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.
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.
104. Davenport, M.P., Zhang, L., Shiver, J.W., Casmiro,
D.R., Ribeiro, R.M. and Perelson, A.S. (2006). Influence of peak viral
load on the extent of CD4+ T-cell depletion in simian HIV infection. Journal
of Acquired Immune Deficiency Syndromes, 41(3), 259-65.
105. De Boer, R.J., Ganusov, V.V., Milutinovic, D., Hodgkin,
P.D. and Perelson, A.S. (2006). Estimating lymphocyte division and death
rates from CFSE data. Bulletin of Mathematical Biology, 68(5),
1011-1031.
106. Deakin, J.E., Olp, J.J., Graves, J.A. and Miller,
R.D. (2006). Physical mapping of immunoglobulin loci IGH@, IGK@, and IGL@
in the opossum (Monodelphis domestica). Cytogenetic and Genome
Research, 114(1), 94H.
107. Deakin, J.E., Parra, Z.E., Graves, J.A.M. and Miller,
R.D. (2006). Physical mapping of T cell receptor loci (TRA@, TRB@, TRD@
and TRG@) in the opossum (Monodelphis domestica). Cytogenetic
and Genome Research, 112(3-4), 342K-U18.
108. Dixit, N.M. and Perelson, A.S. (2006). The metabolism,
pharmacokinetics, and mechanisms of antiviral activity of ribavirin against
hepatitis C virus. Cellular and Molecular Life Sciences, 63(7-8),
832-42.
109. Dragoo, J., Lackey, J., Moore, K., Lessa, E., Cook,
J. and Yates, T. (2006). Phylogeography of the deer mouse (Peromyscus
maniculatus) provides a predictive framework for research on hantaviruses.
Journal of Veneral Virology, 87(Pt 7), 1997-2003.
110. Esponda, F., Jia, H., Forrest, S. and Helman, P.
(2006). Protecting data privacy through hard-to-reverse negative databases.
Information Security Conference.
111. Garver-Apgar, C., Gangestad, S., Thornhill, R.,
Miller, R. and Olp, J. (2006). Major histocompatibility complex alleles,
sexual responsivity, and unfaithfulness in romantic couples. Psychological
Science, 17(10), 830-5.
112. Gerety, R., Spencer, S., Pienta, K. and Forrest,
S. (2006). Modeling somatic evolution in tumorigenesis. PLoS Computational
Biology, 2(8), e108.
113. Gilchrist, M.A. and Wagner, A. (2006). A model of
protein translation including codon bias, nonsense errors,and ribosome
recycling. Journal of Theoretical Biology, 239, 417-434.
114. Gillooly, J.F., Allen, A.P., Savage, V.M., Charnov,
E.L., West, G.B. and Brown, J.H. (2006). Response to Clarke and Fraser:
effects of temperature on metabolic rate. Functional Ecology,
20, 400-404.
115. Gouin, N., Deakin, J.E., Miska, K.B., Miller, R.D.,
Kammerer, C.M., Graves, J.A.M., VandeBerg, J.L. and Samollow, P.B. (2006).
Linkage mapping and physical localization of the major histocompatibility
complex region of the marsupial Monodelphis domestica. Cytogenetic
and Genome Research, 112(3-4), 277-285.
116. Gouin, N., Wright, A., Miska, K., Parra, Z., Samollow,
P., Baker, M. and Miller, R. (2006). Modo-UG, a marsupial nonclassical
MHC class I locus. Immunogenetics, 58(5-6), 96-406.
117. Hlavacek, W.S., Faeder, J.R., Blinov, M.L., Posner,
R.G., Hucka, M. and Fontana, W. (2006). Rules for modeling signal-transduction
systems. Science's Signal Transduction Knowledge Environment,
2006(334), re6.
118. Ingerslev, H.C., Cunningham, C. and Wergeland, H.I.
(2006). Cloning and expression of TNF-alpha, IL-1 beta and COX-2 in an
anadromous and landlocked strain of Atlantic salmon (Salmo salar L.)
during the smolting period. Fish & Shellfish Immunology,
20(4), 450-461.
119. Inoue, H., Stefanovic, D. and Forrest, S. (2006).
On the prediction of Java object lifetimes. IEEE Transactions on Computers,
55(7), 880-892.
120. Jiang, Y., Loker, E. and Zhang, S. (2006). In vivo
and in vitro knockdown of FREP2 gene expression in the snail Biomphalaria
glabrata using RNA interference. Developmental and Comparative
Immunology. 30(10), 855-866.
121. Kim, H. and Perelson, A.S. (2006). Dynamic characteristics
of HIV-1 reservoirs. Current Opinion on HIV and AIDS, 1, 152-156.
122. Kim, H. and Perelson, A.S. (2006). Viral and latent
reservoir persistence in HIV-1 infected patients on therapy. PLoS
Computational Biology, 2(10, e135), 1235-1247.
123. Kodric-Brown, A., Sibly, R.M. and Brown, J.H. (2006).
The allometry of ornaments and weapons. Proceedings of the National Academy
of Sciences, USA, 103(23), 8733-8738.
124. Lieb, B., Dimitrova, K., Kang, H., Braun, S., Gebauer,
W., Martin, A., Hanelt, B., Saenz, S., Adema, C. and Markl, J. (2006).
Red blood with blue-blood ancestry: intriguing structure of a snail hemoglobin.
Proceedings of the National Academy of Sciences, USA, 103(32), 12011-12016.
125. Loker, E. and Brant, S. (2006). Diversification,
dioecy and dimorphism in schistosomes. Trends in Parasitology,
22(11), 521-528.
126. Lorenzen, N., Evensen, O., Cunningham, C., Scapigliati,
G., Alvarez, M.C., Roch, P., Wiegertjes, G., Buchmann, K. and Adams, A.
(2006). Monitoring of the immune system in fish and shellfish. Bulletin
of the European Association of Fish Pathologists, 26(1), 48-49.
127. Martiny, J.B., Bohannan, B.J., Brown, J.H (2006).
Microbial biogeography: putting microorganisms on the map. Nature
Reviews Microbiology, 4(2), 102-12.
128. Mu, F., Unkefer, P.J., Unkefer, C.J. and Hlavacek,
W.S. (2006). Prediction of oxidoreductase-catalyzed reactions based on
atomic properties of metabolites. Bioinformatics, 22, 3082-3088.
129. Parra, Z.E., Arnold, T., Nowak, M.A., Hellman, L.
and Miller, R.D. (2006). TCR gamma chain diversity in the spleen of the
duckbill platypus (Ornithorhynchus anatinus). Developmental
and Comparative Immunology, 30(8), 699-710.
130. Perelson, A.S., Bragg, J.G. and Wiegel, F.W. (2006).
The complexity of the immune system: Scaling laws. In T.S. Deisboeck and
J.Y. Kresh (Eds.) Complex Systems Science in Biomedicine. New York,NY:
Kluwer: 451-459.
131. Powers, K.A., Ribeiro, R.M., Patel, K., Pianko,
S., Nyberg, L., Pockros, P., Conrad, A.J., McHutchison, J. and Perelson,
A.S. (2006). Kinetics of hepatitis C virus reinfection after liver transplantation.
Liver Transplantation, 12(2), 207-216.
132. Qiu, S. and Lane, T. (2006). RNA string kernels
for RNAi off-target evaluation. International Journal of Bioinformatics
Research and Applications, 2(2), 132-146.
133. Qiu, S.B. and Lane, T. (2006). Phase transitions
in gene knockdown networks of transitive RNAi Computational Science. Proceedings
International Conference on Computational Science (pp. 895-903) United
Kingdom.
134. Qiu, S.B., Yang, C.D. and Lane, T. (2006). Efficient
target detection for RNA interference. Proceedings of the First international
Conference on Advances in Grid and Pervasive Computing, (pp. 22-31). Taichun
City, Taiwan.
135. Ribeiro, R.M., Dixit, N.M. and Perelson, A.S. (2006).
Modelling the in vivo growth rate of HIV: implications for vaccination.
In L. A. McNamara (Ed.), Multidisciplinary Approaches to Theory in Medicine
(231-246). Amsterdam: Elsevier.
136. Ribeiro, R.M., Hazenberg, M.D., Perelson, A.S. and
Davenport, M.P. (2006). Naive and memory cell turnover as drivers of CCR5
to CXCR4-tropism switch in HIV-1: Implications for therapy. Journal
of Virology, 80(2), 802-809.
137. Ribeiro, R.M., Powers, K.A., Talal, A.H. and Perelson,
A.S. (2006). Modeling the viral dynamics of HCV in patients treated with
pegylated interferon alpha 2b. In E. R. Schiff (Ed.), Framing the Knowledge
of Viral Hepatitis (pp. 407-420). College Park, GA: IHL Press.
138. Roy, S., Lane, T., Allen, C., Aragon, A. and M,
W.-W. (2006). A hidden-state Markov model for cell population deconvolution.
Journal of Computational Biology, 13(10), 1749-74.
139. Savage, V., E. White, M.E. Moses, S. Ernest, B.J.
Enquist and E. L. Charnov (2006). Technical comment on the illusion of
life history invariants. Science, 312, 5771: 198. DOI: 10.1126/science.1123679.
140. Siddle, H.V., Deakin, J.E., Baker, M.L., Miller,
R.D. and Belov, K. (2006). Isolation of major histocompatibility complex
Class I genes from the tammar wallaby (Macropus eugenii). Immunogenetics,
58(5-6), 487-493.
141. Spencer, S.L., Gerety, R.A., Pienta, K.J. and Forrest,
S. (2006). Modeling somatic evolution in tumorigenesis. PLoS Computational
Biology, 2(8), 939-947.
142. Talal, A.H., Ribeiro, R.M., Powers, K.A., Grace,
M., Cullen, C., Hussain, M., Markatou, M. and Perelson, A.S. (2006). Pharmacodynamics
of PEG-IFN alpha differentiate HIV/HCV coinfected sustained virological
responders from nonresponders. Hepatology, 43(5), 943-53.
143. Vitkup, D., Kharchenko, P. and Wagner, A. (2006).
Influence of metabolic network structure and function on enzyme evolution.
Genome Biology, 7(5), R39.
144 . Wagner, A. (2006). Cooperation is Fleeting in the
World of Transposable Elements. PLoS Computational Biology, 2(12),
e162.
145. Wagner, A. (2006). Periodic extinctions of transposable
elements in bacterial lineages: Evidence from intragenomic variation in
multiple genomes. Molecular Biology and Evolution, 23, 723-733.
146. Wang, Z., Metcalf, B., Ribeiro, R.M., McClure, H.
and Kaur, A. (2006). Th-1-type cytotoxic CD8+ T-lymphocyte responses to
simian immunodeficiency virus (SIV) are a consistent feature of natural
SIV infection in sooty mangabeys. Journal of Virology, 80(6),
2771-2783.
147. Warrender, C., Forrest, S. and Koster, F. (2006).
Modeling intercellular interactions in early Mycobacterium infection.
Bulletin of Mathematical Biology, 68(8), 2233-2261.
148. Wu, H., Huang, Y., Acosta, E.P., Park, J.G., S.,
Y., Rosenkranz, S.L., Kuritzkes, D.R., Eron, J.J., Perelson, A.S. and
Gerber, J.G. (2006). Pharmacodynamics of antiretroviral agents in HIV-1
infected patients: using viral dynamic models that incorporate drug susceptibility
and adherence. Journal of Pharmacokinetics and Pharmacodynamics,
33(4), 399-419.
149. Wu, H., Huang, Y., Dykes, C., Liu, D., Ma, J., Perelson,
A.S. and Demeter, L.M. (2006). Modeling and estimation of replication
fitness of human immunodeficiency virus type 1 in vitro experiments by
using a growth competition assay. Journal of Virology, 80, 2380-2389.
150. Yang, J., Bruno, W.J., Hlavacek, W.S. and Pearson,
J.E. (2006). On imposing detailed balance in complex reaction mechanisms.
Biophysical Journal, 91, 1136-1141.
2005
151. Allen, A.P., Gillooly, J.F. and Brown, J.H. (2005).
Linking the global carbon cycle to individual metabolism. Functional
Ecology, 19, 202-213.
152. Arron, S.T., Ribeiro, R.M., Gettie, A., Blanchard,
J., Yu, J., Perelson, A.S., Ho, D.D. and L., Z. (2005). Impact of thymectomy
on the peripheral T-cell pool in rhesus macaques before and after infection
with simian immunodeficiency virus. European Journal of Immunology,
35, 46-55.
153. Baker, M.L., Belov, K. and Miller, R.D. (2005).
Unusually similar patterns of antibody V segment diversity in distantly
related marsupials. Journal of Immunology, 174(9), 5665-5671.
154. Baker, M.L., Osterman, A.K. and Brumburgh, S. (2005).
Divergent T-cell receptor delta chains from marsupials. Immunogenetics,
57(9), 665-673.
155. Barrantes, G., Ackley, D., Forrest, S. and Stefanovic,
D. (2005). Randomized Instruction Set Randomization. ACM Transactions
on Information Systems Security, (TISSEC) 8(1), 3-40.
156. Belov, K., Deakin, J.E., Papenfuss, A.T., Graves,
J.A.M. and Miller, R.D. (2005). The immune supercomplex: Insights from
the opossum MHC. Tissue Antigens, 66(5), 359-359.
157. Bergthorsson, U. and Roth, J.R. (2005). Natural
isolates of Salmonella enterica serovar Dublin carry a single nadA missense
mutation. Journal of Bacteriology, 187(1), 400-403.
158. Blinov, M.L., Faeder, J.R., Yang, J., Goldstein,
B. and Hlavacek, W.S. (2005). `On-the-fly' or `generate-first' modeling?
Nature Biotechnology, 23, 1344-1345.
159. Blinov, M.L., Yang, J., Faeder, J.R. and Hlavacek,
W.S. (2005). Graph theory for rule-based modeling of biochemical networks.
BioCONCUR 2005. San Francisco, California.
160. Brant, S.V. and Loker, E.S. (2005). Can specialized
pathogens colonize distantly related hosts? Schistosome evolution as a
case study. PLoS Pathogens, 1(3), 167-69.
161. Brown, J.H. and Sax, D.F. (2005). Biological invasions
and scientific objectivity: Reply to Cassey et al. (2005). Austral
Ecology 30: 481-483.
162. Brown, J.H., West, G.B. and Enquist, B.J. (2005).
Yes, West, Brown, and Enquist's model of allometric scaling is both mathematically
correct and biologically relevant. Functional Ecology, 19, 735-738.
163. Burge, J. and Lane, T. (2005). Learning class-discriminative
dynamic Bayesian networks. Proceedings of the 22nd International Machine
Learning Conference, ACM Press.
164. Chao, D.L., Balthrop, J. and Forrest, S. (2005).
Adaptive radio: achieving consensus using negative preferences. 2005 International
ACM SIGGROUP Conference on Supporting Group Work. Sanibel Island, FL:
ACM Press.
165. Chao, D.L., Davenport, M.P., Forrest, S. and Perelson,
A.S. (2005). The effects of thymic selection on the range of T cell cross-reactivity.
European Journal of Immunology, 35(12), 3452-3459.
166. Conant, G.C. and Wagner, A. (2005). The rarity of
gene shuffling in conserved genes. Genome Biology, 6(6), R50.
167. Dahari, H., Major, M., Zhang, X., Mihalik, K., Rice,
C.M., Perelson, A.S., Feinstone, S.M. and Neumann, A.U. (2005). Mathematical
modeling of primary hepatitis C infection: Non-cytolytic clearance and
early blockage of virion production. Gastroenterology, 128, 1056-1066.
168. Davenport, M.P., Zhang, L., Bagchi, A., Fridman,
A., Fu, T.-M., Schleif, W., Shiver, J.W., Ribeiro, R.M. and Perelson,
A.S. (2005). High potency HIV vaccination leads to delayed and reduced
CD8+ T cell expansion, but nevertheless improved viral control. Journal
of Virology, 79, 10059-10062.
169. De Boer, R.J. and Perelson, A.S. (2005). Estimating
division and death rates from CSFE data. Journal of Computational
and Applied Mathematics, 184, 140-164.
170. Di Mascio, M., Percus, P.K., Percus, O.E., Markowitz,
M., Ho, D.D. and Perelson, A.S. (2005). Duration of an intermittent episode
of viremia. Bulletin of Mathematical Biology, 67, 885-900.
171. Dixit, N.M. and Perelson, A.S. (2005). HIV dynamics
with multiple infections of target cells. Proceedings of the National
Academy of Sciences, USA, 102, 8198-8203.
172. Dixit, N.M. and Perelson, A.S. (2005). Influence
of drug pharmacokinetics on HIV pathogenesis and therapy. In H. Wu (Ed.)
Deterministic and Stochastic Models of AIDS and HIV with Intervention
(pp. 287-311). Singapore: World Scientific Press.
173. Esponda, F., Ackley, E.S., Forrest, S. and Helman,
P. (2005). Online negative databases. Journal of Unconventional Computing,
1(3), 201-220.
174. Faeder, J.R., Blinov, M.L., Goldstein, B. and Hlavacek,
W.S. (2005). Combinatorial complexity and dynamical restriction of network
flows in signal transduction. IEE Proceedings - Systems Biology,
2, 5-15.
175. Faeder, J.R., Blinov, M.L., Goldstein, B. and Hlavacek,
W.S. (2005). Rule-based modeling of biochemical networks. Complexity,
10, 22-41.
176. Faeder, J.R., Blinov, M.L. and Hlavacek, W.S. (2005).
Graphical rule-based representation of signal-transduction networks. Proceedings
of theThe 20th ACM Symposium on Applied Computing. Santa Fe, New Mexico:
ACM Press.
177. Forrest, S., Balthrop, J., Glickman, M. and Ackley,
D. (2005). Computation in the Wild. In K. Park and W. Willins (Eds.) The
Internet as a Large-Scale Complex System. New York: Oxford University
Press.
178. Gillooly, J.F., Allen, A.P., Brown, J.H., Elser,
J.J., del Rio, C.M., Savage, V.M., West, G.B., Woodruff, W.H. and Woods,
H.A. (2005). The metabolic basis of whole-organism RNA and phosphorus
content. Proceedings of the National Academy of Sciences, USA,102, 11923-11927.
179. Gillooly, J.F., Allen, A.P., West, G.B. and Brown,
J.H. (2005). The rate of DNA evolution: Effects of body size and temperature
on the molecular clock. Proceedings of the National Academy of Sciences,
USA, 2(1), 140-145.
180. Glickman, M., Balthrop, J. and Forrest, S. (2005).
A machine learning evaluation of an artificial immune system. Evolutionary
Computation, 13(2), 179-212.
181. Friggens, M.M. and Brown, J.H. (2005). Niche partitioning
in the cestode communities of two elasmobranchs. Oikos, 108,
76-84.
182. Goheen, J.R., White, E.P., Ernest, S.K.M. and Brown,
J.H. (2005). Intra-guild compensation regulates species richness in desert
rodents. Ecology, 86(3), 567-573.
183. Grose, J.H., Bergthorsson, U. and Roth, J.R. (2005).
Regulation of NAD synthesis by the trifunctional NadR protein of Salmonella
enterica. Journal of Bacteriology, 187(8), 2774-2782.
184. Grose, J.H., Bergthorsson, U., Xu, Y.P., Sterneckert,
J., Khodaverdian, B. and Roth, J.R. (2005). Assimilation of nicotinamide
mononucleotide requires periplasmic AphA phosphatase in Salmonella
enterica. Journal of Bacteriology, 187(13), 4521-4530.
185. Hertel, L.A., Adema, C.M. and Loker, E.S. (2005).
Differential expression of FREP genes in two strains of Biomphalaria
glabrata following exposure to the digenetic trematodes Schistosoma
mansoni and Echinostoma paraensei. Developmental and
Comparative Immunology, 29(4), 295-303.
187. Ingham, K. and Forrest, S. (2005). Network firewalls.
In V. Sreeharirao (Ed.) Enhancing Computer Security with Smart Technology
(pp. 9-35). CRC Press.
188. Inoue, H. and Forrest, S. (2005). Inferring Java
security policies through dynamic sandboxing. International Conference
on Programming Languages and Compilers.
189. Johansson, J., Salazar, J.N., Aveskogh, M., Munday,
B., Miller, R.D. and Hellman, L. (2005). High variability in complementarity-determining
regions compensates for a low number of V gene families in the lambda
light chain locus of the platypus. European Journal of Immunology,
35(10), 3008-3019.
190. Jones, L.E. and Perelson, A.S. (2005). Opportunistic
infection as a cause of transient viremia in chronically infected HIV
patients under treatment with HAART. Bulletin of Mathematical Biology,
67, 1227-1251.
191. Jung, Y., Nowak, T.S., Zhang, S.M., Hertel, L.A.,
Loker, E.S. and Adema, C.M. (2005). Manganese superoxide dismutase from
Biomphalaria glabrata. Journal of Invertebrate Pathology,
90 (1), 59-63.
192. Lane, T. and Wilson, A. (2005). Toward a topological
theory of relational reinforcement learning for navigation tasks. Proceedings
of the Eighteenth International Florida Artificial Intelligence Research
Society Conference (FLAIRS-2005).
193. Layden-Almer, J.E., Kuiken, C., Ribeiro, R.M., Kunstman,
K.J., Perelson, A.S., Layden, T.J. and Wolinsky, S.M. (2005). HCV NS5A
1a pre-treatment sequence variation and viral kinetics in African Americans
and Caucasians. Journal of Infectious Diseases, 192, 1078-1087.
194. Lotfy, W.M., DeJong, R.J., Abdel-Kader, A. and Loker,
E.S. (2005). A molecular survey of Biomphalaria in Egypt: Is B-glabrata
present. American Journal of Tropical Medicine and Hygiene,
73(1), 131-139.
195. Lotfy, W.M., DeJong, R.J., Black, B.S. and Loker,
E.S. (2005). Specific identification of Egyptian Biomphalaria species
and possible hybrids using the polymerase chain reaction based on nuclear
and mitochondrial loci. Molecular and Cellular Probes,19(1),
21-25.
196. MacDonald, T.T. and Miller, R.D. (2005). Phylogeny
of the gut associated lymphoid tissue. In B. J. Mestecky, M. E. Lamm,
L. Mayer, J. R. McGhee and W. Strober (Eds.), Mucosal Immunology,
3rd Ed.(323-334). London: Academic Press, Elsevier.
197. Morgan, J.A., Dejong, R.J., Adeoye, G.O., Ansa,
E.D., Barbosa, C.S. Brémond, P., Cesari, I.M., Charbonnel, N.,
Corrêa, L.R., Coulibaly, G., D’Andrea, P.S., De Souza, C.
P., Doenhoff, M.J., File, S., Idris, M.A., Incani, R.N., Jarne, P., Karanja,
D.M., Kazibwe, F. Kpikpi, J., Lwambo, N.J., Mabaye, A., Magalhães,
L.A., Makundi, A., Moné, H., Mouahid, G., Muchemi, G.M., Mungai,
B.N., Séne, M., Southgate, V., Tchuenté, L.A., Théron,
A., Yousif, F., Zanotti-Magalhães, E.M., Mkoji, G.M., and Loker,
E.S. (2005). Origin and diversification of the human parasite Schistosoma
mansoni.Molecular Ecology, 14(12), 3889-3902.
198. Murray, J.D. and Perelson, A.S. (2005). Human immunodeficiency
virus: Quasispecies and drug resistance. Multiscale Modeling and Simulation,
3, 300-311.
199. Nowak, T.S. and Loker, E.S. (2005). Echinostoma
paraensei: differential gene transcription in the sporocyst stage.
Experimental Parasitology, 109(2), 94-105.
200. Papenfuss, A.T., Belov, K., Deakin, J.E., Speed,
T.P., Graves, J.A.M. and Miller, R.D. (2005). Annotation of the opossum
major histocompatibility complex and analysis of conserved non-coding
regions . Tissue Antigens, 66(5), 508-508.
201. Perelson, A.S. and Ribeiro, R.M. (2005). Mutagenic
effects of ribavirin in vivo. Journal of Hepatology, 43, 553-555.
202. Pointier, J.P., DeJong, R.J., Tchuem Tchuente, L.A.,
Kristensen, T.K. and Loker, E.S. (2005). A neotropical snail host of Schistosoma
mansoni introduced into Africa and consequences for the schistosomiasis
transmission Biomphalaria tenagophila in Kinshasa (Democratic
Republic of Congo). Acta tropica, 93(2), 191-199.
203. Qiu, S., Adema, C.M. and Lane, T. (2005). A computational
study of off-target effects of RNA interference, Nucleic Acids Research,
33(6), 1834-1847.
204. Qiu, S. and Lane, T. (2005). Parallel computation
of RBF kernels for support vector classifiers. Proceedings of the 2005
SIAM Conference on Data Mining (SIAM-DM 2005), (pp. 334-345). Newport
Beach, CA.
205. Qiu, S. and Lane, T. (2007). Implications of phase
transitions in knockdown networks of transitive RNAi. IEEE Transactions
on Nanobioscience, 6(1), 68-76.
206. Qiu, S.B. and Lane, T. (2005). String kernels of
imperfect matches for off-target detection in RNA interference Computational
Science. ICCS, 2005, Pt 2.
207. Perelson, A.S., Herrmann, E., Micol, F. and Zeuzem,
S. (2005). New kinetic models for the hepatitis C virus. Spiers, C., van
Nimwegen, E., Bolton, D.L., Zavolan, M., Duvall, M., Angleman, S., Siegel,
R., Perelson, A.S. and Lenardo, M.J. (2005). Analysis of human immunodeficiency
virus cytopathicity using a new method for quantitating viral dynamics
in cell culture. Journal of Virology, 79, 4025-4032.
208. Wagner, A. (2005). Circuit topology and the evolution
of robustness in two-gene circadian oscillators. Proceedings of the National
Academy of Sciences, USA, 102, 11775-11780.
209. Wagner, A. (2005). Distributed robustness versus
redundancy as causes of mutational robustness. Bioassays, 27,
176-188.
209. Wagner, A. (2005). Energy constraints on the evolution
of gene expression. Molecular Biology and Evolution, 22, 1365-1374.
210. Wagner, A. (2005). Lessons from a genetic network
about the evolution of dominance. In V. R. Georgetown (Ed.), The biology
of genetic dominance. Texas: Landes Bioscience.
211. Wagner, A. (2005). Robustness, neutrality, and evolvability.
FEBS Letters, 579, 1772-1778.
212. Wagner, A. and Wright, J. (2005). Compactness and
cycles in signal transduction and transcriptional regulation networks:
a signature of natural selection? Advances in Complex Systems,
7, 419-432.
213. Wall, M.E., Dunlop, M.J. and Hlavacek, W.S. (2005).
Multiple functions of a feed-forward-loop gene circuit. Journal of
Molecular Biology, 349, 501-514.
214. West, G.B. and Brown, J.H. (2005). The origin of
allometric scaling laws in biology from genomes to ecosystems: towards
a quantitative unifying theory of biological structure and organization.
Journal of Experimental Biology, 208, 1575-1592.
215. White, E.P. and Brown, J.H. (2005). The Template:
Patterns and Processes of Spatial Variation. In J. Lovett, B. Turner and
T. Weathers (Eds.), Ecosystem Function in Heterogeneos Landscapes. New
York:Springer.
216. Wilson, W.D., Johnson, P.T.J., Sutherland, D.R.,
Mone, H. and Loker, E.S. (2005). A molecular phylogenetic study of the
genus Ribeiroia (Digenea): Trematodes known to cause limb malformations
in amphibians Journal of Parasitology, 91(5), 1040-1045.
217. Wu, H., Huang, Y., Acosta, E.P., Rosenkranz, S.L.,
Kuritzkes, D.R., Eron, J.J., Perelson, A.S. and Gerber, J.G. (2005). Modeling
long-term HIV dynamics and antiretroviral response: Effects of drug potency,
pharmacokinetics, adherence, and drug resistance. Journal of Acquired
Immune Deficiency Syndromes, 39, 272-283.
218. Wu, J.T., Wein, L.M. and Perelson, A.S. (2005).
Optimization of influenza vaccine selection. Operations Research,
53, 456-476.
219. Zhao, W.Z., Fanning, L. and Lane, T. (2005). RNA
interference-based gene family knockdown via computational set covering.
Artificial Intelligence in Medicine, 35(1-2), 61-73.
220. Zhao, W.Z., Fanning, M.L. and Lane, T. (2005). Efficient
RNAi-based gene family knockdown via set cover optimization. Artificial
Intelligence in Medicine, 35(1-2), 61-73.
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.
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.