Publications

2009

Aebersold, R. 2009. “A Stress Test for Mass Spectrometry-Based Proteomics.” Nat Methods 6 (6): 411–12. Cite
Aebersold, R., C. Auffray, E. Baney, E. Barillot, A. Brazma, C. Brett, S. Brunak, et al. 2009. “Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008).” Mol Oncol 3 (1): 9–17. Cite
Akiyoshi, B., C. R. Nelson, J. Ranish, and S. Biggins. 2009. “Analysis of Ipl1-Mediated Phosphorylation of the Ndc80 Kinetochore Protein in Saccharomyces Cerevisiae.” Genetics 183 (4): 1591–95. Cite
Akiyoshi, B., C. R. Nelson, J. Ranish, and S. Biggins. 2009. “Quantitative Proteomic Analysis of Purified Yeast Kinetochores Identifies a PP1 Regulatory Subunit.” Genes Dev 23 (24): 2887–99. Cite
Anderson, N. L., N. G. Anderson, T. W. Pearson, C. H. Borchers, A. G. Paulovich, S. D. Patterson, M. Gillette, R. Aebersold, and S. A. Carr. 2009. “A Human Proteome Detection and Quantitation Project.” Mol Cell Proteomics 8 (5): 883–86. Cite
Auffray, C., Z. Chen, and L. Hood. 2009. “Systems Medicine: The Future of Medical Genomics and Healthcare.” Genome Med 1 (1): 2. Cite
Beck, M., J. A. Malmstrom, V. Lange, A. Schmidt, E. W. Deutsch, and R. Aebersold. 2009. “Visual Proteomics of the Human Pathogen Leptospira Interrogans.” Nat Methods 6 (11): 817–23. Cite
Bell, A. W., E. W. Deutsch, C. E. Au, R. E. Kearney, R. Beavis, S. Sechi, T. Nilsson, and J. J. Bergeron. 2009. “A HUPO Test Sample Study Reveals Common Problems in Mass Spectrometry-Based Proteomics.” Nat Methods 6 (6): 423–30. Cite
Bochud, P. Y., D. Sinsimer, A. Aderem, M. R. Siddiqui, P. Saunderson, S. Britton, I. Abraham, et al. 2009. “Polymorphisms in Toll-like Receptor 4 (TLR4) Are Associated with Protection against Leprosy.” Eur J Clin Microbiol Infect Dis 28 (9): 1055–65. Cite
Bollyky, P. L., J. B. Bice, I. R. Sweet, B. A. Falk, J. A. Gebe, A. E. Clark, V. H. Gersuk, A. Aderem, T. R. Hawn, and G. T. Nepom. 2009. “The Toll-like Receptor Signaling Molecule Myd88 Contributes to Pancreatic Beta-Cell Homeostasis in Response to Injury.” PLoS OnePLoS ONE 4 (4): e5063. Cite
Boyle, J., H. Rovira, C. Cavnor, D. Burdick, S. Killcoyne, and I. Shmulevich. 2009. “Adaptable Data Management for Systems Biology Investigations.” BMC Bioinformatics 10: 79. Cite
Brentnall, T. A., S. Pan, M. P. Bronner, D. A. Crispin, H. Mirzaei, K. Cooke, Y. Tamura, et al. 2009. “Proteins That Underlie Neoplastic Progression of Ulcerative Colitis.” Proteomics Clin Appl 3 (11): 1326–37. Cite
Brock, Amy, Hannah Chang, and S. Huang. 2009. “Non-Genetic Heterogeneity--a Mutation-Independent Driving Force for the Somatic Evolution of Tumours.” Nature Reviews. Genetics 10 (5): 336–42. https://doi.org/10.1038/nrg2556. Cite
Carapito, C., C. Klemm, R. Aebersold, and B. Domon. 2009. “Systematic LC-MS Analysis of Labile Post-Translational Modifications in Complex Mixtures.” J Proteome Res 8 (5): 2608–14. Cite
Carter, G. W., and A. M. Dudley. 2009. “Systems Genetics and Complex Traits.” In Encyclopedia of Complexity and Systems Science. New York: Springer Publishing. Cite
Carter, G. W., D. J. Galas, and T. Galitski. 2009. “Maximal Extraction of Biological Information from Genetic Interaction Data.” PLoS Comput Biol 5 (4): e1000347. Cite
Chan, T. M., W. Longabaugh, H. Bolouri, H. L. Chen, W. F. Tseng, C. H. Chao, T. H. Jang, et al. 2009. “Developmental Gene Regulatory Networks in the Zebrafish Embryo.” Biochim Biophys Acta 1789 (4): 279–98. Cite
Chaturvedi, C. P., A. M. Hosey, C. Palii, C. Perez-Iratxeta, Y. Nakatani, J. Ranish, F. J. Dilworth, and M. Brand. 2009. “Dual Role for the Methyltransferase G9a in the Maintenance of Beta-Globin Gene Transcription in Adult Erythroid Cells.” Proc Natl Acad Sci U S A 106 (43): 18303–8. Cite
Chung, Y., S. H. Chang, G. J. Martinez, X. O. Yang, R. Nurieva, H. S. Kang, L. Ma, et al. 2009. “Critical Regulation of Early Th17 Cell Differentiation by Interleukin-1 Signaling.” Immunity 30 (4): 576–87. Cite
Claassen, M., R. Aebersold, and J. M. Buhmann. 2009. “Proteome Coverage Prediction with Infinite Markov Models.” Bioinformatics 25 (12): i154-60. Cite
David-Fung, E. S., R. Butler, G. Buzi, M. A. Yui, R. A. Diamond, M. K. Anderson, L. Rowen, and E. V. Rothenberg. 2009. “Transcription Factor Expression Dynamics of Early T-Lymphocyte Specification and Commitment.” Dev Biol 325 (2): 444–67. Cite
Di Paolo, N. C., E. A. Miao, Y. Iwakura, K. Murali-Krishna, A. Aderem, R. A. Flavell, T. Papayannopoulou, and D. M. Shayakhmetov. 2009. “Virus Binding to a Plasma Membrane Receptor Triggers Interleukin-1 Alpha-Mediated Proinflammatory Macrophage Response in Vivo.” Immunity 31 (1): 110–21. Cite
Diercks, A., H. Kostner, and A. Ozinsky. 2009. “Resolving Cell Population Heterogeneity: Real-Time PCR for Simultaneous Multiplexed Gene Detection in Multiple Single-Cell Samples.” PLoS OnePLoS ONE 4 (7): e6326. Cite
Diercks, A. H., A. Ozinsky, C. L. Hansen, J. M. Spotts, D. J. Rodriguez, and A. Aderem. 2009. “A Microfluidic Device for Multiplexed Protein Detection in Nano-Liter Volumes.” Anal Biochem 386 (1): 30–35. Cite
Domon, B., B. Bodenmiller, C. Carapito, Z. Hao, A. Huehmer, and R. Aebersold. 2009. “Electron Transfer Dissociation in Conjunction with Collision Activation to Investigate the Drosophila Melanogaster Phosphoproteome.” J Proteome Res 8 (6): 2633–39. Cite
Eddy, James A., Donald Geman, and Nathan D. Price. 2009. “Relative Expression Analysis for Identifying Perturbed Pathways.” Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 2009: 5456–59. https://doi.org/10.1109/IEMBS.2009.5334063. Cite
Edelman, Lucas B., Giuseppe Toia, Donald Geman, Wei Zhang, and Nathan D. Price. 2009. “Two-Transcript Gene Expression Classifiers in the Diagnosis and Prognosis of Human Diseases.” BMC Genomics 10. https://doi.org/10.1186/1471-2164-10-583. Cite
Eisenacher, M., L. Martens, T. Hardt, M. Kohl, H. Barsnes, K. Helsens, J. Hakkinen, et al. 2009. “Getting a Grip on Proteomics Data - Proteomics Data Collection (ProDaC).” Proteomics 9 (15): 3928–33. Cite
Fagarasanu, A., F. D. Mast, B. Knoblach, Y. Jin, M. J. Brunner, M. R. Logan, J. N. Glover, et al. 2009. “Myosin-Driven Peroxisome Partitioning in S. Cerevisiae.” J Cell Biol 186 (4): 541–54. Cite
Fedorov, V. B., A. V. Goropashnaya, O. Toien, N. C. Stewart, A. Y. Gracey, C. Chang, S. Qin, et al. 2009. “Elevated Expression of Protein Biosynthesis Genes in Liver and Muscle of Hibernating Black Bears (Ursus Americanus).” Physiol Genomics 37 (2): 108–18. Cite
Foltz, G., J. G. Yoon, H. Lee, T. C. Ryken, Z. Sibenaller, M. Ehrich, L. Hood, and A. Madan. 2009. “DNA Methyltransferase-Mediated Transcriptional Silencing in Malignant Glioma: A Combined Whole-Genome Microarray and Promoter Array Analysis.” Oncogene 28 (29): 2667–77. Cite
Foster, David V., Jacob G. Foster, S. Huang, and Stuart A. Kauffman. 2009. “A Model of Sequential Branching in Hierarchical Cell Fate Determination.” Journal of Theoretical Biology 260 (4): 589–97. https://doi.org/10.1016/j.jtbi.2009.07.005. Cite
Fu, E., K. E. Nelson, S. A. Ramsey, J. O. Foley, K. Helton, and P. Yager. 2009. “Modeling of a Competitive Microfluidic Heterogeneous Immunoassay: Sensitivity of the Assay Response to Varying System Parameters.” Anal Chem 81 (9): 3407–13. Cite
Fulton, D. L., S. Sundararajan, G. Badis, T. R. Hughes, W. W. Wasserman, J. Roach, and R. Sladek. 2009. “TFCat: The Curated Catalog of Mouse and Human Transcription Factors.” Genome Biol 10 (3): R29. Cite
Galas, D. J., and L. Hood. 2009. “Systems Biology and Emerging Technologies Will Catalyze the Transition from Reactive Medicine to Predictive, Personalized, Preventive and Participatory (P4) Medicine.” Interdisciplinary Bio Central 1 (2): 0006. Cite
Gehlenborg, N., W. Yan, I. Lee, H. Yoo, K. Nieselt, D. Hwang, R. Aebersold, and L. Hood. 2009. “Prequips–an Extensible Software Platform for Integration, Visualization and Analysis of LC-MS/MS Proteomics Data.” Bioinformatics 25 (5): 682–83. Cite
Gehlenborg, N., D. Hwang, I. Lee, H. Yoo, D. Baxter, B. Petritis, R. Pitstick, et al. 2009. “The Prion Disease Database: A Comprehensive Transcriptome Resource for Systems Biology Research in Prion Diseases.” Database : The Journal of Biological Databases and Curation 2009: bap011. Cite
Ghosh, D., X. Yan, and Q. Tian. 2009. “Gene Regulatory Networks in Embryonic Stem Cells and Brain Development.” Birth Defects Res C Embryo Today 87 (2): 182–91. Cite
Gillespie, M. A., F. Le Grand, A. Scime, S. Kuang, J. von Maltzahn, V. Seale, A. Cuenda, J. Ranish, and M. A. Rudnicki. 2009. “P38-Gamma-Dependent Gene Silencing Restricts Entry into the Myogenic Differentiation Program.” J Cell Biol 187 (7): 991–1005. Cite
Glatter, T., A. Wepf, R. Aebersold, and M. Gstaiger. 2009. “An Integrated Workflow for Charting the Human Interaction Proteome: Insights into the PP2A System.” Mol Syst Biol 5: 237. Cite
Glusman, G., and A. Smit. 2009. “Genome Organization.” In Encyclopedia of Complexity and Systems Science, 4:4160–78. New York: Springer. Cite
Goetze, S., E. Qeli, C. Mosimann, A. Staes, B. Gerrits, B. Roschitzki, S. Mohanty, et al. 2009. “Identification and Functional Characterization of N-Terminally Acetylated Proteins in Drosophila Melanogaster.” PLoS Biol 7 (11): e1000236. Cite
Goudreault, M., L. M. D’Ambrosio, M. J. Kean, M. J. Mullin, B. G. Larsen, A. Sanchez, S. Chaudhry, et al. 2009. “A PP2A Phosphatase High Density Interaction Network Identifies a Novel Striatin-Interacting Phosphatase and Kinase Complex Linked to the Cerebral Cavernous Malformation 3 (CCM3) Protein.” Mol Cell Proteomics 8 (1): 157–71. Cite
Gradolatto, A., S. K. Smart, S. Byrum, L. P. Blair, R. S. Rogers, E. A. Kolar, H. Lavender, et al. 2009. “A Noncanonical Bromodomain in the AAA ATPase Protein Yta7 Directs Chromosomal Positioning and Barrier Chromatin Activity.” Mol Cell Biol 29 (17): 4604–11. Cite
Gstaiger, M., and R. Aebersold. 2009. “Applying Mass Spectrometry-Based Proteomics to Genetics, Genomics and Network Biology.” Nat Rev Genet 10 (9): 617–27. Cite
Hawn, T. R., D. Scholes, S. S. Li, H. Wang, Y. Yang, P. L. Roberts, A. E. Stapleton, et al. 2009. “Toll-like Receptor Polymorphisms and Susceptibility to Urinary Tract Infections in Adult Women.” PLoS OnePLoS ONE 4 (6): e5990. Cite
Hawn, T. R., D. Scholes, H. Wang, S. S. Li, A. E. Stapleton, M. Janer, A. Aderem, W. E. Stamm, L. P. Zhao, and T. M. Hooton. 2009. “Genetic Variation of the Human Urinary Tract Innate Immune Response and Asymptomatic Bacteriuria in Women.” PLoS OnePLoS ONE 4 (12): e8300. Cite
Heath, J. R., M. E. Davis, and L. Hood. 2009. “Nanomedicine Targets Cancer.” Sci Am 300 (2): 44–51. Cite
Hemmi, H., J. Idoyaga, K. Suda, N. Suda, K. Kennedy, M. Noda, A. Aderem, and R. M. Steinman. 2009. “A New Triggering Receptor Expressed on Myeloid Cells (Trem) Family Member, Trem-like 4, Binds to Dead Cells and Is a DNAX Activation Protein 12-Linked Marker for Subsets of Mouse Macrophages and Dendritic Cells.” J Immunol 182 (3): 1278–86. Cite
Hertz, A. L., A. T. Bender, K. C. Smith, M. Gilchrist, P. S. Amieux, A. Aderem, and J. A. Beavo. 2009. “Elevated Cyclic AMP and PDE4 Inhibition Induce Chemokine Expression in Human Monocyte-Derived Macrophages.” Proc Natl Acad Sci U S A 106 (51): 21978–83. Cite