Publications

2010

Amon, L. M., W. Law, M. P. Fitzgibbon, J. A. Gross, K. O’Briant, A. Peterson, C. Drescher, D. B. Martin, and M. McIntosh. 2010. “Integrative Proteomic Analysis of Serum and Peritoneal Fluids Helps Identify Proteins That Are Up-Regulated in Serum of Women with Ovarian Cancer.” PLoS OnePLoS ONE 5 (6): e11137. Cite
Ao, P., D. J. Galas, L. Hood, L. Yin, and X. M. Zhu. 2010. “Towards Predictive Stochastic Dynamical Modeling of Cancer Genesis and Progression.” Interdiscip Sci 2 (2): 140–44. Cite
Arpanaei, A., B. Winther-Jensen, E. Theodosiou, P. Kingshott, T. J. Hobley, and O. R. Thomas. 2010. “Surface Modification of Chromatography Adsorbents by Low Temperature Low Pressure Plasma.” J Chromatogr A 1217 (44): 6905–16. Cite
Auffray, C., T. Ideker, D. J. Galas, and L. Hood. 2010. “The Hallmarks of Cancer Revisited through Systems Biology and Network Modeling.” In Cancer Systems Biology, Bioinformatics and Medicine: Research and Clinical Applications. Springer Science & Business Media B.V. Cite
Bare, J. C., T. Koide, D. J. Reiss, D. Tenenbaum, and N. S. Baliga. 2010. “Integration and Visualization of Systems Biology Data in Context of the Genome.” BMC Bioinformatics 11: 382. Cite
Beck, C., H. Morbach, M. Beer, M. Stenzel, D. Tappe, S. Gattenlohner, U. Hofmann, P. Raab, and H. J. Girschick. 2010. “Chronic Nonbacterial Osteomyelitis in Childhood: Prospective Follow-up during the First Year of Anti-Inflammatory Treatment.” Arthritis Res Ther 12 (2): R74. Cite
Berrington, W. R., M. Macdonald, S. Khadge, B. R. Sapkota, M. Janer, D. A. Hagge, G. Kaplan, and T. R. Hawn. 2010. “Common Polymorphisms in the NOD2 Gene Region Are Associated with Leprosy and Its Reactive States.” J Infect Dis 201 (9): 1422–35. Cite
Bodenmiller, B., S. Wanka, C. Kraft, J. Urban, D. Campbell, P. G. Pedrioli, B. Gerrits, et al. 2010. “Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast.” Sci Signal 3 (153): rs4. Cite
Bracha, Abigail L., Arvind Ramanathan, S. Huang, Donald E. Ingber, and Stuart L. Schreiber. 2010. “Carbon Metabolism-Mediated Myogenic Differentiation.” Nature Chemical Biology 6 (3): 202–4. https://doi.org/10.1038/nchembio.301. Cite
Burdick, D. B., C. C. Cavnor, J. Handcock, S. Killcoyne, J. Lin, B. Marzolf, S. A. Ramsey, et al. 2010. “SEQADAPT: An Adaptable System for the Tracking, Storage and Analysis of High Throughput Sequencing Experiments.” BMC Bioinformatics 11: 377. Cite
Carter, G. W., C. G. Rush, F. Uygun, N. A. Sakhanenko, D. J. Galas, and T. Galitski. 2010. “A Systems-Biology Approach to Modular Genetic Complexity.” Chaos 20 (2): 026102. Cite
Chandrasekaran, Sriram, and Nathan D. Price. 2010. “Probabilistic Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks in Escherichia Coli and Mycobacterium Tuberculosis.” Proceedings of the National Academy of Sciences of the United States of America 107 (41): 17845–50. https://doi.org/10.1073/pnas.1005139107. Cite
Cheng, L., W. Lu, B. Kulkarni, T. Pejovic, X. Yan, J. H. Chiang, L. Hood, K. Odunsi, and B. Lin. 2010. “Analysis of Chemotherapy Response Programs in Ovarian Cancers by the Next-Generation Sequencing Technologies.” Gynecol Oncol 117 (2): 159–69. Cite
Christensen, G. B., A. B. Baffoe-Bonnie, A. George, I. Powell, J. E. Bailey-Wilson, J. D. Carpten, G. G. Giles, et al. 2010. “Genome-Wide Linkage Analysis of 1,233 Prostate Cancer Pedigrees from the International Consortium for Prostate Cancer Genetics Using Novel SumLINK and SumLOD Analyses.” Prostate 70 (7): 735–44. Cite
Sol, A. del, R. Balling, L. Hood, and D. J. Galas. 2010. “Diseases as Network Perturbations.” Curr Opin Biotechnol 21 (4): 566–71. Cite
Deutsch, E. W. 2010. “Mass Spectrometer Output File Format MzML.” Methods Mol Biol 604: 319–31. Cite
Deutsch, E. W. 2010. “The PeptideAtlas Project.” Methods Mol Biol 604: 285–96. Cite
Deutsch, E. W., L. Mendoza, D. Shteynberg, T. Farrah, H. Lam, N. Tasman, Z. Sun, et al. 2010. “A Guided Tour of the Trans-Proteomic Pipeline.” Proteomics 10 (6): 1150–59. Cite
Deutsch, E. W., D. Shteynberg, H. Lam, Z. Sun, J. K. Eng, C. Carapito, P. D. von Haller, et al. 2010. “Trans-Proteomic Pipeline Supports and Improves Analysis of Electron Transfer Dissociation Data Sets.” Proteomics 10 (6): 1190–95. Cite
Diercks, A. K., A. Schwab, W. Rittgen, A. Kruspel, E. Heuss, and J. Schenkel. 2010. “Environmental Influences on the Production of Pre-Implantation Embryos.” Theriogenology 73 (9): 1238–43. Cite
Dilworth, D. J., R. A. Saleem, R. S. Rogers, H. Mirzaei, J. Boyle, and J. D. Aitchison. 2010. “QTIPS: A Novel Method of Unsupervised Determination of Isotopic Amino Acid Distribution in SILAC Experiments.” J Am Soc Mass Spectrom 21 (8): 1417–22. Cite
Eddy, James A., Leroy Hood, Nathan D. Price, and Donald Geman. 2010. “Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC).” PLoS Computational Biology 6 (5). https://doi.org/10.1371/journal.pcbi.1000792. Cite
Eddy, James A., Jaeyun Sung, Donald Geman, and Nathan D. Price. 2010. “Relative Expression Analysis for Molecular Cancer Diagnosis and Prognosis.” Technology in Cancer Research & Treatment 9 (2): 149–59. Cite
Edelman, Lucas B., Sriram Chandrasekaran, and Nathan D. Price. 2010. “Systems Biology of Embryogenesis.” Reproduction, Fertility, and Development 22 (1). https://doi.org/10.1071/RD09215. Cite
Edelman, Lucas B., James A. Eddy, and Nathan D. Price. 2010. “In Silico Models of Cancer.” Wiley Interdisciplinary Reviews. Systems Biology and Medicine 2 (4): 438–59. https://doi.org/10.1002/wsbm.75. Cite
Erkkila, T., S. Lehmusvaara, P. Ruusuvuori, T. Visakorpi, I. Shmulevich, and H. Lahdesmaki. 2010. “Probabilistic Analysis of Gene Expression Measurements from Heterogeneous Tissues.” Bioinformatics 26 (20): 2571–77. Cite
Ezeji, Thaddeus, Caroline Milne, Nathan D. Price, and Hans P. Blaschek. 2010. “Achievements and Perspectives to Overcome the Poor Solvent Resistance in Acetone  and Butanol-Producing Microorganisms.” Applied Microbiology and Biotechnology 85 (6): 1697–1712. https://doi.org/10.1007/s00253-009-2390-0. Cite
Facciotti, M. T., W. L. Pang, F. Y. Lo, K. Whitehead, T. Koide, K. Masumura, M. Pan, et al. 2010. “Large Scale Physiological Readjustment during Growth Enables Rapid, Comprehensive and Inexpensive Systems Analysis.” BMC Syst Biol 4: 64. Cite
Fitzgerald, L. M., S. K. McDonnell, E. E. Carlson, W. Langeberg, L. M. McIntosh, K. Deutsch, E. A. Ostrander, D. J. Schaid, and J. L. Stanford. 2010. “Genome-Wide Linkage Analyses of Hereditary Prostate Cancer Families with Colon Cancer Provide Further Evidence for a Susceptibility Locus on 15q11-Q14.” Eur J Hum Genet 18 (10): 1141–47. Cite
Flamez, D., I. Roland, A. Berton, B. Kutlu, D. Dufrane, M. C. Beckers, E. De Waele, et al. 2010. “A Genomic-Based Approach Identifies FXYD Domain Containing Ion Transport Regulator 2 (FXYD2)Gammaa as a Pancreatic Beta Cell-Specific Biomarker.” Diabetologia 53 (7): 1372–83. Cite
Foltz, G., J. G. Yoon, H. Lee, L. Ma, Q. Tian, L. Hood, and A. Madan. 2010. “Epigenetic Regulation of Wnt Pathway Antagonists in Human Glioblastoma Multiforme.” Genes & Cancer 1 (1): 81. Cite
Galas, D. J., M. Nykter, G. W. Carter, N. D. Price, and I. Shmulevich. 2010. “Biological Information as Set-Based Complexity.” IEEE Transactions on Information Theory 56 (2): 667–77. Cite
Gehlenborg, N., S. I. O’Donoghue, N. S. Baliga, A. Goesmann, M. A. Hibbs, H. Kitano, O. Kohlbacher, et al. 2010. “Visualization of Omics Data for Systems Biology.” Nat Methods 7 (3 Suppl): S56-68. Cite
Gilchrist, M., Jr Henderson, A. Morotti, C. D. Johnson, A. Nachman, F. Schmitz, K. D. Smith, and A. Aderem. 2010. “A Key Role for ATF3 in Regulating Mast Cell Survival and Mediator Release.” Blood 115 (23): 4734–41. Cite
Gizzatkulov, N. M., I. I. Goryanin, E. A. Metelkin, E. A. Mogilevskaya, K. V. Peskov, and O. V. Demin. 2010. “DBSolve Optimum: A Software Package for Kinetic Modeling Which Allows Dynamic Visualization of Simulation Results.” BMC Syst Biol 4: 109. Cite
Glusman, G., B. Marzolf, K. Wang, J.-H. Cho, B. Kutlu, and Q. Tian. 2010. “Bioinformatics Strategies for Understanding Gene Expression in Human Pluripotent Cells.” In Human Stem Cell Technology and Biology: A Research Guide and Laboratory Manual. Wiley-Blackwell. Cite
Handcock, J., E. W. Deutsch, and J. Boyle. 2010. “MspecLINE: Bridging Knowledge of Human Disease with the Proteome.” BMC Med Genomics 3: 7. Cite
Himeda, C. L., J. Ranish, R. C. Pearson, M. Crossley, and S. D. Hauschka. 2010. “KLF3 Regulates Muscle-Specific Gene Expression and Synergizes with Serum Response Factor on KLF Binding Sites.” Mol Cell Biol 30 (14): 3430–43. Cite
Holstein Sherwood, C. A., P. R. Gafken, and D. B. Martin. 2010. “Collision Energy Optimization of B- and y-Ions for Multiple Reaction Monitoring Mass Spectrometry.” J Proteome Res, November. Cite
Huang, S. 2010. “Cell Lineage Determination in State Space: A Systems View Brings Flexibility to Dogmatic Canonical Rules.” PLOS Biol 8 (5): e1000380. https://doi.org/10.1371/journal.pbio.1000380. Cite Download
Johanneson, B., S. K. McDonnell, D. M. Karyadi, P. Quignon, L. McIntosh, S. M. Riska, L. M. Fitzgerald, et al. 2010. “Family-Based Association Analysis of 42 Hereditary Prostate Cancer Families Identifies the Apolipoprotein L3 Region on Chromosome 22q12 as a Risk Locus.” Hum Mol Genet 19 (19): 3852–62. Cite
Jung, S., M. Marelli, R. A. Rachubinski, D. R. Goodlett, and J. D. Aitchison. 2010. “Dynamic Changes in the Subcellular Distribution of Gpd1p in Response to Cell Stress.” J Biol Chem 285 (9): 6739–49. Cite
Kaur, A., P. T. Van, C. R. Busch, C. K. Robinson, M. Pan, W. L. Pang, D. J. Reiss, J. DiRuggiero, and N. S. Baliga. 2010. “Coordination of Frontline Defense Mechanisms under Severe Oxidative Stress.” Mol Syst Biol 6 (July): 393. Cite
Kim, Pan-Jun, and Nathan D. Price. 2010. “Macroscopic Kinetic Effect of Cell-to-Cell Variation in Biochemical Reactions.” Physical Review Letters 104 (14): 148103. Cite
Lam, H., E. W. Deutsch, and R. Aebersold. 2010. “Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics.” J Proteome Res 9 (1): 605–10. Cite
Lee, H. J., J. E. Suk, C. Patrick, E. J. Bae, J. H. Cho, S. Rho, D. Hwang, E. Masliah, and S. J. Lee. 2010. “Direct Transfer of Alpha-Synuclein from Neuron to Astroglia Causes Inflammatory Responses in Synucleinopathies.” J Biol Chem 285 (12): 9262–72. Cite
Lee, L. W., S. Zhang, A. Etheridge, L. Ma, D. Martin, D. J. Galas, and K. Wang. 2010. “Complexity of the MicroRNA Repertoire Revealed by Next-Generation Sequencing.” RNA 16 (11): 2170–80. Cite
Lin, B., A. Madan, J. G. Yoon, X. Fang, X. Yan, T. K. Kim, D. Hwang, L. Hood, and G. Foltz. 2010. “Massively Parallel Signature Sequencing and Bioinformatics Analysis Identifies Up-Regulation of TGFBI and SOX4 in Human Glioblastoma.” PLoS OnePLoS ONE 5 (4): e10210. Cite
Ma, Shuyi, Cory C. Funk, and Nathan D. Price. 2010. “Systems Approaches to Molecular Cancer Diagnostics.” Discovery Medicine 10 (55): 531–42. Cite
Mansson, M., R. K. Phipps, L. Gram, M. H. Munro, T. O. Larsen, and K. F. Nielsen. 2010. “Explorative Solid-Phase Extraction (E-SPE) for Accelerated Microbial Natural Product Discovery, Dereplication, and Purification.” J Nat Prod 73 (6): 1126–32. Cite