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p p e n d i x A 6 103 U.S. Department Office of of Energy Science U.S. - Experimen “Systems al. 2004. et T., M. Facciotti, Predictive Building for tal Design—Considerations Systems,” for Prokaryotic Models Regulatory Network 5(1), 527–44. Current - Valida and Mapping 2007. “Large-Scale J. J., et al. Faith, a from Regulation Transcriptional coli tion of Escherichia PLoS Biology 5, e8. Profiles,” Compendium of Expression 2008. Delong. and E. F. Fenchel, T. G., P. Falkowski, Biogeochemi- Earth’s Drive Engines That Microbial “The Science 320(5879), 1034–39. cal Cycles,” - 2005. “Bioinformat and J. Snape. Tiwari, D., B. Field, for Environmental Support Management ics and Data PLoS Biology 3(8), 1352–53. Genomics,” M. J., et al. 2007. “Emergent Follows, Science Ocean,” a Model Communities in of Microbial 315(5820), 1843–46. Environmental J. K, et al. 2008. “Towards Fredrickson, - Microbiol Reviews ,” of Shewanella Biology Systems ogy 6(8), 592–603. of Genomics 2006. “Comparative et al. Y., S. Gerdes, - of Bacteriol Journal in ,” NAD Biosynthesis ogy 188(8), 3012–23. in of the Nation 2008. “State C., and R. Stevens. Goble, - of Biomedi Journal for ,” Integration Data 41(5), 687–93. cal Informatics Frame- Integration MeDICi Gorton, I., et al. 2008. “The Streaming Data Performance for High A Platform work: on IEEE/IFIP Conference Working Seventh Applications,” , 95–104. Architecture Software : N., et al. 2008. “Comparative Gupta, - Genom Comparative and Spectrometry Mass Combining Research ,” Multiple ics to Analyze 18(7), 1133–42. Signal- for Modeling S., et al. 2006. “Rules W. Hlavacek, Science STKE 2006(334), re6. Systems,” Transduction Biocura- of Future Rhee. 2008. “The Y. D., and S. Howe, 455, 47–50. Nature tion,” 2008. “Formulating N., and B. O. Palsson. Jamshidi, Era,” in the Post-Genome Kinetic Models Genome-Scale Biology Systems Molecular 4(171). - Partition et al. 2006. “Niche Z. I., E. R. Zinser, Johnson, Along Ocean-Scale Ecotypes ing Among Science 311(5768), 1737–40. Gradients,” Environmental Inte- Bioinformatics: New M. B., et al. 2006. “The Jones, to the Biosphere,” the Gene from Data grating Ecological 37, and , of , Review Annual 519–44. Biol- Systems Meaning of 2005. “The W. M. Kirschner, 121(4), 503–04. ogy,”

Genome BiologyGenome ,” NRC-1 10101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101

(8), R52.

10101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101 Bibliography - Micro 2004. Systems of . Academy American biology: Genomics. Microbial Beyond - Biol in Synthetic Standard the A. 2008. “Setting Arkin, 26(7), 771–74. Nature ogy,” of Structuring 2007. “Microbial Malfatti. and F. Azam, F., Microbiology Reviews 5(10), Nature Ecosystems,” Marine 782–91. Molecules, “Microbes, 2004. Worden. Z. A. and Azam,F., Science 303(5664), 1622–24. Ecosystems,” and Marine Networks Gene to Infer M., et al. 2007. “How Bansal, Biology Systems Molecular 3, 78. Profiles,” Expression from - Integra Two-Way Firegoose: J. C., et al. 2007. “The Bare, Web Bioinformatics Different from Data tion of Diverse - BMC Bioinformat Applications,” with Desktop Resources ics, 8(456). Bonneau, R., et al. 2004. “Comprehensive De Novo Structure Prediction in a Systems-Biology Context for Sp. Halobacterium the Appendix 6 5 An Algorithm Inferelator: Bonneau, R., et al. 2006. “The from Regulatory Networks for Learning Parsimonious Biology Genome Novo,” De Sets Data Systems-Biology 7(5), R36. Model Predictive et al. 2007. “A Bonneau, R., N. Baliga, Living in a Free of Control Transcriptional for 131(7), 1354–65. Cell Cell,” 2008. “Refinement Canton, B., A. Labno, and D. Endy. and Parts Biological of Synthetic and Standardization Biotechnology26(7), 787–93. Nature Devices,” - Biol in Systems to Progress Cassman, M. 2005. “Barriers 438(7071), 1079. Nature ogy,” is a Signal 1998. “Sucrose J., and D. R. Bush. T. Chiou, of the Proceedings in Assimilate Partitioning,” Molecule of America States of the United of Sciences Academy National 95(8), 4784–88. Automated the 2007. “Toward M., et al. DeJongh, in the Networks Metabolic of Genome-Scale Generation 8(139). BMC Bioinformatics SEED,” - 1997. “Explor O. Brown. and P. R. Iyer, V. J. L., DeRisi, - Expres of Gene Control and Genetic ing the Metabolic Science 278, 680–686. Scale,” sion on a Genomic Sys- Distributed Annotation R. D. 2001. “The Dowell, 2(7). BMC Bioinformatics tem,” Tran- Gene of Program et al. 2004. “The P., Eichenberger, During Type Cell Differentiating scription for a Single PLoS Biology 2(10), e328. subtilis,” in Bacillus Sporulation Workshop GTL Knowledgebase Appendix 6 10101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101

Kitano, H. 2002. “: A Brief Overview,” Sci- Reiss, D. J., N. S. Baliga, and R. Bonneau. 2006. “Inte- ence 295(5560), 1662–64. grated Biclustering of Heterogeneous Genome-Wide Klamt, S., et al. 2008. “Modeling the Electron Transport Datasets for the Inference of Global Regulatory Networks,” Chain of Purple Non-Sulfur ,” Molecular Systems BMC Bioinformatics 7(280). Biology 4(156). Rodionov, D. A. 2007. “Comparative Genomic Recon- Laub, M. T., et al. 2000. “Global Analysis of the Genetic struction of Transcriptional Regulatory Networks in Bacte- Network Controlling a Bacterial Cell Cycle,” Science ria,” Chemical Reviews 107(8), 3467–97. 290(5499), 2144–48. Rodionov, D. A., et al. 2007. “Genomic Identification Laws, E. A., et al. 2000. “Temperature Effects on Export and Reconstitution of a Complete Biosynthetic Production in the Open Ocean,” Global Biogeochemical Pathway for the Osmolyte Di-Myo-Inositol-Phosphate,” Cycles 14(4), 1231–46. Proceedings of the National Academy of Sciences of the United Liu, Y., J. Zhou, et al. 2003. “ Dynamics of States of America 104(11), 4279–84. Deinococcus radiodurans Recovering from Ionizing Radia- tion,” Proceedings of the National Academy of Sciences of the Rodionov, D. A., et al. 2008a. “Transcriptional Regulation United States of America 100(7), 4191–96. of NAD Metabolism in Bacteria: Genomic Reconstruction of NiaR (YrxA) Regulon,” Nucleic Acids Research 36(6), Lynch, C. 2008. “: How Do Your Data Grow?” 2032–46. Nature 455, 28–29. Marx, J. 2004. “The Roots of Plant-Microbe Collabora- Rodionov, D. A., et al. 2008b. “Transcriptional Regulation tions,” Science 304(5668), 234–36. of NAD Metabolism in Bacteria: NrtR Family of Nudix- Related Regulators,” Nucleic Acids Research 36(6), 2047–59. Masuda, N., and G. M. Church. 2003. “Regulatory Net- work of Acid Resistance in Escherichia coli,” Molecu- Rodionov, D. A., et al. 2009. “A Novel Class of Modular lar Microbiology 48, 699–712. Transporters for Vitamins in Prokaryotes,” Journal of Bacte- Nature. 2008a. “A Place for Everything,” Nature 453, 2. riology 191(1), 42–51. Nature. 2008b. “ Cleverness Required,” Nature Rohde, A., et al. 2007. “ During the 455, 1. Induction, Maintenance, and Release of Dormancy in Apical Buds of Poplar,” Journal of Experimental Osterman, A. L. 2006. “A Hidden Metabolic Pathway 58(15/16), 4047–60. Exposed,” Proceedings of the National Academy of Sciences of the United States of America 103(15), 5637–38. Shannon, P. T., et al. 2006. “The Gaggle: An Open-Source Software System for Integrating Bioinformatics Software Osterman, A. L., and R. Overbeek. 2003. “Missing and Data Sources,” BMC Bioinformatics 7(176). Genes in Metabolic Pathways: A Comparative Genom- ics Approach,” Current Opinion in 7(2), Shetty, R. P., D. Endy, and T. F. Knight, Jr. 2008. “Engi- 238–51. neering BioBrick Vectors from BioBrick Parts,” Journal of 2(5). Osterman, A. L., and T. P. Begley. 2007. “A Subsystems- Based Approach to the Identification of Drug Targets in Slepchenko, B. M., et al. 2003. “Quantitative Cell Biol- Bacterial .” In Systems Biological Approaches in ogy with the Virtual Cell,” Trends in 13(11), Infectious Diseases, 131–70. From the Progress in Drug 570–76. Research series 64, Birkhäuser Basel. Smith, A. K., et al. 2007. “LinkHub: A Semantic Web Sys- Overbeek, R., et al. 2005. “The Subsystems Approach to tem That Facilitates Cross-Database Queries and Informa- Genome Annotation and Its Use in the Project to Annotate tion Retrieval in ,” BMC Bioinformatics 8(Suppl 1000 Genomes,” Nucleic Acids Research 33(17), 5691–702. 3), S5. Pinchuk, G., D. Rodionov, C. Yang, et al. 2009. “Genomic Smith, B., et al. 2007. “The OBO Foundry: Coordinated Reconstruction of Shewanella oneidensis MR-1 Metabolism Evolution of Ontologies to Support Biomedical Data Inte- Reveals a Previously Uncharacterized Machinery for Lactate gration,” Nature Biotechnology 25(11), 1251–55. Utilization,” Proceedings of the National Academy of Sciences Stein, L. D. 2003. “Integrating Biological Databases,” of the United States of America, published online before Nature Reviews 4(5), 337–45. print February 5. DOI: 10.1073/pnas.0806798106.

U.S. Department of Energy GTL Knowledgebase Workshop 104 Appendix 6 10101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101010101

Stein, L. D. 2008. “Towards a Cyberinfrastructure for the National Academy of Sciences of the United States of America Biological Sciences: Progress, Visions and Challenges,” 99(16), 10,876–80. Nature 9, 678–88. Yang, C., et al. 2006. “ and Experi- Taylor, C. F., et al. 2007. “The Minimum Information mental Characterization of N-Acetylglucosamine Utiliza- About a Proteomics Experiment (MIAPE),” Nature Biotech- tion Pathway of Shewanella oneidensis,” Journal of Biological nology 25(8), 887–93. Chemistry 281(40), 29,872–85. U.S. DOE. 2006. Breaking the Biological Barriers to Yang, C., et al. 2008. “Glycerate 2-Kinase of Thermotoga Cellulosic Ethanol: A Joint Research Agenda, DOE/SC- maritima and Genomic Reconstruction of Related Meta- 0095, U.S. Department of Energy Office of Science and bolic Pathways,” Journal of Bacteriology 190(5), 1773–82. Office of Energy Efficiency and Renewable Energy (http:// Ye, Y. Z., et al. 2005. “Automatic Detection of Subsystem/ genomicsgtl.energy.gov/biofuels/b2bworkshop.shtml). Pathway Variants in Genome Analysis,” Bioinformatics 21, U.S. DOE 2008. Carbon Cycling and Biosequestration: Inte- i478–86. grating Biology and Climate Through Systems Science, DOE/ Yun, W., et al. 1998. “X-Ray Imaging and Microspectros- SC-108, U.S. Department of Energy Office of Science copy of Plants and Fungi,” Journal of Synchrotron Radiation (http://genomicsgtl.energy.gov/carboncycle/). 5, 1390–95. Vaughn, M. W., G. N. Harrington, and D. R. Bush. 2002. “Sucrose-Mediated Transcriptional Regulation of Sucrose Symporter Activity in the Phloem,” Proceedings of the

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