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Amplification of CRKL Induces Transformation and Epidermal Growth Factor Receptor Inhibitor Resistance in Human Non-Small Cell Lung Cancers.
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A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
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Expression of the p53 Target CDIP Correlates with Sensitivity to TNFα-Induced Apoptosis in Cancer Cells.
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Absolute quantification of somatic DNA alterations in human cancer.
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RNA-SeQC: RNA-seq metrics for quality control and process optimization.
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Scientific Publications

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2012

Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.Udeshi, ND, Mani D. R., Eisenhaure T., Mertins P., Jaffe JD, Clauser KR, Hacohen N., and Carr SA Molecular & cellular proteomics : MCP, 2012/04/14, (2012) Read More / View Supplemental Materials

STK33 kinase inhibitor BRD-8899 has no effect on KRAS-dependent cancer cell viability.Luo, T., Masson K., Jaffe JD, Silkworth W., Ross NT, Scherer CA, Scholl C., Fröhling S., Carr SA, Stern AM, Schreiber SL, and Golub T. R. Proceedings of the National Academy of Sciences of the United States of America, 2012/02/21, Volume 109, Issue 8, p.2860-5, (2012) Read More / View Supplemental Materials

Identifying cellular targets of small-molecule probes and drugs with biochemical enrichment and SILAC.Ong, SE, Li X., Schenone M., Schreiber SL, and Carr SA Methods in molecular biology (Clifton, N.J.), 2012/01/09, Volume 803, p.129-40, (2012) Read More / View Supplemental Materials

2011

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.Mertins, P., Udeshi ND, Clauser KR, Mani D. R., Patel J., Ong SE, Jaffe JD, and Carr SA Molecular & cellular proteomics : MCP, 2011/12/30, (2011) Read More / View Supplemental Materials

The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.Naba, A., Clauser KR, Hoersch S., Liu H., Carr SA, and Hynes R. O. Molecular & cellular proteomics : MCP, 2011/12/09, (2011) Read More / View Supplemental Materials

Systematic discovery of TLR signaling components delineates viral-sensing circuits.Chevrier, N., Mertins P., Artyomov MN, Shalek AK, Iannacone M., Ciaccio MF, Gat-Viks I., Tonti E., Degrace MM, Clauser KR, Garber M., Eisenhaure TM, Yosef N., Robinson J., Sutton A., Andersen MS, Root DE, von Andrian U., Jones RB, Park H., et al. Cell, 2011/11/11, Volume 147, Issue 4, p.853-67, (2011) Read More / View Supplemental Materials

Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation.Tucker, EJ, Hershman SG, Köhrer C., Belcher-Timme CA, Patel J., Goldberger OA, Christodoulou J., Silberstein JM, McKenzie M., Ryan MT, Compton AG, Jaffe JD, Carr SA, Calvo SE, RajBhandary UL, Thorburn DR, and Mootha VK Cell metabolism, 2011/09/07, Volume 14, Issue 3, p.428-34, (2011) Read More / View Supplemental Materials

Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics.Gerszten, RE, Asnani A., and Carr SA Circulation research, 2011/08/05, Volume 109, Issue 4, p.463-74, (2011) Read More / View Supplemental Materials

Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry.Zhao, L., Whiteaker JR, Pope ME, Kuhn E., Jackson A., Anderson NL, Pearson TW, Carr SA, and Paulovich AG Journal of visualized experiments : JoVE, 2011/07/31, Issue 53, (2011) Read More / View Supplemental Materials

AAK1 identified as an inhibitor of neuregulin-1/ErbB4-dependent neurotrophic factor signaling using integrative chemical genomics and proteomics.Kuai, L., Ong SE, Madison JM, Wang X., Duvall JR, Lewis TA, Luce CJ, Conner SD, Pearlman DA, Wood JL, Schreiber SL, Carr SA, Scolnick EM, and Haggarty SJ Chemistry & biology, 2011/07/29, Volume 18, Issue 7, p.891-906, (2011) Read More / View Supplemental Materials

Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity.Yu, M., Romer KA, Nieland TJ, Xu S., Saenz-Vash V., Penman M., Yesilaltay A., Carr SA, and Krieger M. Proceedings of the National Academy of Sciences of the United States of America, 2011/07/26, Volume 108, Issue 30, p.12243-8, (2011) Read More / View Supplemental Materials

Selective killing of cancer cells by a small molecule targeting the stress response to ROS.Raj, L., Ide T., Gurkar AU, Foley M., Schenone M., Li X., Tolliday NJ, Golub T. R., Carr SA, Shamji AF, Stern AM, Mandinova A., Schreiber SL, and Lee SW Nature, 2011/07/13, Volume 475, Issue 7355, p.231-4, (2011) Read More / View Supplemental Materials

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease.Addona, TA, Shi X., Keshishian H., Mani D. R., Burgess M., Gillette MA, Clauser KR, Shen D., Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, and Carr SA Nature biotechnology, 2011/06/19, Volume 29, Issue 7, p.635-43, (2011) Read More / View Supplemental Materials

Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry.Whiteaker, JR, Zhao L., Abbatiello SE, Burgess M., Kuhn E., Lin C., Pope ME, Razavi M., Anderson NL, Pearson TW, Carr SA, and Paulovich AG Molecular & cellular proteomics : MCP, 2011/04/01, Volume 10, Issue 4, p.M110.005645, (2011) Read More / View Supplemental Materials

Lipid profiling identifies a triacylglycerol signature of insulin resistance and improves diabetes prediction in humans.Rhee, EP, Cheng S., Larson MG, Walford GA, Lewis GD, McCabe E., Yang E., Farrell L., Fox CS, O'Donnell CJ, Carr SA, Vasan RS, Florez JC, Clish CB, Wang TJ, and Gerszten RE The Journal of clinical investigation, 2011/04/01, Volume 121, Issue 4, p.1402-11, (2011) Read More / View Supplemental Materials

Metabolite profiles and the risk of developing diabetes.Wang, TJ, Larson MG, Vasan RS, Cheng S., Rhee EP, McCabe E., Lewis GD, Fox CS, Jacques PF, Fernandez C., O'Donnell CJ, Carr SA, Mootha VK, Florez JC, Souza A., Melander O., Clish CB, and Gerszten RE Nature medicine, 2011/04/01, Volume 17, Issue 4, p.448-53, (2011) Read More / View Supplemental Materials

2010

Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease.Bradner, JE, Mak R., Tanguturi SK, Mazitschek R., Haggarty SJ, Ross K., Chang CY, Bosco J., West N., Morse E., Lin K., Shen JP, Kwiatkowski NP, Gheldof N., Dekker J., DeAngelo DJ, Carr SA, Schreiber SL, Golub T. R., and Ebert BL Proceedings of the National Academy of Sciences of the United States of America, 2010/07/13, Volume 107, Issue 28, p.12617-22, (2010) Read More / View Supplemental Materials

Rictor phosphorylation on the Thr-1135 site does not require mammalian target of rapamycin complex 2.Boulbes, D., Chen CH, Shaikenov T., Agarwal NK, Peterson TR, Addona TA, Keshishian H., Carr SA, Magnuson MA, Sabatini DM, and Sarbassov dos D. Molecular cancer research : MCR, 2010/06/01, Volume 8, Issue 6, p.896-906, (2010) Read More / View Supplemental Materials

Metabolic signatures of exercise in human plasma.Lewis, GD, Farrell L., Wood MJ, Martinovic M., Arany Z., Rowe GC, Souza A., Cheng S., McCabe EL, Yang E., Shi X., Deo R., Roth FP, Asnani A., Rhee EP, Systrom DM, Semigran MJ, Vasan RS, Carr SA, Wang TJ, et al. Science translational medicine, 2010/05/26, Volume 2, Issue 33, p.33ra37, (2010) Read More / View Supplemental Materials

Optimizing performance of glycopeptide capture for plasma proteomics.Berven, FS, Ahmad R., Clauser KR, and Carr SA Journal of proteome research, 2010/04/05, Volume 9, Issue 4, p.1706-15, (2010) Read More / View Supplemental Materials

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.Tabb, DL, Vega-Montoto L., Rudnick PA, Variyath AM, Ham AJ, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling B., Tegeler TJ, Wang M., Wang P., et al. Journal of proteome research, 2010/02/05, Volume 9, Issue 2, p.761-76, (2010) Read More / View Supplemental Materials

Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics.Rodriguez, H., Tezak Z., Mesri M., Carr SA, Liebler DC, Fisher SJ, Tempst P., Hiltke T., Kessler LG, Kinsinger CR, Philip R., Ransohoff DF, Skates SJ, Regnier FE, Anderson NL, Mansfield E., and Workshop Participants Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.237-43, (2010) Read More / View Supplemental Materials

Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry.Abbatiello, SE, Mani D. R., Keshishian H., and Carr SA Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.291-305, (2010) Read More / View Supplemental Materials

Integration of proteomic-based tools for improved biomarkers of myocardial injury.Gerszten, RE, Carr SA, and Sabatine M. Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.194-201, (2010) Read More / View Supplemental Materials

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.Paulovich, AG, Billheimer D., Ham AJ, Vega-Montoto L., Rudnick PA, Tabb DL, Wang P., Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B., Tegeler TJ, Variyath AM, Wang M., Whiteaker JR, Zimmerman LJ, Fenyo D., Carr SA, et al. Molecular & cellular proteomics : MCP, 2010/02/01, Volume 9, Issue 2, p.242-54, (2010) Read More / View Supplemental Materials

Introduction: Advances in protein analysis for the clinical laboratory.Hortin, GL, Carr SA, and Anderson NL Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.149-51, (2010) Read More / View Supplemental Materials

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.Rudnick, PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P., Blonder N., Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M., Neubert TA, Schilling B., Tabb DL, Tegeler TJ, Vega-Montoto L., Variyath AM, et al. Molecular & cellular proteomics : MCP, 2010/02/01, Volume 9, Issue 2, p.225-41, (2010) Read More / View Supplemental Materials

Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration.Regnier, FE, Skates SJ, Mesri M., Rodriguez H., Tezak Z., Kondratovich MV, Alterman MA, Levin JD, Roscoe D., Reilly E., Callaghan J., Kelm K., Brown D., Philip R., Carr SA, Liebler DC, Fisher SJ, Tempst P., Hiltke T., Kessler LG, et al. Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.165-71, (2010) Read More / View Supplemental Materials

A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint.van Vugt, MA, Gardino AK, Linding R., Ostheimer GJ, Reinhardt HC, Ong SE, Tan CS, Miao H., Keezer SM, Li J., Pawson T., Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR, and Yaffe MB PLoS biology, 2010/01/26, Volume 8, Issue 1, p.e1000287, (2010) Read More / View Supplemental Materials

2009

ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.Markljung, E., Jiang L., Jaffe JD, Mikkelsen TS, Wallerman O., Larhammar M., Zhang X., Wang L., Saenz-Vash V., Gnirke A., Lindroth AM, Barrés R., Yan J., Strömberg S., De S., Pontén F., Lander E. S., Carr SA, Zierath JR, Kullander K., et al. PLoS biology, 2009/12/01, Volume 7, Issue 12, p.e1000256, (2009) Read More / View Supplemental Materials

Empirical Bayes analysis of quantitative proteomics experiments.Margolin, AA, Ong SE, Schenone M., Gould R., Schreiber SL, Carr SA, and Golub T. R. PloS one, 2009/10/14, Volume 4, Issue 10, p.e7454, (2009) Read More / View Supplemental Materials

Proteomic and genetic approaches identify Syk as an AML target.Hahn, CK, Berchuck JE, Ross KN, Kakoza RM, Clauser K., Schinzel AC, Ross L., Galinsky I., Davis TN, Silver SJ, Root DE, Stone RM, DeAngelo DJ, Carroll M., Hahn WC, Carr SA, Golub T. R., Kung AL, and Stegmaier K. Cancer cell, 2009/10/06, Volume 16, Issue 4, p.281-94, (2009) Read More / View Supplemental Materials

Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution.Keshishian, H., Addona T., Burgess M., Mani D. R., Shi X., Kuhn E., Sabatine MS, Gerszten RE, and Carr SA Molecular & cellular proteomics : MCP, 2009/10/01, Volume 8, Issue 10, p.2339-49, (2009) Read More / View Supplemental Materials

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.Addona, TA, Abbatiello SE, Schilling B., Skates SJ, Mani D. R., Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H., Hall SC, Allen S., Blackman RK, Borchers CH, Buck C., Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, et al. Nature biotechnology, 2009/07/01, Volume 27, Issue 7, p.633-41, (2009) Read More / View Supplemental Materials

Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry.Kuhn, E., Addona T., Keshishian H., Burgess M., Mani D. R., Lee RT, Sabatine MS, Gerszten RE, and Carr SA Clinical chemistry, 2009/06/01, Volume 55, Issue 6, p.1108-17, (2009) Read More / View Supplemental Materials

Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx).Rudomin, EL, Carr SA, and Jaffe JD Journal of proteome research, 2009/06/01, Volume 8, Issue 6, p.3154-60, (2009) Read More / View Supplemental Materials

Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells.Burkard, ME, Maciejowski J., Rodriguez-Bravo V., Repka M., Lowery DM, Clauser KR, Zhang C., Shokat KM, Carr SA, Yaffe MB, and Jallepalli PV PLoS biology, 2009/05/05, Volume 7, Issue 5, p.e1000111, (2009) Read More / View Supplemental Materials

A human proteome detection and quantitation project.Anderson, NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M., Aebersold R., and Carr SA Molecular & cellular proteomics : MCP, 2009/05/01, Volume 8, Issue 5, p.883-6, (2009) Read More / View Supplemental Materials

Identifying the proteins to which small-molecule probes and drugs bind in cells.Ong, SE, Schenone M., Margolin AA, Li X., Do K., Doud MK, Mani D. R., Kuai L., Wang X., Wood JL, Tolliday NJ, Koehler AN, Marcaurelle LA, Golub T. R., Gould RJ, Schreiber SL, and Carr SA Proceedings of the National Academy of Sciences of the United States of America, 2009/03/24, Volume 106, Issue 12, p.4617-22, (2009) Read More / View Supplemental Materials

Prediction of high-responding peptides for targeted protein assays by mass spectrometry.Fusaro, VA, Mani D. R., Mesirov J. P., and Carr SA Nature biotechnology, 2009/02/01, Volume 27, Issue 2, p.190-8, (2009) Read More / View Supplemental Materials

Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy.Du, J., Bernasconi P., Clauser KR, Mani D. R., Finn SP, Beroukhim R., Burns M., Julian B., Peng XP, Hieronymus H., Maglathlin RL, Lewis TA, Liau LM, Nghiemphu P., Mellinghoff IK, Louis DN, Loda M., Carr SA, Kung AL, and Golub T. R. Nature biotechnology, 2009/01/01, Volume 27, Issue 1, p.77-83, (2009) Read More / View Supplemental Materials

2008

Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?Carr, SA, and Anderson L. Clinical chemistry, 2008/11/01, Volume 54, Issue 11, p.1749-52, (2008) Read More / View Supplemental Materials

Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification.Jaffe, JD, Keshishian H., Chang B., Addona TA, Gillette MA, and Carr SA Molecular & cellular proteomics : MCP, 2008/10/01, Volume 7, Issue 10, p.1952-62, (2008) Read More / View Supplemental Materials

Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury.Lewis, GD, Wei R., Liu E., Yang E., Shi X., Martinovic M., Farrell L., Asnani A., Cyrille M., Ramanathan A., Shaham O., Berriz G., Lowry PA, Palacios IF, Taşan M., Roth FP, Min J., Baumgartner C., Keshishian H., Addona T., et al. The Journal of clinical investigation, 2008/10/01, Volume 118, Issue 10, p.3503-12, (2008) Read More / View Supplemental Materials

A mitochondrial protein compendium elucidates complex I disease biology.Pagliarini, DJ, Calvo SE, Chang B., Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C., Boneh A., Chen WK, Hill DE, Vidal M., Evans JG, Thorburn DR, Carr SA, and Mootha VK Cell, 2008/07/11, Volume 134, Issue 1, p.112-23, (2008) Read More / View Supplemental Materials

Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity.Shaham, O., Wei R., Wang TJ, Ricciardi C., Lewis GD, Vasan RS, Carr SA, Thadhani R., Gerszten RE, and Mootha VK Molecular systems biology, 2008/01/01, Volume 4, p.214, (2008) Read More / View Supplemental Materials

2007

Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution.Keshishian, H., Addona T., Burgess M., Kuhn E., and Carr SA Molecular & cellular proteomics : MCP, 2007/12/01, Volume 6, Issue 12, p.2212-29, (2007) Read More / View Supplemental Materials

Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.Lowery, DM, Clauser KR, Hjerrild M., Lim D., Alexander J., Kishi K., Ong SE, Gammeltoft S., Carr SA, and Yaffe MB The EMBO journal, 2007/05/02, Volume 26, Issue 9, p.2262-73, (2007) Read More / View Supplemental Materials

PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase.Sancak, Y., Thoreen CC, Peterson TR, Lindquist RA, Kang SA, Spooner E., Carr SA, and Sabatini DM Molecular cell, 2007/03/23, Volume 25, Issue 6, p.903-15, (2007) Read More / View Supplemental Materials

2006

PEPPeR, a platform for experimental proteomic pattern recognition.Jaffe, JD, Mani D. R., Leptos KC, Church GM, Gillette MA, and Carr SA Molecular & cellular proteomics : MCP, 2006/10/01, Volume 5, Issue 10, p.1927-41, (2006) Read More / View Supplemental Materials

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.Lamb, J., Crawford ED, Peck D., Modell JW, Blat IC, Wrobel MJ, Lerner J., Brunet JP, Subramanian A., Ross KN, Reich M., Hieronymus H., Wei G., Armstrong SA, Haggarty SJ, Clemons PA, Wei R., Carr SA, Lander E. S., and Golub T. R. Science (New York, N.Y.), 2006/09/29, Volume 313, Issue 5795, p.1929-35, (2006) Read More / View Supplemental Materials

mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s.Frias, MA, Thoreen CC, Jaffe JD, Schroder W., Sculley T., Carr SA, and Sabatini DM Current biology : CB, 2006/09/19, Volume 16, Issue 18, p.1865-70, (2006) Read More / View Supplemental Materials

Protein biomarker discovery and validation: the long and uncertain path to clinical utility.Rifai, N., Gillette MA, and Carr SA Nature biotechnology, 2006/08/01, Volume 24, Issue 8, p.971-83, (2006) Read More / View Supplemental Materials

Systematic identification of human mitochondrial disease genes through integrative genomics.Calvo, S., Jain M., Xie X., Sheth SA, Chang B., Goldberger OA, Spinazzola A., Zeviani M., Carr SA, and Mootha VK Nature genetics, 2006/05/01, Volume 38, Issue 5, p.576-82, (2006) Read More / View Supplemental Materials

2005

Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics.Carr, SA, Annan RS, and Huddleston MJ Methods in enzymology, 2005/01/01, Volume 405, p.82-115, (2005) Read More / View Supplemental Materials

2004

Selective detection of glycopeptides on ion trap mass spectrometers.Sullivan, B., Addona TA, and Carr SA Analytical chemistry, 2004/06/01, Volume 76, Issue 11, p.3112-8, (2004) Read More / View Supplemental Materials

1969

Place of pattern in proteomic biomarker discovery.Gillette, MA, Mani D. R., and Carr SA Journal of proteome research, 2005/1/1, Volume 4, Issue 4, p.1143-54, (1969) Read More / View Supplemental Materials