, T.L., Schrenk, U.M., Clauson, M., Pacheco, D.M. and Perelson, A.S. (2003). Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) dynamics during HCV treatment in HCV/HIV coinfection. Journal of Infectious Diseases, 188(10), 1498-1507.

304. Zhang, S.-M. and Loker, E.S. (2003). The FREP gene family in the snail Biomphalaria glabrata: additional members, and evidence consistent with alternative splicing and FREP retrosequences. Developmental and Comparative Immunology, 27(3), 175-187.

305. Zhang, S.-M., Wang, D.Q. and Zhang, Y.-P. (2003). Mitochondrial DNA variation, effective female population size and population history of the endangered Chinese sturgeon, Acipenser sinensis. Conservation Genetics, 4(6), 673-683.

Publications by Non-CETI Investigators Utilizing CETI Supported Core Facilities:

1. Alo, D. and Turner, T.F. (2005). Effects of habitat fragmentation on effective population size in the endangered Rio Grande silvery minnow. Conservation Biology, 19(4), 1138-1148.

2. Ashford, R.U., Mehta, J.A. and Cripps, R. (2004). Delayed presentation is no barrier to satisfactory outcome in the management of open tibial fractures. Injury, 35(4), 411-6.

3. Baker, P.W., Tanaka, K.K., Klitgord, N. and Cripps, R.M. (2005). Adult myogenesis in Drosophila melanogaster can proceed independently of myocyte enhancer factor-2. Genetics, 170(4), 1747-59.

4. Barton, L.L., Goulhen, F., Bruschi, M., Woodards, N.A., Plunkett, R.M. and Rietmeijer, F.J. (2007). The bacterial metallome: composition and stability with specific reference to the anaerobic bacterium Desulfovibrio desulfuricans. Biometals, 20(3-4), 291-302.

5. Cripps, R.L., Martin-Gronert, M.S. and Ozanne, S.E. (2005). Fetal and perinatal programming of appetite. Clinical Science (Lond),109(1), 1-11.

6. Cripps, R.M., Lovato, T.L. and Olson, E.N. (2004). Positive autoregulation of the Myocyte enhancer factor-2 myogenic control gene during somatic muscle development in Drosophila. Developmental Biology, 267(2), 536-47.

7. Dragoo, J.W., Matthes, D.K., Aragon, A., Hass, C.C. and Yates, T.L. (2004). Identification of skunk species submitted for rabies testing in the desert southwest. Journal of Wildlife Diseases, 40(2), 371-376.

8. Driscoll, T.R., Cripps, R. and Brotherhood, J.R. (2007). Heat-related injuries resulting in hospitalisation in Australian sport. Journal of Science and Medicine in Sport. (E publication ahead of print).

9. Goethert, H., Cook, J., Lance, E. and Telford, S. (2006). Fay and Rausch 1969 revisited: Babesia microti in Alaskan small mammals. Journal of Parasitology, 92(4), 826-31.

10. Hafner, M.S., Light, J.E., Hafner, D.J., Brant, S.V., Spradling, T.A. and Demastes, J.W. (2006). Cryptic species in the mexican pocket gopher, Cratogeomys merriami. Journal of Mammalogy, 86, 1095-1108.

11. Hass, C.C. and Dragoo, J.W. (2006). Rabies in hooded and striped skunks in Arizona. Journal of Wildlife Diseases, 42(4), 825-9.

12. Hendren, J.D., Shah, A.P., Arguelles, A.M. and Cripps, R.M. (2007). Cardiac expression of the Drosophila Sulphonylurea receptor gene is regulated by an intron enhancer dependent upon the NK homeodomain factor Tinman. Mechanisms and Development, 124(6), 416-26.

13. Herranz, R., Diaz-Castillo, C., Nguyen, T.P., Lovato, T.L., Cripps, R.M. and Marco, R. (2004). Expression patterns of the whole troponin C gene repertoire during Drosophila development. Gene Expression Patterns, 4(2), 183-90.

14. Hunter, A.J., Northup, D.E., Dahm, C.N. and Boston, P.J. (2005). Persistent coliform contamination in Lechuguilla Cave pools - response: Barton and Pace discussion. Journal of Cave and Karst Studies, 67(2), 133-135.

15. Jackel, B., Cripps, R., Guntay, S. and Bruchertseifer, H. (2005). Development of semi-automated system for preparation of (188)Re aqueous solutions of high and reproducible activity concentrations. Applied Radiation and Isotopes, 63(3), 299-304.

16. Johnson, G.V. and Barton, L.L. (2007). Inhibition of iron deficiency stress response in cucumber by rare earth elements. Plant Physiology and Biochemistry, 45(5), 302-308.

17. Kim, H. and Nelson, M.A. (2005). Molecular and functional analyses of poi-2, a novel gene highly expressed in sexual and perithecial tissues of Neurospora crassa. Eukaryotic Cell, 4(5), 900-910.

18. Long, S.W. and Faguy, D.M. (2004). Anucleate and titan cell phenotypes caused by insertional inactivation of the structural maintenance of chromosomes (smc) gene in the archaeon Methanococcus voltae. Molecular Microbiology, 52(6), 1567-1577.

19. Lovato, T.L., Benjamin, A.R. and Cripps, R.M. (2005). Transcription of Myocyte enhancer factor-2 in adult Drosophila myoblasts is induced by the steroid hormone ecdysone. Developmental Biology, 288(2), 612-21.

20. Martinez, M.J., Roy, S., Archuletta, A.B., Wentzell, P.D., Anna-Arriola, S.S., Rodriguez, A.L., Aragon, A.D., Quinones, G.A., Allen, C. and Werner-Washburne, M. (2004). Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Molecular Biology of the Cell, 15(12), 5295-5305.

21. McPhee, M.V. and Turner, T.F. (2004). No genetic evidence for hybridization between Rio Grande sucker, Catostomus plebeius, and the introduced white sucker, Catostomus commersoni, in the Rio Grande. Environmental Biology of Fishes, 71(1), 85-93.

22. Moyer, G.R., Osborne, M.J. and Turner, T.F. (2005). Genetic and ecological dynamics of species replacement in an arid-land river system. Molecular Ecology, 14(4), 1263-73.

23. Moyer, G.R., Winemiller, K.O., McPhee, M.V. and Turner, T.F. (2005). Historical demography, selection, and coalescence of mitochondrial and nuclear genes in Prochilodus species of northern South America. Evolution, 59(3), 599-610.

24. Northup, D.E., Barns, S.M., Yu, L.E., Spilde, M.N., Schelble, R.T., Dano, K.E., Crossey, L.J., Connolly, C.A., Boston, P.J., Natvig, D.O. and Dahm, C.N. (2003). Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environmental Microbiology, 5(11), 1071-86.

25. Osborne, M., Benavides, M., Alo, D. and Turner, T. (2006). Genetic effects of hatchery propagation and rearing in the endangered Rio Grande silvery minnow, Hybognathus amarus. Reviews in Fisheries Science, 14(1-2), 127-138.

26. Osborne, M.J., Benavides, M.A. and Turner, T.F. (2005). Genetic heterogeneity among pelagic egg samples and variance in reproductive success in an endangered freshwater fish, Hybognathus amarus (Cyprinidae). Environmental Biology of Fishes, 73(4), 463-472.

27. Powell, A.J., Jacobson, D.J., Salter, L. and Natvig, D.O. (2003). Variation among natural isolates of Neurospora on small spatial scales. Mycologia, 95(5), 809-819.

28. Ryan, K., Hendren, J., Helander, L. and Cripps, R. (2007). The NK homeodomain transcription factor Tinman is a direct activator of seven-up in the Drosophila dorsal vessel. Developmental Biology, 302(2), 694-702.

29. Ryan, K.M., Hoshizaki, D.K. and Cripps, R.M. (2005). Homeotic selector genes control the patterning of seven-up expressing cells in the Drosophila dorsal vessel. Mechanisms of Development, 122(9), 1023-33.

30. Smythe, T.L. and Stricker, S.A. (2005). Germinal vesicle breakdown is not fully dependent on MAPK activation in maturing oocytes of marine nemertean worms. Molecular Reproduction and Development, 70(1), 91-102.

31. Spilde, M.N., Northup, D.E., Boston, P.J., Schelble, R.T., Dano, K.E., Crossey, L.J. and Dahm, C.N. (2005). Geomicrobiology of cave ferromanganese deposits: A field and laboratory investigation. Geomicrobiology Journal, 22(3-4), 99-116.

32. Stricker, S. (2006). Structural reorganizations of the endoplasmic reticulum during egg maturation and fertilization. Seminars in Cell and Developmental Biology, 17(2), 303-13.

33. Stricker, S. and Smythe, T. (2006). Differing mechanisms of cAMP- versus seawater-induced oocyte maturation in marine nemertean worms I. The roles of serine/threonine kinases and phosphatases. Molecular Reproduction and Development, 73(12), 1578-90.

34. Stricker, S. and Smythe, T. (2006). Differing mechanisms of cAMP- versus seawater-induced oocyte maturation in marine nemertean worms II. The roles of tyrosine kinases and phosphatases. Molecular Reproduction and Development, 73(12), 1564-77.

Last updated 11/03/2008


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