Publications

Frühwirth R., Mani D.R., and S. Pyne. (2011) "Clustering with position-specific constraints on variance: Applying redescending M-estimators to label-free LC-MS data analysis." BMC Bioinformatics 12: 358. Abstract

Tucker E.J., S.G. Hershman, et al. (2011) "Mutations in MTFMT Underlie a Human Disorder of Formylation Causing Impaired Mitochondrial Translation." Cell Metab 14(3): 428-434. Abstract

Burgener A., S. Rahman, et al. (2011) "A comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers." J Proteome Res. Under revision.

Zhao L., J.R. Whiteaker, et al. (2011) "Quantification of proteins using Peptide immunoaffinity enrichment coupled with mass spectrometry." J Vis Exp 53: pii: 2812. Abstract

Yu M., K.A. Romer, et al. (2011) "Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity." Proc Natl Acad Sci USA 108(30): 12243-12248. Abstract

Kuai L., S.E. Ong, et al. (2011) "AAK1 Identified as an Inhibitor of Neuregulin-1/ErbB4-Dependent Neurotrophic Factor Signaling Using Integrative Chemical Genomics and Proteomics." Chem Biol 18(7): 891-906. Abstract

Addona T.A., X. Shi, et al. (2011) "A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease." Nature Biotechnol. 29(7): 635-643. Abstract

Raj L., T. Ide, et al. (2011)  "Selective killing of cancer cells by a small molecule targeting the stress response to ROS." Nature 475(7355): 231-234. Abstract

Gerszten R.E., A. Asnani, et al. (2011) "Status and Prospects for Discovery and Verification of New Biomarkers of Cardiovascular Disease by Proteomics." Circ Res 209(4): 463-474. Abstract

Rhee E.P., S. Cheng, et al. (2011) "Lipid Profiling Identifies a Triacylglycerol Signature of Insulin Resistance and Improves Diabetes Prediction in Humans."  J Clin Investigation 121(4): 1402-1411. Abstract

Wang T.J., M.G. Larson, et al. (2011) "Metabolite Profiles and the Risk of Developing Diabetes."  Nat Med 17(4): 448-453. Abstract

Whiteaker J.R., L. Zhao, et al. (2011) "Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry." Mol Cell Proteomics 10(4): M110.005645. Abstract

Lewis, G. D., L. Farrell, et al. (2010) "Metabolic signatures of exercise in human plasma." Sci Transl Med 2:33ra37. Abstract

Boulbes, D., C. H. Chen, et al. (2010) "Rictor phosphorylation on the Thr-1135 site does not require mammalian target of rapamycin complex 2." Mol Cancer Res 8:896-906. Abstract

Bradner, J. E., R. Mak, et al. (2010) "Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease." Proc Natl Acad Sci U S A 107:12617-22. Abstract

van Vugt, M. A., A. K. Gardino, et al. (2010) "A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint." PLoS Biol 8:e1000287. Abstract

Tabb, D. L., L. Vega-Montoto, et al. (2010) "Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry." J Proteome Res 9:761-76. Abstract

Rodriguez, H., Z. Tezak, et al. (2010) "Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics." Clin Chem 56:237-43. Abstract

Regnier, F. E., S. J. Skates, et al. (2010) "Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration." Clin Chem 56:165-71. Abstract

Paulovich, A. G., D. Billheimer, et al. (2010) "A CPTAC Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance." Mol Cell Proteomics 9:242-54. Abstract

Hortin, G. L., S. A. Carr, et al. (2010) "Introduction: Advances in protein analysis for the clinical laboratory." Clin Chem 56:149-51. Abstract

Gerszten, R. E., S. A. Carr, et al. (2010) "Integration of proteomic-based tools for improved biomarkers of myocardial injury." Clin Chem 56:194-201. Abstract

Abbatiello, S. E., D. R. Mani, et al. (2010) "Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry." Clin Chem 56:291-305. Abstract

Rudnick, P. A., K. R. Clauser, et al. (2010) "Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses." Mol Cell Proteomics 9:225-41. Abstract

Berven, F. S., R. Ahmad, et al. (2010) "Optimizing performance of glycopeptide capture for plasma proteomics." J Proteome Res 9:1706-15. Abstract

Hahn, C. K., J. E. Berchuck, et al. (2009) "Proteomic and genetic approaches identify Syk as an AML target." Cancer Cell 16:281-94. Abstract

Keshishian, H., T. Addona, et al. (2009) "Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution." Mol Cell Proteomics 8:2339-49. Abstract

Burkard, M. E., J. Maciejowski, et al. (2009) "Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells." PLoS Biol 7:e1000111. Abstract

Anderson, N. L., N. G. Anderson, et al. (2009) "A human proteome detection and quantitation project." Mol Cell Proteomics 8:883-6. Abstract

Ong, S. E., M. Schenone, et al. (2009) "Identifying the proteins to which small-molecule probes and drugs bind in cells." Proc Natl Acad Sci U S A 106:4617-22. Abstract

Rudomin, E. L., S. A. Carr, et al. (2009) "Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx)." J Proteome Res 8:3154-60. Abstract

Kuhn, E., T. Addona, et al. (2009) "Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry." Clin Chem 55:1108-17. Abstract

Addona, T. A., S. E. Abbatiello, et al. (2009) "Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma." Nat Biotechnol 27:633-41. Abstract

Du, J., P. Bernasconi, et al. (2009) "Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy." Nat Biotechnol 27:77-83. Abstract

Fusaro, V. A., D. R. Mani, et al. (2009) "Prediction of high-responding peptides for targeted protein assays by mass spectrometry." Nat Biotechnol 27:190-8. Abstract

Markljung, E., L. Jiang, et al. (2009) "ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth." PLoS Biol 7:e1000256. Abstract

Margolin, A. A., S. E. Ong, et al. (2009) "Empirical Bayes analysis of quantitative proteomics experiments." PLoS One 4:e7454. Abstract

Lewis, G. D., R. Wei, et al. (2008) "Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury." J Clin Invest 118:3503-12. Abstract

Jaffe, J. D., H. Keshishian, et al. (2008) "Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification." Mol Cell Proteomics 7:1952-62. Abstract PDF

Carr, S. A. and L. Anderson (2008) "Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?" Clin Chem 54:1749-52. Abstract

Pagliarini, D. J., S. E. Calvo, et al. (2008) "A mitochondrial protein compendium elucidates complex I disease biology." Cell 134:112-23. Abstract

Shaham, O., R. Wei, et al. (2008) "Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity." Mol Syst Biol 4:214. Abstract

Lowery, D. M., K. R. Clauser, et al. (2007) "Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate." Embo J 26:2262-73. Abstract

Sancak, Y., C. C. Thoreen, et al. (2007) "PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase." Mol Cell 25:903-15. Abstract

Keshishian, H., T. Addona, et al. (2007) "Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution." Mol Cell Proteomics 6:2212-29. Abstract

Lamb, J., E. D. Crawford, et al. (2006) "The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease." Science 313:1929-35. Abstract

Frias, M. A., C. C. Thoreen, et al. (2006) "mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s." Curr Biol 16:1865-70. Abstract

Jaffe, J. D., D. R. Mani, et al. (2006) "PEPPeR, a platform for experimental proteomic pattern recognition." Mol Cell Proteomics 5:1927-41. Abstract

Calvo, S., M. Jain, et al. (2006) "Systematic identification of human mitochondrial disease genes through integrative genomics." Nat Genet 38:576-82. Abstract

Rifai, N., M. A. Gillette, et al. (2006) "Protein biomarker discovery and validation: the long and uncertain path to clinical utility." Nat Biotechnol 24:971-83. Abstract

Gillette, M. A., D. R. Mani, et al. (2005) "Place of pattern in proteomic biomarker discovery." J Proteome Res 4:1143-54. Abstract

Carr, S. A., R. S. Annan, et al. (2005) "Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics." Methods Enzymol 405:82-115. Abstract

Sullivan, B., T. A. Addona, et al. (2004) "Selective detection of glycopeptides on ion trap mass spectrometers." Anal Chem 76:3112-8. Abstract