Biosciences Division

News

  • New ORNL process brings nanoparticles into focus

    Scientists can study the biological impacts of engineered nanomaterials on cells within the body with greater resolution than ever because of a procedure developed by researchers at the Department of Energy's Oak Ridge National Laboratory.

  • Audio Spot: New medicine therapeutics company is spinout from ORNL

    A Company, NellOne Therapeutics, has been formed through Battelle Ventures to research the potential for a new therapy that could help heart patients, according to Oak Ridge National Laboratory scientist Cymbeline Culiat.

2007 Publications/Presentations

Borole, A. P., Davison, B. H., “Improving activity of salt-lyophilized enzymes in organic media,” Appl. Biochem. Biotechnol. (2007).

Chen, G., “PRAP: An automated de novo repeat finder pipeline for prokaryotic genomes,” The 2007 World Congress in Computer Science Computer Engineering, and Applied Computing, Las Vegas, NV, June 2007.

Chesler, E. J., Langston, M. A., “Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data,” RECOMB 2005 Workshops on Systems Biology, San Diego, CA, December 2005. Paper in Conference Proceedings (Book) 4023/200 150-165 (2007).

Chourey, K., Thompson, M. R., Morrell-Falvey, J. L., Verberkmoes, N. C., Brown, S. D., Shah, M. B., Zhou, J., Doktycz, M. J., Hettich, R. L., Thompson, D. K., “Global Molecular and Morphological Effects of 24-Hour Chromium(VI)Exposure on Shewanella oneidensis MR-1,” Appl. Environ. Microbiol. 72(9) 6331-6344 (2007).

Desikan, R., Armel, S. E., Meyer III, H. M., Thundat, T. G., “Effect of chain length on nanomechanics of alkanethiol self-assembly,” Nanotechnology (2007).

Garten Jr, C. T., Kang, S., Brice, D. J., Schadt, C. W., Zhou, J., “Variability in Soil Properties at Different Spatial Scales (1 m to 1 km) in a Deciduous Forest Ecosystem,” Soil Biol. Biochem.39(10) 2621-2627 (2007).

Gatti, D., Maki, A., Chesler, E. J., Kirova, R., Kosyk, O., Lu, L., Manly, K., Matthews, D. B., Qu, Y., Williams, R., Perkins, A., Langston, M. A., Threadgill, D., Rusyn, I., “Genome-level analysis of genetic regulation of liver gene expression networks,” Hepatology (2007).

Hancock, J. M., Adams, N., Aidinis, V., Blake, J. A., Bogue, M., Brown, S. D., Chesler, E. J., Davidson, D., Duran, C., Eppig, J. T., Gailus-Durner, V., Gkoutos, G. V., Greenaway, S., Angelis, M. H., Kollias, G., Leblanc, S., Lee, K., Lengger, C., Maier, H., Mallon, A., Masuya, H., Melvin, D., Muller, W., Parkinson, H., Proctor, G., Reuveni, E., Schofield, P., Shukla, A., Smith, C., Toyoda, T., Vasseur, L., Wakana, S., Walling, A., White, J., Wood, J., Zouberakis, M.., “Integration of Mouse Phenome Data Resources,” Mammal. Genome. (2007).

Hervey, IV, W. J., Strader, M. B., Strader, M. B., Hurst, G. B., “Comparison of Digestion Protocols for Microgram Quantities of Enriched Protein Samples,” J. Proteome Res. (2007).

Hu, Z., “Nanoscale Energy Conversion and Its Applications,” ASME Intl Conf on Integration & Commercialization of Micro and Nano-Systems, Sanya, Hainan, China, Jan. 2007.

Kane, S. R., Chakicherla, A. Y., Chain, P. S., Schmidt, R., Shin, M., Legler, T. C., Scow, K. M., Larimer, F. W., Lucas, S., Richardson, P. M., Hristova, K. R., “Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1,” J. Bacteriol. 189(5) 1931-1945 (2007).

Kuklin, A., Mynatt, R., Klebig, M., Kiefer, L., Wilkison, W. O., Woychik, R. P., Michaud III, E. J., “Liver-specific expression of the agouti gene in transgenic mice promotes liver carcinogenesis in the absence of obesity and diabetes,” Mol. Canc.3(17) 1-10 (2007).

Langston, M. A., Perkins, A., Saxton, A., Scharff, J., Voy, B. H., “Innovative Computational Methods For Transcriptomic Data Analysis: A Case Study in the Use Of FPT For Practical Algorithm Design and Implementation,” Comput. J.1 (2007).

Lo, I., Denef, V., Verberkmoes, N. C., Shah, M. B., Goltsman, D., DiBartolo, G., Tyson, G. W., Allen, E. E., Ram, R. J., Detter, J. C., Richardson, P., Thelen, M. P., Hettich, R. L., Banfield, J. F., “Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria,” Nature446(1) 537 (2007).

Luo, W., Zhou, J., Wu, W., Yan, T., Criddle, C., Jardine, P. M., Gu, B., “Electron Donor Effects on Bioreduction Rates of Uranium and Microbial Community under Varying Bicarbonate and Sulfate Conditions,” Appl. Environ. Microbiol. (2007).

Lykidis, A., Mavromatis, K., Ivanova, N., Anderson, I., Land, M. L., DiBartolo, G., Martinez, M., Lapidus, A. L., Lucas, S., Copeland, A., Richardson, P. M., Wilson, D. B., Kyripides, N. C., “Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX,” J. Bacteriol. 189(6) 2477-2486 (2007).

Lynch, R. M. Voy, B. H. Glass, D. F. Mahurin, S. M. Saxton, A. Donnel, R. L. Cheng, M., “Assessing the pulmonary toxicity of single-walled carbon nanohorns,” Nanotoxicology (2007).

Lynch, R. M. Voy, B. H. Zhao, B. Mahurin, S. M. Thundat, T. G. Cheng, M. Passian, A. Venmar, K. T. Tetard, L., “IN-VIVO EXPOSURE CHARACTERIZATION AND VISUALIZATION OF SWNH AGGREGATES,” The 3rd International Symposium on Nanotechnology, Occupational and Environmental Health, Taipei, Taiwan Aug. 2007. Conference Proceedings.

Madden, A., Palumbo, A. V., Ravel, B., Vishnivetskaya, T. A., Phelps, T. J., Schadt, C. W., Brandt, C. C., “Geochemical consequences of electron donor selection for bioremediation of contaminated sediments,” Environ. Sci. Technol. (2007).

Madden, A., Smith, A., Balkwill, Dr. D., Fagan, L. A., Phelps, T. J., “Microbial Uranium Immobilization Independent of Nitrate Reduction,” Environ. Microbiol. (2007).

Madden, M. E., Ulrich, S. M., Onstott, T., Phelps, T. J., “Salinity-induced hydrate dissociation: A mechanism for recent CH4 release on Mars,” Geophys. Res. Lett. (2007).

Martin, M. Z., Wullschleger, S. D., Garten Jr, C. T., Palumbo, A. V., “Measurement of carbon for carbon sequestration and site monitoring,” (2007).

Martin, M. Z., Wullschleger, S. D., Vass, A. A., Martin, R. C., Grissino-Mayer, H., “High-Resolution Laser-Induced Breakdown Spectroscopy used in Homeland Security and Forensic Applications,” Bull. Las. Spectrosc. Soc . , India 14 23-35 (2007).

Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A. C., Rigoutsos, I., Salamov, A., Korzeniewski, F., Land, M. L., Lapidus, A. L., Grigoriev, I., Hugenholtz, P., Kyripides, N. C., “Use of simulated data sets to evaluate the fidelity of metagenomic processing methods,” Nature Methods (2007).

Moon, J., Roh, Y., Lauf, R. J., Vali, H., Yeary, L. W., Phelps, T. J., “Microbial preparation of metal-substituted magnetite nanoparticles,” J. Microbiol. Meth. 70(1) 150-158 (2007).

Moon, J., Roh, Y., Yeary, L. W., Lauf, R. J., Rawn, C. J., Love, L. J., Phelps, T. J., “Microbial formation of lanthanide-substituted magnetites by Thermoanaerobacter sp. TOR-39,” Extremophiles (2007).

Moon, J., Yeary, L. W., Rondinone, A. J., Rawn, C. J., Kirkham, M. J., Roh, Y., Love, L. J., Phelps, T. J., “Magnetic response of microbially synthesized transition metal- and lanthanide-substituted nano-sized magnetites,” J. Magn. Magn. Mater.313(2) 283-292 (2007).

Narasimhan, C. N., Tabb, D. L., Verberkmoes, N. C., Thompson, M. R., Hettich, R. L.,
Uberbacher, E. C., “MASPIC: Intensity-Based Tandem Mass Spectrometry Scoring Scheme That Improves Peptide Identification at High Confidence,” Anal. Chem. 12(77) 7581-7593 (2005).

New, J. R., Huang, J., Chesler, E. J., “Dynamic Visualization of Co-expression in Systems Genetics Data,” IEEE Trans. Visual. Comput. Graph. (2007).

Palumbo, A. V., Amonette, J. E., Phillips, J. R., Fagan, L. A., McNeilly, M. S., Daniels, W. L., “Fly Ash Characteristics and Carbon Sequestration Potential,” World of Coal Ash 2007, Covington, KY, May 2007.

Palumbo, A. V., Phillips, J. R., Fagan, L. A., McNeilly, M. S., Ruther, R. E., Fisher, L. S., Amonette, J. E., “Comparing Metal Leaching and Toxicity from High pH, Low pH, and High Ammonia Fly Ash,” Fuel.86 1623-1630 (2007).

Pan, C., Oda, Y., Lankford, P. K., Zhang, B., Samatova, N. F., Pelletier, D. A., Harwood, C. S., Hettich, R. L., “Characterization of Anaerobic Catabolism of p-Coumarate in Rhodopseudomonas palustris by Integrating Transcriptomics and Quantitative Proteomics,” J. Bacteriol. (2007).

Paquit, V. C., Ferrell, T. L., Meriaudeau, F., Price, J. R., Seulin, R., Tobin Jr, K. W., Farahi, R. H., “Near-infrared imaging and structured light ranging for automatic catheter insertion," SPIE Medical Imaging 2006, San Diego, CA, Feb. 2006. SPIE 6141.

Paquit, V. C., Price, J. R., Meriaudeau, F., Tobin Jr, K. W., Ferrell, T. L., “Combining near-infrared illuminants to optimize venous imaging,” SPIE Medical Imaging Symposium, Visualization and Image-guided Procedures Conf., San Diego, CA, Feb. 2007.

Pinnaduwage, L. A., Boiadjiev, V. I., Fernando, G. W., Hawk, J. E., Wijewardhana, L. R., Gehl, A. C., “An Energy Conservation Approach to Adsorbate-Induced Surface Stress and the Extraction of Binding Energy Using Nanomechanics,” Phys. Rev. B. (2007).

Pinnaduwage, L. A., Zhao, W., Gehl, A. C., Allman, S. L., “Quantitative Analysis of Ternary Vapor Mixtures Using a Microcantilever-Based Electronic Nose,” Appl. Phys. Lett. (2007).

Podar, M., Abulencia, C., Walcher, M., Hutchinson, D., Zengler, K., Garcia, J., Holland, T., Cotton, D., Hauser, L. J., Keller, M., “Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities,” Appl. Environ. Microbiol. (2007).

Savidor, A., Donahoo, R. S., Hurtado-Gonzales, O., Land, M. L., Shah, M. B., Lamour, K. H., McDonald, W. H., “Cross-species proteomics reveals processes in early infection of Phytophthora,” Science (2007).

Savidor, A., Donahoo, R. S., Hurtado-Gonzales, O., Verberkmoes, N. C., Shah, M. B., Lamour, K. H., McDonald, W. H., “Expressed Peptide Tags: An additional layer of data for genome annotation,” J. Proteome Res.5(11) 3048-3058 (2007).

Senesac, L. R., Thundat, T. G., “Explosive Vapor Detection Using Microcantilever Sensors,” Submitted (2007).

Sullivan, C. J., Venkataraman, S., Retterer, S. T., Allison, D. P., Doktycz, M. J., “Comparison of the Identation and Elasticity of E.coli and its Spheroplasts by AFM,” Ultramicroscopy (2007).

Tetard, L., Venmar, K. T., Lynch, R. M., Glass, D. F., Voy, B. H., Passian, A., Cheng, M., Thundat, T. G., “Intercellular Revelation of Inhaled Nanoparticles,” Nature Methods. (2007).

Thompson, M. R., Verberkmoes, N. C., Chourey, K., Shah, M. B., Thompson, D. K., Hettich, R. L., “Dosage-Dependent Proteome Response of Shewanella oneidensis MR-1 to Acute Chromate Challenge,” J. Proteome Res.6(5) 1745-1757 (2007).

Weiner, R. M., Taylor II, L. E., Henrissat, B., Hauser, L. J., Land, M. L., Coutinho, P. M., Rancurel, C., Saunders, E. H., Longmire, A. G., Zhang, H., Bayer, E., Gilbert, H. J., Larimer, F. W., Zhulin, I. B., Lamed, R., Richardson, P. M., Borovok, I., Hutcheson, S., “Complete Genome Sequence of the Complex Carbohydrate-Degrading Marine Bacterium, Saccharophagus degradans strain 2-40,” Proc. Natl. Acad. Sci. USA (2007).

Woodward, J., Kennel, S. J., Mirzadeh, S., Dai, S., Rondinone, A. J., “Biodistribution of radioactive Cd 125mTe/ZnS nanoparticles targeted with antibody to murine lung endothelium,” Nanotechnology 18(17) 175103 (2007).

Zhang, B., Verberkmoes, N. C., Langston, M. A., Uberbacher, E. C., Hettich, R. L., Samatova, N. F., “Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics,” J. Proteome Res.5(11) 2909-2918 (2007).

Zhang, Y., Chesler, E. J., Langston, M. A., “An Efficient Algorithm for Finding Bicliques in Bipartite Graphs, with Applications,” The 13th Annual International Computing and Combinatorics Conference (COCOON), University of Alberta, Informatics Core, Alberta, Canada, J. Bioinf. Comput. Biol. July 2007.

Zhang, Y., Ding, S., Mielenz, J. R., Cui, J., Elander, R. T., Laser, M., Himmel, M., McMillan, J. R., Lynd, L., “Fractionating Recalcitrant Lignocellulose at Modest Reaction Conditions,” Biotechnol. Bioeng. (2007).

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