Publications

2008

Aderem, A. 2008. “Alan Aderem: From Molecules to Megabytes. Interviewed by Nicole LeBrasseur.” J Cell Biol 180 (2): 252–53. Cite
Aderem, A., and I. Shmulevich. 2008. “Taming Data.” Cell Host Microbe 4 (4): 312–13. Cite
Andrecut, M., S. Huang, and S. A. Kauffman. 2008. “Heuristic Approach to Sparse Approximation of Gene Regulatory Networks.” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 15 (9): 1173–86. https://doi.org/10.1089/cmb.2008.0087. Cite
Ao, P., D. J. Galas, L. Hood, and X. Zhu. 2008. “Cancer as Robust Intrinsic State of Endogenous Molecular-Cellular Network Shaped by Evolution.” Med Hypotheses 70 (3): 678–84. Cite
Baliga, N. S. 2008. “Systems Biology. The Scale of Prediction.” Science 320 (5881): 1297–98. Cite
Balleza, E., E. R. Alvarez-Buylla, A. Chaos, S. Kauffman, I. Shmulevich, and M. Aldana. 2008. “Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms.” PLoS OnePLoS ONE 3 (6): e2456. Cite
Bao, Xin-Yu, Cesare Soci, Darija Susac, Jon Bratvold, David P. R. Aplin, Wei Wei, Ching-Yang Chen, Shadi A. Dayeh, Karen L. Kavanagh, and Deli Wang. 2008. “Heteroepitaxial Growth of Vertical GaAs Nanowires on Si (111) Substrates by Metal−Organic Chemical Vapor Deposition.” Nano Letters 8 (11): 3755–60. https://doi.org/10.1021/nl802062y. Cite
Bochud, P. Y., T. R. Hawn, M. R. Siddiqui, P. Saunderson, S. Britton, I. Abraham, A. T. Argaw, et al. 2008. “Toll-like Receptor 2 (TLR2) Polymorphisms Are Associated with Reversal Reaction in Leprosy.” J Infect Dis 197 (2): 253–61. Cite
Bochud, P. Y., J. W. Chien, K. A. Marr, W. M. Leisenring, A. Upton, M. Janer, S. D. Rodrigues, et al. 2008. “Toll-like Receptor 4 Polymorphisms and Aspergillosis in Stem-Cell Transplantation.” N Engl J Med 359 (17): 1766–77. Cite
Bodenmiller, B., D. Campbell, B. Gerrits, H. Lam, M. Jovanovic, P. Picotti, R. Schlapbach, and R. Aebersold. 2008. “PhosphoPep–a Database of Protein Phosphorylation Sites in Model Organisms.” Nat Biotechnol 26 (12): 1339–40. Cite
Boyle, J., C. Cavnor, S. Killcoyne, and I. Shmulevich. 2008. “Systems Biology Driven Software Design for the Research Enterprise.” BMC Bioinformatics 9: 295. Cite
Brusniak, M. Y., B. Bodenmiller, D. Campbell, K. Cooke, J. Eddes, A. Garbutt, H. Lau, et al. 2008. “Corra: Computational Framework and Tools for LC-MS Discovery and Targeted Mass Spectrometry-Based Proteomics.” BMC Bioinformatics 9: 542. Cite
Carter, G. W., V. Thorsson, and T. Galitski. 2008. “Integrated Network Modeling of Molecular and Genetic Interactions.” In Sourcebook of Models for Biomedical Research, 67–74. Humana Press. Cite
Chang, Hannah H., Martin Hemberg, Mauricio Barahona, Donald E. Ingber, and S. Huang. 2008. “Transcriptome-Wide Noise Controls Lineage Choice in Mammalian Progenitor Cells.” Nature 453 (7194): 544–47. https://doi.org/10.1038/nature06965. Cite
Charles, J. F., M. B. Humphrey, X. Zhao, E. Quarles, M. C. Nakamura, A. Aderem, W. E. Seaman, and K. D. Smith. 2008. “The Innate Immune Response to Salmonella Enterica Serovar Typhimurium by Macrophages Is Dependent on TREM2-DAP12.” Infect Immun 76 (6): 2439–47. Cite
Chen, Meng, Misook Ha, Erika Lackey, Jianlin Wang, and Z. Jeffrey Chen. 2008. “RNAi of Met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids.” Genetics 178 (April): 1845–58. https://doi.org/10.1534/genetics.107.086272. Cite
Chi, Y., M. Welcker, A. A. Hizli, J. J. Posakony, R. Aebersold, and B. E. Clurman. 2008. “Identification of CDK2 Substrates in Human Cell Lysates.” Genome Biol 9 (10): R149. Cite
Deutsch, E. W., C. A. Ball, J. J. Berman, G. S. Bova, A. Brazma, R. E. Bumgarner, D. Campbell, et al. 2008. “Minimum Information Specification for in Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).” Nat Biotechnol 26 (3): 305–12. Cite
Deutsch, E. W., H. Lam, and R. Aebersold. 2008. “Data Analysis and Bioinformatics Tools for Tandem Mass Spectrometry in Proteomics.” Physiol Genomics 33 (1): 18–25. Cite
Deutsch, E. W., H. Lam, and R. Aebersold. 2008. “PeptideAtlas: A Resource for Target Selection for Emerging Targeted Proteomics Workflows.” EMBO Rep 9 (5): 429–34. Cite
Dishaw, L. J., M. G. Mueller, N. Gwatney, J. P. Cannon, R. N. Haire, R. T. Litman, C. T. Amemiya, et al. 2008. “Genomic Complexity of the Variable Region-Containing Chitin-Binding Proteins in Amphioxus.” BMC Genet 9: 78. Cite
E, P., D. B, F. C, D. O, V. T, and D. G. Am. 2008. “The Inactivation of a New Peptidoglycan Hydrolase Pmp23 Leads to Abnormal Septum Formation in Streptococcus Pneumoniae.” Open Microbiol J 2: 107–14. Cite
Fan, R., O. Vermesh, A. Srivastava, B. K. Yen, L. Qin, H. Ahmad, G. A. Kwong, et al. 2008. “Integrated Barcode Chips for Rapid, Multiplexed Analysis of Proteins in Microliter Quantities of Blood.” Nat Biotechnol 26 (12): 1373–78. Cite
Gavin, A. C., R. Aebersold, and A. J. Heck. 2008. “Meeting Report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology.” Mol Cell Proteomics 7 (11): 2288–91. Cite
Geiss, G. K., R. E. Bumgarner, B. Birditt, T. Dahl, N. Dowidar, D. L. Dunaway, H. P. Fell, et al. 2008. “Direct Multiplexed Measurement of Gene Expression with Color-Coded Probe Pairs.” Nat Biotechnol 26 (3): 317–25. Cite
Georgescu, C., W. Longabaugh, D. D. Scripture-Adams, E. S. David-Fung, M. A. Yui, M. A. Zarnegar, H. Bolouri, and E. V. Rothenberg. 2008. “A Gene Regulatory Network Armature for T Lymphocyte Specification.” Proc Natl Acad Sci U S A 105 (51): 20100–105. Cite
Gilchrist, M., Jr Henderson, A. E. Clark, R. M. Simmons, X. Ye, K. D. Smith, and A. Aderem. 2008. “Activating Transcription Factor 3 Is a Negative Regulator of Allergic Pulmonary Inflammation.” J Exp Med 205 (10): 2349–57. Cite
Gradolatto, A., R. S. Rogers, H. Lavender, S. D. Taverna, C. D. Allis, J. D. Aitchison, and A. J. Tackett. 2008. “Saccharomyces Cerevisiae Yta7 Regulates Histone Gene Expression.” Genetics 179 (1): 291–304. Cite
Hershberg, R., M. Lipatov, P. M. Small, H. Sheffer, S. Niemann, S. Homolka, J. Roach, et al. 2008. “High Functional Diversity in Mycobacterium Tuberculosis Driven by Genetic Drift and Human Demography.” PLoS Biol 6 (12): e311. Cite
Himeda, C. L., J. Ranish, and S. D. Hauschka. 2008. “Quantitative Proteomic Identification of MAZ as a Transcriptional Regulator of Muscle-Specific Genes in Skeletal and Cardiac Myocytes.” Mol Cell Biol 28 (20): 6521–35. Cite
Hoffmann, Martin, Hannah H. Chang, S. Huang, Donald E. Ingber, Markus Loeffler, and Joerg Galle. 2008. “Noise-Driven Stem Cell and Progenitor Population Dynamics.” PloS One 3 (8): e2922. https://doi.org/10.1371/journal.pone.0002922. Cite
Hohmann, L. J., J. K. Eng, A. Gemmill, J. Klimek, O. Vitek, G. E. Reid, and D. B. Martin. 2008. “Quantification of the Compositional Information Provided by Immonium Ions on a Quadrupole-Time-of-Flight Mass Spectrometer.” Anal Chem 80 (14): 5596–5606. Cite
Hood, L. 2008. “Gene Regulatory Networks and Embryonic Specification.” Proc Natl Acad Sci U S A 105 (16): 5951–52. Cite
Hood, L. E. 2008. “Wu and Kabat 1970: A Transforming View of Antibody Diversity.” J Immunol 180 (11): 7055–56. Cite
Hood, L. 2008. “A Personal Journey of Discovery: Developing Technology and Changing Biology.” Annu Rev Anal Chem (Palo Alto Calif) 1: 1–43. Cite
Hood, L., L. Rowen, D. J. Galas, and J. D. Aitchison. 2008. “Systems Biology at the Institute for Systems Biology.” Brief Funct Genomic Proteomic 7 (4): 239–48. Cite
Huertas-Vazquez, A., C. L. Plaisier, D. Weissglas-Volkov, J. Sinsheimer, S. Canizales-Quinteros, I. Cruz-Bautista, E. Nikkola, et al. 2008. “TCF7L2 Is Associated with High Serum Triacylglycerol and Differentially Expressed in Adipose Tissue in Families with Familial Combined Hyperlipidaemia.” Diabetologia 51 (January): 62–69. https://doi.org/10.1007/s00125-007-0850-6. Cite
Hwang, D., N. Zhang, H. Lee, E. Yi, H. Zhang, I. Lee, L. Hood, and R. Aebersold. 2008. “MS-BID: A Java Package for Label-Free LC-MS-Based Comparative Proteomic Analysis.” Bioinformatics 24 (22): 2641–42. Cite
Johanneson, B., S. K. McDonnell, D. M. Karyadi, S. J. Hebbring, L. Wang, K. Deutsch, L. McIntosh, et al. 2008. “Fine Mapping of Familial Prostate Cancer Families Narrows the Interval for a Susceptibility Locus on Chromosome 22q12.3 to 1.36 Mb.” Hum Genet 123 (1): 65–75. Cite
Kauffman, S., R. K. Logan, R. Este, R. Goebel, D. Hobill, and I. Shmulevich. 2008. “Propagating Organization: An Enquiry.” Biology and Philosophy 23 (1): 27–45. Cite
Klimek, J., J. S. Eddes, L. Hohmann, J. Jackson, A. Peterson, S. Letarte, P. R. Gafken, et al. 2008. “The Standard Protein Mix Database: A Diverse Data Set to Assist in the Production of Improved Peptide and Protein Identification Software Tools.” J Proteome Res 7 (1): 96–103. Cite
Korb, M., A. G. Rust, V. Thorsson, C. Battail, B. Li, D. Hwang, K. A. Kennedy, et al. 2008. “The Innate Immune Database (IIDB).” BMC Immunol 9: 7. Cite
Lähdesmäki, H., and I. Shmulevich. 2008. “Learning the Structure of Dynamic Bayesian Networks from Time Series and Steady State Measurements.” Machine Learning 71 (2): 185–217. Cite
Lahdesmaki, H., A. G. Rust, and I. Shmulevich. 2008. “Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources.” PLoS OnePLoS ONE 3 (3): e1820. Cite
Lam, H., E. W. Deutsch, J. S. Eddes, J. K. Eng, S. E. Stein, and R. Aebersold. 2008. “Building Consensus Spectral Libraries for Peptide Identification in Proteomics.” Nat Methods 5 (10): 873–75. Cite
Lange, V., P. Picotti, B. Domon, and R. Aebersold. 2008. “Selected Reaction Monitoring for Quantitative Proteomics: A Tutorial.” Mol Syst Biol 4: 222. Cite
Lange, V., J. A. Malmstrom, J. Didion, N. L. King, B. P. Johansson, J. Schafer, J. Rameseder, et al. 2008. “Targeted Quantitative Analysis of Streptococcus Pyogenes Virulence Factors by Multiple Reaction Monitoring.” Mol Cell Proteomics 7 (8): 1489–1500. Cite
Lausted, Christopher, Zhiyuan Hu, and Leroy Hood. 2008. “Quantitative Serum Proteomics from Surface Plasmon Resonance Imaging.” Mol Cell Proteomics 7 (December): 2464–74. https://doi.org/10.1074/mcp.M800121-MCP200. Cite
Lee, W. W., D. Cui, M. Czesnikiewicz-Guzik, R. Z. Vencio, I. Shmulevich, A. Aderem, C. M. Weyand, and J. J. Goronzy. 2008. “Age-Dependent Signature of Metallothionein Expression in Primary CD4 T Cell Responses Is Due to Sustained Zinc Signaling.” Rejuvenation Res 11 (6): 1001–11. Cite