Biosciences Division

2004 Publications

Allain, L. R., D. N. Stratis-Cullum, and T. Vo-Dinh, "Investigation of microfabrication of biological sample arrays using piezoelectric and bubble-jet printing technologies," Anal. Chim. Acta 518(1-2): 77-85 (2004).

Armbrust, E. V., J. A. Berges, C. Bowler, B. R. Green, D. Martinez, N. H. Putnam, S. G. Zhou, A. E. Allen, K. E. Apt, M. Bechner, M. A. Brzezinski, B. K. Chaal, A. Chiovitti, A. K. Davis, M. S. Memarest, J. C. Detter, T. Glavina, D. Goodstein, M. Z. Hadi, U. Hellsten, M. Hildebrand, B. D. Jenkins, J. Jurka, V. V. Kapitonov, N. Kroger, W. W. Y. Lau, T. W. Lane, F. W. Larimer, J. C. Lippmeier, S. Lucas, M. Medina, A. Montsant, M. Obornik, M. S. Parker, B. Palenik, G. J. Pazour, P. M. Richardson, T. A. Rynearson, M. A. Saito, D. C. Schwartz, K. Thamatrakoin, K. Valentin, A. Vardi, F. P. Wilkerson, and D. S. Rokhsar, "The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism," Science 306(5693): 79-86 (2004).

Askari, M.D.F. and T. Vo-Dinh, "Implication of mitochondrial involvement in apoptotic activity of fragile histidine triad gene: Application of synchronous luminescence spectroscopy," Biopolymers 73(4): 510-523 (2004).

Austin, C. P., J. F. Battey, A. Bradley, M. Bucan, M. Capecchi, F. S. Collins, W. F. Dove, G. Duyk, S. Dymecki, J. T. Eppig, F. B. Grieder, N. Heintz, G. Hicks, T. R. Insel, A. Joyner, B. H. Koller, K. C. K. Lloyd, T. Magnuson, M. W. Moore, A. Nagy, J. D. Pollock, A. D. Roses, A. T. Sands, B. Seed, W. C. Skarnes, J. Snoddy, P. Soriano, D. J. Stewart, F. Stewart, B. Stillman, H. Varmus, L. Varticovski, I. M. Verma, T. F. Vogt, H. von Melchner, J. Witkowski, R. P. Woychik, W. Wurst, G. D. Yancopoulos, S. G. Young, and B. Zambrowicz, "The knockout mouse project," Nature Genetics 36(9): 921-924 (2004).

Baker, E. J., L. Galloway, B. Jackson, D. Schmoyer, and J. Snoddy, "MuTrack: a genome analysis system for large-scale mutagenesis in the mouse," BMC Bioinformatics 5: Art. 11 (2004).

Barton, J. W., T. Kuritz, L. E. O'Connor, C. Y. Ma, M. P. Maskarinec, and B. H. Davison, "Reductive transformation of methyl parathion by the cyanobacterium Anabaena sp. Strain PCC7120," Appl. Microbial. Biotechnol. 65: 330-335 (2004).

Bast, C., G. Rusch, D. Krewski, and K. Bakshi, "Acute Exposure Guideline Levels (AGELs) for Uranium Hexafluoride," The Toxicologist 78(15), 2004.

Borole, A. P., C. L. Cheng, and B. H. Davison, "Substrate Desolvation as a Governing Factor in Enzymatic Transformations of PAHs in Aqueous-Acetonitrile Mixtures," Biotechnol. Prog., 20(4), 1251-1254 (2004).

Borole, A., S. Dai, C. L. Cheng, M. Rodriguez, and B. H. Davison, "Performance of chloroperoxidase stabilization in mesoporous sol-gel glass using in situ glucose oxidase peroxide generation," Appl. Biochem. & Biotech. 113-116: 273-285 (2004).

Bult, C., W. A. Kibbe, J. Snoddy, M. Vitaterna, D. Swanson, S. Pretel, Y. X. Li, M. M. Hohman, E. Rinchik, J. S. Takahashi, W. N. Frankel, and D. Goldowitz, "A genome end-game: understanding gene function in the nervous system," Nature Neuroscience 7(5): 484-485 (2004).

Bunick, C. G., M. R. Nelson, S. Mangahas, M. J. Hunter, J. H. Sheehan, L. S. Mizoue, G. J. Bunick, and W. J. Chazin, "Designing sequence to control protein function in an EF-hand protein," J. Amer. Chem. Soc. 126(19): 5990-5998 (2004).

Chain, P. S. G., E. Carniel, F. W. Larimer, J. Lamerdin, P. O. Stoutland, W. M. Regala, A. M. Georgescu, L. M. Vergez, M. L. Land, V. L. Motin, R. R. Brubaker, J. Fowler, J. Hinnebusch, M. Marceau, C. Medigue, M. Simonet, V. Chenal-Francisque, B. Souza, D. Dacheux, J. M. Elliott, A. Derbise, L. J. Hauser, and E. Garcia, "Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis," PNAS 101(38): 13826-13831 (2004).

Chick, W. S. H., S. E. Mentzer, D. A. Carpenter, E. M. Rinchik, and Y. You, "Modification of an existing chromosomal inversion to engineer a balancer for mouse chromosome 15," Genetics 167(2): 889-895 (2004).

Churchill, G., D. C. Airey, H. Allayee, J. M. Angel, A. D. Attie, J. Beatty, W. D. Beavis, J. K. Belknap, B. Bennett, W. Berrettini, A. Bleich, M. Bogue, K. W. Broman, K. J. Buck, E. Buckler, M. Bermeister, E. J. Chesler, J. M. Cheverud, S. Clapcote, M. N> Cook, R. D. Cox, J. C. Crabbe, W. E. Crusio, A. Darvasi, C. F. Deschnepper, R. W. Doerge, C. R. Farber, J. Forejt, D. Gaile, S. J. Garlow, H. Geiger, H. Gershenfeld, T. Gordon, J. Gu, W. K. Gu, G. de Haan, N. L. Hayes, C. Heller, H. Himmelbauer, R. Hitzemann, K. Hunter, H. C. Hsu, F. A. Iraqi, B. Ivandic, H. J. Jacob, R. C. Jansen, K. J. Jjepsen, D. K. Johnson, T. E. Johnson, G. Kempermann, C. Kendziorski, M. Kotb, R. F. Kooy, B. Llamas, F. Lammert, J. M. Lassalle, P. R. Lowenstein, L. Lu, A. Lusiss, K. F., Manly, R. Marcucio, D. Matthews, J. F. Medrano, D. R. Miller, G. Mittleman, B. A. Mock, J. S. Mogil, X. Montagutelli, G. Morahan, D. G. Morris, R. Mott, J. H. Nadeau, H. Nagase, R. S. Nowakowski, B. F. O'Hara, A. V. Osadchuk, G. P. Page, B. Paigen, K. Paigen, A. A. Palmer, H. J. Pan, L. Peltonen-Palotie, J. Peirce, D. Pomp, M. Pravenec, D. R. Prows, Z. H. Qi, R. H,. Reeves, J. Roder, G. D. Rosen, E. E. Schadt, L. C. Schalkwyk, Z. Seltzer, K. Shimomure, S. M. Shou, M. J. Sillanpaa, L. D. Siracusa, H. W. Snoeck, J. L. Spearow, K. Svenson, L. M. Taratine, D. Threadgill, La. A. Toth, W. Valdar, F. P. M. de Villena, C. Warden, S. Whatley, R. W. Williams, T. Wiltshire, N. J. Yi, D. B. Zhang, and F. Zou, "The Collaborative Cross, a community resource for the genetic analysis of complex traits," Nature Genetics 36(11): 1133-1137 (2004).

Coffman, E. A., A. V. Melechko, D. P. Allison, M. L. Simpson, and M. J. Doktycz, "Surface patterning of silica nanostructures using bio-inspired templates and directed synthesis," Langmuir 20(20): 8431-8436 (2004).

Culha, M., D. L. Stokes, G. D. Griffin, and T. Vo-Dinh, "Screening for the breast cancer gene (BRCA1) using a biochip systems and molecular beacon probes immobilized on solid surfaces," J. Biomed. Optics 9(3): 439-443 (2004).

Culha, M., D. L. Stokes, G. D. Griffin, and T. Vo-Dinh, "Application of a miniature biochip using the molecular beacon probe in breast cancer gene BRCA1 detection," Biosensors & Bioelectronics 19(9): 1007-1012 (2004).

Davison, B. H., N. P. Nghiem, G. L. Richardson, "Succinic acid adsorption from fermentation broth and regeneration," Appl. Biochem. & Biotech. 113-116: 653-669 (2004).

DeNardo, G. L., S. J. Kennel, J. A. Siegel, and S. J. DeNardo, "Radiometals as payloads for radioimmunotherapy for lymphoma, "Clinical Lymphoma 5:S5-S10 Suppl.1 (2004).

Dhar, M. S., C. S. Sommardahl, T. Kirkland, S. Nelson, R. Donnell, D. K. Johnson, L. W. Castellani, "Mice heterozygous for Atp10c, a putative amphipath, represent a novel model of obesity and type 2 diabetes," J. Nutrition 134(4): 799-805 (2004).

Dhar, M. S., L. J. Hauser, R. D. Nicholis, D. K. Johnson, "Physical mapping of the pink-eyed dilution complex in mouse chromosome 7 shows that Atp10c is the only transcript between Gabrb3 and Ube3a," DNA Sequence 15(4): 306-309 (2004).

Doktycz, M. J., J. E. Johnson, and M. J. Cornett, "Hybrid valve structure for high throughput, low volume liquid handling applications," J. Assoc. Lab. Auto. 9(4): 250-256 (2004).

Elso, C. M., X. C. Lu, C. T. Culiat, J. C. Rutledge, N. L. A. Cacheiro, W. M. Generoso, L. J. Stubbs, "Heightened susceptibility to chronic gastritis, hyperphasia and metaplasia in Kcnq1 mutant mice," Human Molecular Genetics 13(220: 2813-2821 (2004).

Erdmann, N., Y. Liu, and L. Harrington, "Distinct dosage requirements for the maintenance of long and short telomeres in mTert heterozygous mice," Proc. Natl. Acad. Sci. U.S.A. 101(16): 6080-6085 (2004).

Farahi, R. H., A. Passian, T. L. Ferrell, and T. Thundat, "Microfluidic manipulation via Marangoni forces," Applied Physics Letters 85(18): 4237-4239 (2004).

Finkelstein, M. and B. H. Davison, "Introduction to the proceedings of the twenty-fifth symposium on biotechnology for fuels and chemicals," Appl. Biochem. & Biotech. 113-16: iii-viii (2004).

Fletcher, B. L., E. D. Hullander, A. V. Melechko, T. E. McKnight, K. L. Klein, D. K. Hensley, J. L. Morrell, M. L. Simpson, and M. J. Doktycz, "Microarrays of biomimetic cells formed by the controlled synthesis of carbon nanofiber membranes," Nano Letters 4(10): 1809-1814 (2004).

Gilbert, E. S. , N. A. Koshurnikova, M. E. Sokolnikov, N. S. Shilnikova, D. L. Preston, E. Ron, P. V. Okatenko, V. F. Khokhryakov, E. K. Vasilenko, S. Miller, K. Eckerman, and S. A. Romanov, "Lung cancer in Mayak workers," Radiation Research 162(5): 505-516 (2004).

Gupta, V., C. B. Peterson, L. T. Dice, T. Uchiki, J. Racca, J. T. Guo, Ying Xu, R. Hettich, X. L. Zhao, R. Rothstein, and C. G. Dealwis, "Sm11p is a dimmer in solution: Characterization of denaturation and of recombinant Sm11p," Biochem. 43(26): 8568-8578 (2004).

Hamre, K. M., D. B. Matthews, E. Rinchik, E. Chesler, D. Goldowitz, and G. Mittleman, "Behavioral responses to ethanol or cocaine, including locomotor activation and anxiolytic response, in ENU-mutagenized mice," Alcoh.-Clin. & Exper. Res. 28(5): 90A-90A Suppl. S (2004).

Hanson, B. L., P. Langan, A. K. Katz, X. M. Li, J. M. Harp, J. P. Glusker, B. P. Schoenborn, and G. J. Bunick, "A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase," Acta Crystal. Sec. D - Biol. Crystal. 60: 241-249 Part 2 (2004).

Hanson, B. L., C. Alexander, J. M. Harp, and G. J. Bunick, "Preparation and crystallization of nucleosome core particle," Meth. Enzymology 375: PT A, 44-62 (2004).

Harp, J. M., B. L. Hanson, and G. J. Bunick, "The core particle of the nucleosome," New Compreh. Biochem. 39: 13-44 (2004).

Hendrickson, E. L., R. Haul, Y Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J. A. Dodsworth, W. Gillett, D. E. Graham, M. Hackett, A. K. Haydock, A. Kang, M. L. Land, R. Levy, T. J. Lie, T. A. Major, B. C. Moore, I. Porat, A. Palmeiri, G. Rouse, C. Saenphimmachak, D. Soll, S. Van Dien, T. Wang, W. B. Whitman, Q. Xia, Y. Zhang, F. W. Larimer, M. V. Olson, and J. A. Leigh, "Complete genome sequence of the genetically tractable hydorgenotrophic methanogen Methanococcus maripaludis," Journal of Bacteriology 186(20): 6956-6969 (2004).

Hoyt, P. R. and M. J. Doktycz, "Optimized beadmilling of tissues for high-throughput RNA production and microarray-based analyses," Anal. Biochem. 332(1): 100-108 (September 2004).

Hu, Z., T. Seeley, S. Kossek, and T. Thundat, "Calibration of optical cantilever deflection readers," Rev. Sci. Instruments 75(2): 400-404 (2004).

Hurst, G. B., T. K. Lankford, and S. J. Kennel, "Mass spectrometric detection of affinity purified crosslinked peptides," J. Amer. Soc. Mass Spect. 15(6): 832-839 (2004).

Jamasbi, R. J., S. J. Kennel, L. C. Waters, L. J. Foote, and J. M. Ramsey, "Genetic analysis of Pseudomonas aeruginosa by enterobacterial repetitive intergenic consensus polymerase chain reaction (PCR) and arbitrarily primed PCR: Gel analysis compared with microchip gel electrophoresis," Infec. Cont. & Hosp. Epidem. 25(1): 65-71 (2004).

Jeon, S., Y. Braiman, and T. Thundat, "Torsional spring constant obtained for an atomic force microscope cantilever," Appl. Phys. Lett. 84(10): 1795-1797 (2004).

Jeon, S. Y., Y. Braiman, and T. Thundat, "Cross talk between bending, twisting, and buckling modes of three types of microcantilever sensors," Review of Scientific Instruments 75(11): 4841-4844 (2004).

Kasili, P. M., J. M. Song, and T. Vo-Dinh, "Optical sensor for the detection of caspase-9 activity in a single cell," J. Amer. Chem. Soc. 126(9): 2799-2806 (2004).

Kasili, P. M. and T. Vo-Dinh, "Detection of polycyclic aromatic compounds in single living cells using optical nanoprobes," Polycyc. Aromat. Comp. 24(3): 221-235 (2004).

Kennel, S. J., T. Lankford, L. Foote, M. Wall, and S. Davern, "Phage Display Selection of scFv to Murine Endothelial Cell Membranes," Hybridoma & Hybridomics 23(4): 205-211 (2004).

Klasson, K. T., P. A.Taylor, J. F. Walker, S. A. Jones, R. L. Cummins, and S. A. Richardson, "Investigation of a centrifugal separator for in-well oil water separation," Petroleum Science and Technology 22(9-10): 1143-1159 (2004).

Kuklin, A. I., R. L. Mynatt, M. L. Klebig, L. L. Kiefer, W. O. Wilkison, R. P. Woychik, and E. J. Michaud, "Liver-specific expression of the agouti gene in transgenic mice promotes liver carcinogenesis in the absence of obesity and diabetes," Mol. Cancer 3:17-26 (2004).

Kumar, P., A. Mehta, S. M. Mahurin, S. Dai, M. D. Dadmun, B. G. Sumpter, and M. D. Barnes, "Formation of oriented nanostructures from single molecules of conjugated polymers in microdroplets of solution: The role of solvent," Macromol. 37(16): 6132-6140 (August 2004).

Langston, M., "Practical FPT implementations and applications," Parameterized and Exact Computations, Proceedings Lecture Notes in Computer Science 3162: 291-291 (2004).

Larimer, F. W., P. Chain, L. Hauser, J. Lamerdin, S. Malfatti, L. Do, M. L. Land, D. A. Pelletier, J. T. Beatty, A. S. Lang, F. R. Tabita, J. L. Gibson, T. E. Hanson, C. Bobst, J.L.T.Y. Torres, C. Peres, F. H. Harrison, J. Gibson, and C. S. Harwood, "Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris," Nat. Biotech. 22(1): 55-61 (2004).

Lee, T. H., P. Kumar, A. Mehta, K. W. Xu, R. M. Dickson, and M. D. Barnes, "Oriented semiconducting polymer nanostructures as on-demand room-temperature single-photon sources," Appl. Phys. Lett. 85(1): 100-102 (2004).

Leggett, R. W., "A biokinetic model for carbon dioxide and bicarbonate," Rad. Prot. Dos. 108(3): 203-213 (2004).

Lereu, A. L., A. Passian, R. J. Warmack, T. L. Ferrell, and T. Thundat, "Effect of thermal variations on the Knudsen forces in the transitional regime," Appl. Phys. Lett. 84(6): 1013-1015 (2004).

Liu, Y., B. E. Snow, V. A. Kickhoefer, N. Erdmann, W. Zhou, A. Wakeham, M. Gomez, L. H. Rome, and L. Harrington, "Vault poly (ADP-Ribose) polymerase is associated with mammalian telomerase and is dispensable for telomerase function and vault structure in vivo," Molecular and Cellular Biology 24(12): 5314-5323 (2004).

Martinez, D., L. F. Larrondo, N. Putnam, M. D. S. Gelpke, K. Huang, J. Chapman, K. G. Helfenbein, P. Ramaiya, J. C. Detter, F. Larimer, P. M. Coutinho, B. Henrissat, R. Berka, D. Cullen, and D. Rokhsar, "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78," Nat. Biotech. doi:10.1038/nbt 967, Published online http://www.nature.com/naturebiotechnology/ (2004).

Martinez, D., L. F. Larrondo, N. Putnam, M. D. S. Gelpke, K. Huang, J. Chapman, K. G. Helfenbein, P. Ramaiya, J. C. Detter, F. Larimer, P. M. Coutinho, B. Henrissat, R. Berka, D. Cullen, and D. Rokhsar, "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78," Nat. Biotech. 22(6): 695-700 (2004).

McKeown, C. K. and B. H. Davison, "A simplified method to create quantitative, "fixed" uranyl-contaminated metal coupons," Health Phys. 86(5): S113-S115 Suppl. S (2004).

Mobley, J., B. M. Cullum, A. L. Wintenberg, S. S. Frank, R. A. Maples, D. L. Stokes, and T. Vo-Dinh, "Single-board computer based control system for a portable Raman device with integrated chemical identification," Rev. Sci. Instrum. 75(6): 2016-2023 (2004).

Moussa, H. M., K. F. Eckerman, and L. W. Townsend, "Electron absorbed fractions based on a new model of the anterior nasal passage," Health Phys. 86(1): 19-24 (2004).

Nath, S., S. K. Ghosh, S. Panigahi, T. Thundat, and T. Pal, "Synthesis of selenium nanoparticle and its photocatalytic application for decolorization of methylene blue under UV irradiation," Langmuir 20(18):7880-7883 (2004).

Pal, A., D. L. Stokes, and T. Vo-Dihn, "Photchemically prepared gold metal film in a carbohydrate-based polymer: A practical, solid substrate for surface-enhanced Raman scattering," Current Science 87(4): 486-491 (2004).

Pappas, C. T., J. Scram, O. V. Moskvin, P. S. Ivanov, R. C. Mackenzie, M. Choudhary, M. L. Land, F. W. Larimer, S. Kaplan, and M. Gomelsky, "Construction and validation of the Rhodobacter sphaeroides 2.4.1 DNA microarray: Transcriptome flexibility at diverse growth modes," J. Bact. 186(14): 4748-4758 (2004).

Passian, A., A. Wig, A. L. Lereu, P. G. Evans, F. Meriaudeau, T. Thundat, and T. L. Ferrell, "Probing large area surface plasmon interference in thin metal films using photon scanning tunneling microscopy," Ultramicros. 100(3-4): 429-436 (2004).

Passian, A., A. Wig, A. L. Lereu, F. Meriaudeau, T. Thundat, and T. L. Ferrell, "Photon tunneling via surface plasmon coupling," Applied Physics Letters 85(16): 3420-3422 (2004).

Pei, J. H., F. Tian, and T. Thundat, "Glucose biosensor based on the microcantilever," Anal. Chem. 76(2): 292-297 (2004).
Pinnaduwage, L. A., T. Thundat, J. E. Hawk, D. L. Hedden, R. Britt, E. J. Houser, S. Stepnowski, R. A. McGill, and D. Bubb, "Detection of 2,4-dinitrotoluene using microcantilever sensors," Sens. & Actu. B - Chem. 99(2-3): 223-229 (2004).

Pinnaduwage, L. A., T. Thundat, A. Gehl, S. D. Wilson, D. L. Hedden, and R. T. Lareau, "Desorption characteristics of uncoated silicon microcantilever surfaces for explosive and common nonexplosive vapors," Ultramicros. 100(3-4): 211-216 (2004).

Pinnaduwage, L. A., A. Wig, D. L. Hedden, A. Gehl, D. Yi, T. Thundat, and R. T. Lareau, "Detection of trinitrotoluene via deflagration on a microcantilever," J. Appl. Phys. 95(10): 5871-5875 (2004).

Pinnaduwage, L. A., D. Yi, F. Tian, T. Thundat, and R. T. Lareau, "Adsorption of trinitrotoluene on uncoated silicon microcantilever surfaces," Langmuir 20(7): 2690-2694 (2004).

Pinnaduwage, L. A., D. L. Hedden, A. Gehl, V. I. Boiadjiev, J. E. Hawk, R. H. Farahi, T. Thundat, E. J. Houser, S. Stepnowski, R. A. McGill, L. Deel, and R. T. Lareau, "A sensitive, handheld vapor sensor based on microcantilevers," Review of Scientific Instruments 75(11): 4554-4557 (2004).

Qiu, X. Y., R. A. Hurt, L. Y. Wu, C. H. Chen, J. M. Tiedje, and Z. Zhou, "Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR," Journal of Microbiological Methods 59(2): 199-210 (2004).

Razumovskaya, J., V. Olman, D. Xu, E. C. Uberbacher, N. C. VerBerkmoes, R. L. Hettich, and Y. Xu, "A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with SEQUEST," Proteomics 4(4): 961-969 (2004).

Regan, J. D., J. E. Trosko, and W. L. Carrier, "Evidence for excision of ultraviolet-induced pyrimidine dimmers from the DNA of human cells in vitro," (Reprinted) DNA Repair 3(1): 92-98 (2004).

Russell, L. B., "Effects of male germ-cell stage on the frequency, nature, and spectrum of induced specific-locus mutations in the mouse," Genetica 122(1): 25-36 (2004).

Son, C. D., H. Sargsyan, F. Naider, and J. M. Becker, "Identification of ligand binding regions of the Saccharomyces cerevisiae alpha-factor pheromone receptor by photoaffinity cross-linking," Biochemistry 43(41): 13193-13203 (2004).

Setlow, R. B., J. D. Regan, J. German, and W. L. Carrier, "Evidence that xeroderma pigmentosum cells do not perform the firststep in the repair of ultraviolet damage to their DNA (reprinted from Proc. Natl. Acad. Sci. U.S.A., Vol. 64, pg. 1035-1041, 1969) DNA Repair 3(2): 188-194 (2004).

Sharp, J. S., J. M. Becker, and R. L. Hettich, "Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry," Anal. Chem. 76(3): 672-683 (2004).

Schuller, H. M., B. Porter, A. Riechert, K. Walker, and R. Schmoyer, "Neuroendocrine lung carcinogenesis in hamsters in inhibited by green tea or theophylline while the development of adenocarcinomas is promoted: implications for chemoprevention in smokers," Lung Cancer 45(1): 11-18 (2004).

Son, C. D., J. Sargsyan, F. Naider, and J. M. Becker, "Identification of ligand binding regions of the Saccharomyces cerevisiae alpha-factor pheromone receptor by photoaffinity cross-linking," Biochemistry 43(41): 13193-13203 (2004).

Song, J. M., P. M. Kasili, G. D. Griffin, and T. Vo-Dinh, "Detection of cytochrome c in a single cell using an optical nanobiosensor," Appl. Chem. 76(9): 2591-2594 (2004).

Song, J. M. and T. Vo-Dinh, "Miniature biochip system for detection of Escherichia coli O157 : H7 based on antibody-immobilized capillary reactors and enzyme-linked immunosorbent assay," Anal. Chim. Acta 507(1): 115-121 (2004).

Stokes, D. L., Z. H. Chi, and T. Vo-Dinh, "Surface-enhanced-Raman-scattering-inducing nanoprobe for spectrochemical analysis," Appl. Spect. 58(3): 292-298 (2004).

Strader, M. B., N. C. VerBerkmoes, D. L. Tabb, H. M. Connelly, J. W. Barton, B. D. Bruce, D. A. Pelletier, B. H. Davison, R. L. Hettich, F. W. Larimer, and G. B. Hurst, "Characterization of the 70S ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach," Journal of Proteome Research 3(5): 965-978 (2004).

Tang, Y. J., J. Fang, X. H. Xu, H. F. Ji, G. M. Brown, and T. Thundat, "Detection of femtomolar concentrations of HF using an SiO2 microcantilever," Anal. Chem. 76(9): 2478-2481 (2004).

Tian, F., J. H. Pei, D. L. Hedden, G. M. Brown, and T. Thundat, "Observation of the surface stress induced in microcantilevers by electrochemical redox processes," Ultramicros. 100(3-4): 217-223 (2004).

Urs, S., C. Smith, B. Campbell, A. M. Saxton, J. Taylor, B. Zhang, J. Snoddy, B. J. Voy, and N. Moustaid-Moussa, "Gene expression profiling in human preadipocytes and adipocytes by microarray analysis," J. Nutrition 134(4): 762-770 (2004).

Vass, A. A., R. R. Smith, C. V. Thompson, M. N. Burnett, D. A. Wolf, J. A. Synstelien, N. Dulgerian, and B. A. Eckenrode, "Decompositional odor analysis database," J. For. Sci. 49(4): 760-769 (2004).

Vo-Dinh, T., G. Griffin, D. L. Stokes, D. N. Stratis-Cullum, M. Askari, and A. Wintenberg, "Multi-functional biochip for medical diagnostics and pathogen detection," Opt. Sens.: Indus. Envir. & Diag. Appl. 1: 121-143 (2004).

Vo-Dinh, T., D. L. Stokes, M. B. Wabuyele, M. E. Martin, J. M. Song, R. Jagannathan, E. Michaud, R. J. Lee, and X. G. Pan, "A hyperspectral imaging system for in vivo optical diagnosis," IEEE Engineering in Medicine and Biology 23(5): 40-49 (2004).

Wang, L. H, B. E. Hingerty, R. Shapior, and S. Broyde, "Structural and stereoisomer effects of model estrogen quinine-derived DNA adducts: N-6-(2-hydroxyestron-6(alpha, beta)-yl)-2 '-deoxyadenosine and N-2-(2-hydroxyestron-6(alpha,beta)-yl)-2 '-deoxyguanosine," Chem. Res. Tox. 17(30): 311-324 (2004).

Wang, Y. X., B. J. Voy, S. Urs, S. Kim, M. Soltani-Bejnood, N. Quigley, Y. R. Heo, M. Standridge, B. Andersen, M. Dhar, R. Joshi, P. Wortman, J. W. Taylor, J. Chun, M Leuze, K. Claycombe, a. M. Saxton, and N. Moustaid-Moussa, "The human fatty acid synthase gene and de novo lipogenesis are coordinately regulated in human adipose tissue," Journal of Nutrition 134(5): 1032-1038 (2004).

Warner, G. F. and D. M. Opersko, "A new black coral (Anthozoa : Antipatharia) from a reef wall environmental in Jamaica," Bull. Marine Sci. 74(1): 169-174 (2004).

Wig, A., A. Passian, E. Arakawa, T. L. Ferrell, and T. Thundat, "Optical thin-film interference effects in microcantilevers," J. Appl. Phys. 95(3): 1162-1165 (2004).

Yan, X. D., Y. J. Tang, H. F. Ji, Y. Lvov, and T. Thundat, "Detection of organophosphates using an acetyl cholinesterase (AChE) coated microcantilever," Instrum. Sci. & Tech. 32(2): 175-183 (2004).

Young, R., C. Bast, J. Hinz, D. Krewski, and K. Bakshi, "Acute Exposure Guideline Levels (AEGLs) for Uranium Hexafluoride," The Toxicologist 78(15), 2004.

Zhang, B., D. Schmoyer, S. Kirov, and J. Snoddy, "GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies," BMC Bioinformatics 5: Art. 16 (2004).

Zhu, J. H., C. T. Liu, and C. H. Chen, "Effect of iron additions on environmental embrittlement of NiTi-base alloys," Intermetallics 12(7-9): 859-686, Sp. Iss. SI (July-September 2004).

Zou, Y., H. X. Ma, I. G. Minko, S. M. Shell, Z. G. Yang, Y. X. Qu, Y. Xu, N. E. Geacintov, and R. S. Lloyd, "DNA damage recognition of mutated forms of UvrB proteins in nucleotide excision repair," Biochem. 43(14): 4196-4205 (2004).

Books/Book Chapters

C. B. Bast and J. Hinz, "Hydrogen Chloride," in Acute Exposure Guideline Levels for Selected Airborne Chemicals, pp.77-122, Publisher The National Academies Press, Washington, D.C., 2004.

C. B. Bast and G. Rusch, "Uranium Hexafluoride," in Acute Exposure Guideline Levels for Selected Airborne Chemicals, pp.250-291, Publisher The National Academies Press, Washington, D.C., 2004.

Finkelstein, Mark, James D. McMillan, Brian H. Davison, and Barbara Evans, eds., Biotechnology for Fuels and Chemicals, The Twenty-Fifth Symposium Mulchandani, Ashok, ex. ed., in Applied Biochemistry and Biotechnology, Vols. 113-116, (Proceedings of the Twenty-Fifth Symposium on Biotechnology for Fuels and Chemicals, May 4-7, 2003, Breckenridge, CO) Humana Press, Totowa, New Jersey, (2004).

Xu, Ying, "Computation Genome Annotation," in Microbial Functional Genomics, Chapter 3, Publisher Wiley-Liss, Hoboken, New Jersey, March 2004.

Xu, Ying, "Computation Methods for Functional Prediction of Genes," in Microbial Functional Genomics, Chapter 5, Publisher Wiley-Liss, Hoboken, New Jersey, March 2004.

Xu, Ying, "Microarray Gene Expression Data Analysis," in Microbial Functional Genomics, Chapter 7, Publisher Wiley-Liss, Hoboken, New Jersey, March 2004.

Zhou, J., D. K. Thompson, Y. Xu, and J. M. Tiedje, Microbial Functional Genomics, Publisher Wiley-Liss, Hoboken, New Jersey, March 2004.

Reports (ORNL-TMs)

Bernal, S. M. and J. S. Bogard, Protocols for Thermoluminescence and Optically Stimulated Luminescence Research at DOSAR. ORNL/TM-2004/172 (August 2004).

Eckerman, K. F. and A. L. Sjoreen, Radiological Toolbox User's Manual. ORNL/TM-2004/27 (January 2004).

Geist, A. L., T. Zacharia, R. C. Mann, G. Michaels, G. Heffelfinger, J. Gephart, A. Adamson, and J. Wyrick, Report on Three Genomes to Life Workshops: Data Infrastructure, Modeling and Simulation, and Protein Structure Prediction. R04 119579 (January 2004).

Klasson, K. T., W. B. Ridenour, B. H. Davison, and J. McFarlane, Direct Capture of Organic Acids from Fermentation Media Using Ionic Liquids. ORNL/TM-2004/192, Oak Ridge National Laboratory (August 2004).

Sauers, I., D. R. James, A. R. Ellis, C. E. Easterly, and J. S. Hsu, Preliminary Measurements of Dielectric and Toxic Properties of Potential Refrigerants for Two-Phase Cooling of Power Electronics and Motors. ORNL/TM-2004/210 (September 2004).

Genome Management Information Systems Products (A. E. Adamson, J. L. Bownas, D. K. Casey, S. A. Estes, B. K. Mansfield, S. A. Martin, M. D. Mills, K. Nylander, and J. M. Wyrick)

Report on Three Genomes to Life Workshops: Data Infrastructure, Modeling and Simulation, and Protein Structure Prediction, July 22-24, 2003, 30 pp., January 2004.

DOE Genomics:GTL Contractor-Grantee Workshop II, Washington, D.C., February 29-March 2, 2004, 162 pp., February 2004.

Genomes to Life Program Overview, 2-page flyer, February 2004.

GTL Briefing Book, February 2004. (Internal)

Genomics and Its Impact on Science and Society, 12 pp., March 2004.

Human Genome Landmarks: Selected Traits and Disorders Mapped to Chromosomes, poster, March 2004.

DOE Genomics:GTL; Merging Technologies, Computing, and Microbial Systems to Build a New Foundation for Energy and Environmental Solutions, 6-page brochure, April 2004.

GTL Briefing Presentation for Office of Science and Office of Management and Budget, April 2004. (Internal)

GTL Briefing Presentation, "Questions and Answers," for Office of Science and Office of Management and Budget, April 2004. (Internal)

Microbial Genomics Research, 6-page brochure prepared for DOE OBER, July 2004.

Genomes:GTL; Accelerating Discovery for Energy and Environment http://doegenomestolife.org, initiated October 2004.

GTL BERAC Subcommittee on Protein Production Facility, speaker preparation, October 2004. (Internal)

Search the ORNL Publications Database for Division Publications