Recent Proteomics Platform Publications

Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.Abelin, JG, Patel J., Lu X., Feeney CM, Fagbami L., Creech AL, Hu R., Lam D., Davison D., Pino L., Qiao JW, Kuhn E., Officer A., Li J., Abbatiello S., Subramanian A., Sidman R., Snyder E., Carr SA, and Jaffe JD Molecular & cellular proteomics : MCP, 2016/05/01, Volume 15, Issue 5, p.1622-41, (2016) Read More / View Supplemental Materials
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Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.Tabb, DL, Wang X., Carr SA, Clauser KR, Mertins P., Chambers MC, Holman JD, Wang J., Zhang B., Zimmerman LJ, Chen X., Gunawardena HP, Davies SR, Ellis MJ, Li S., Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M., et al. Journal of proteome research, 2016/03/04, Volume 15, Issue 3, p.691-706, (2016) Read More / View Supplemental Materials
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An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.Ruggles, KV, Tang Z., Wang X., Grover H., Askenazi M., Teubl J., Cao S., McLellan MD, Clauser KR, Tabb DL, Mertins P., Slebos R., Erdmann-Gilmore P., Li S., Gunawardena HP, Xie L., Liu T., Zhou JY, Sun S., Hoadley KA, et al. Molecular & cellular proteomics : MCP, 2016/03/01, Volume 15, Issue 3, p.1060-71, (2016) Read More / View Supplemental Materials
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Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2.Hung, V., Udeshi ND, Lam SS, Loh KH, Cox KJ, Pedram K., Carr SA, and Ting AY Nature protocols, 2016/03/01, Volume 11, Issue 3, p.456-75, (2016) Read More / View Supplemental Materials
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Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8 and S100A9.Schneider, RK, Schenone M., Ferreira MV, Kramann R., Joyce CE, Hartigan C., Beier F., Brümmendorf TH, Germing U., Platzbecker U., Büsche G., Knüchel R., Chen MC, Waters CS, Chen E., Chu LP, Novina CD, Lindsley RC, Carr SA, and Ebert BL Nature medicine, 2016/03/01, Volume 22, Issue 3, p.288-97, (2016) Read More / View Supplemental Materials
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Identification of cancer-cytotoxic modulators of PDE3A by predictive chemogenomics.de Waal, L., Lewis TA, Rees MG, Tsherniak A., Wu X., Choi PS, Hartigan C., Faloon PW, Hickey MJ, Tolliday N., Carr SA, Clemons PA, Munoz B., Wagner BK, Shamji AF, Koehler AN, Schenone M., Burgin AB, Schreiber SL, Greulich H., et al. Nature chemical biology, 2016/02/01, Volume 12, Issue 2, p.102-8, (2016) Read More / View Supplemental Materials
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Multiplexed Immunoaffinity Enrichment of Peptides with Anti-peptide Antibodies and Quantification by Stable Isotope Dilution Multiple Reaction Monitoring Mass Spectrometry.Kuhn, E., and Carr SA Methods in molecular biology (Clifton, N.J.), 2016/01/01, Volume 1410, p.135-67, (2016) Read More / View Supplemental Materials
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Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.Hoofnagle, AN, Whiteaker JR, Carr SA, Kuhn E., Liu T., Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E., Chen J., Crimmins DL, Davies SR, Gao Y., Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M., Meyer MR, Qian WJ, et al. Clinical chemistry, 2016/01/01, Volume 62, Issue 1, p.48-69, (2016) Read More / View Supplemental Materials
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Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.Whiteaker, JR, Halusa GN, Hoofnagle AN, Sharma V., Maclean B., Yan P., Wrobel JA, Kennedy J., Mani D. R., Zimmerman LJ, Meyer MR, Mesri M., Boja E., Carr SA, Chan DW, Chen X., Chen J., Davies SR, Ellis MJ, Fenyö D., et al. Methods in molecular biology (Clifton, N.J.), 2016/01/01, Volume 1410, p.223-36, (2016) Read More / View Supplemental Materials
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Corrigendum: 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, 2015/10/22, Volume 526, Issue 7574, p.596, (2015) Read More / View Supplemental Materials
Responses to Bacteria, Virus and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia.Valim, C., Ahmad R., Lanaspa M., Tan Y., Acácio S., Gillette MA, Almendinger KD, Milner DA Jr, Madrid L., Pellé K., Harezlak J., Silterra J., Alonso PL, Carr SA, Mesirov J. P., Wirth DF, Wiegand RC, and Bassat Q. American journal of respiratory and critical care medicine, 2015/10/15, (2015) Read More / View Supplemental Materials
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Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis.Kroksveen, AC, Jaffe JD, Aasebø E., Barsnes H., Bjørlykke Y., Franciotta D., Keshishian H., Myhr KM, Opsahl JA, van Pesch V., Teunissen CE, Torkildsen Ø., Ulvik RJ, Vethe H., Carr SA, and Berven FS Proteomics, 2015/10/01, Volume 15, Issue 19, p.3361-9, (2015) Read More / View Supplemental Materials
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Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase.Chen, CL, Hu Y., Udeshi ND, Lau TY, Wirtz-Peitz F., He L., Ting AY, Carr SA, and Perrimon N. Proceedings of the National Academy of Sciences of the United States of America, 2015/09/29, Volume 112, Issue 39, p.12093-8, (2015) Read More / View Supplemental Materials
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Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.Abbatiello, SE, Schilling B., Mani D. R., Zimmerman LJ, Hall SC, Maclean B., Albertolle M., Allen S., Burgess M., Cusack MP, Gosh M., Hedrick V., Held JM, Inerowicz HD, Jackson A., Keshishian H., Kinsinger CR, Lyssand J., Makowski L., Mesri M., et al. Molecular & cellular proteomics : MCP, 2015/09/01, Volume 14, Issue 9, p.2357-74, (2015) Read More / View Supplemental Materials
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Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.Keshishian, H., Burgess MW, Gillette MA, Mertins P., Clauser KR, Mani D. R., Kuhn EW, Farrell LA, Gerszten RE, and Carr SA Molecular & cellular proteomics : MCP, 2015/09/01, Volume 14, Issue 9, p.2375-93, (2015) Read More / View Supplemental Materials
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Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow.Svinkina, T., Gu H., Silva JC, Mertins P., Qiao J., Fereshetian S., Jaffe JD, Kuhn E., Udeshi ND, and Carr SA Molecular & cellular proteomics : MCP, 2015/09/01, Volume 14, Issue 9, p.2429-40, (2015) Read More / View Supplemental Materials
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A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.Parnas, O., Jovanovic M., Eisenhaure TM, Herbst RH, Dixit A., Ye CJ, Przybylski D., Platt RJ, Tirosh I., Sanjana NE, Shalem O., Satija R., Raychowdhury R., Mertins P., Carr SA, Zhang F., Hacohen N., and Regev A. Cell, 2015/07/30, Volume 162, Issue 3, p.675-86, (2015) Read More / View Supplemental Materials
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Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS.Krönke, J., Fink EC, Hollenbach PW, MacBeth KJ, Hurst SN, Udeshi ND, Chamberlain PP, Mani D. R., Man HW, Gandhi AK, Svinkina T., Schneider RK, McConkey M., Järås M., Griffiths E., Wetzler M., Bullinger L., Cathers BE, Carr SA, Chopra R., et al. Nature, 2015/07/09, Volume 523, Issue 7559, p.183-8, (2015) Read More / View Supplemental Materials
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The extracellular matrix: Tools and insights for the "omics" era.Naba, A., Clauser KR, Ding H., Whittaker CA, Carr SA, and Hynes R. O. Matrix biology : journal of the International Society for Matrix Biology, 2015/07/08, (2015) Read More / View Supplemental Materials
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On Credibility, Clarity, and Compliance.Burlingame, A., Carr SA, Bradshaw RA, and Chalkley RJ Molecular & cellular proteomics : MCP, 2015/07/01, Volume 14, Issue 7, p.1731-3, (2015) Read More / View Supplemental Materials
Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.Begun, J., Lassen KG, Jijon HB, Baxt LA, Goel G., Heath RJ, Ng A., Tam JM, Kuo SY, Villablanca EJ, Fagbami L., Oosting M., Kumar V., Schenone M., Carr SA, Joosten LA, Vyas JM, Daly M. J., Netea MG, Brown GD, et al. Cell reports, 2015/06/30, Volume 11, Issue 12, p.1905-18, (2015) Read More / View Supplemental Materials
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Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling.Chou, DH, Vetere A., Choudhary A., Scully SS, Schenone M., Tang A., Gomez R., Burns SM, Lundh M., Vital T., Comer E., Faloon PW, Dančík V., Ciarlo C., Paulk J., Dai M., Reddy C., Sun H., Young M., Donato N., et al. Journal of the American Chemical Society, 2015/06/24, Volume 137, Issue 24, p.7929-34, (2015) Read More / View Supplemental Materials
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Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.Maier, VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A., Das PP, Chevrier N., Cifuentes-Rojas C., Orkin SH, Carr SA, Jaffe JD, Mertins P., and Lee JT Molecular & cellular proteomics : MCP, 2015/06/01, Volume 14, Issue 6, p.1435-46, (2015) Read More / View Supplemental Materials
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Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.Jovanovic, M., Rooney MS, Mertins P., Przybylski D., Chevrier N., Satija R., Rodriguez EH, Fields AP, Schwartz S., Raychowdhury R., Mumbach MR, Eisenhaure T., Rabani M., Gennert D., Lu D., Delorey T., Weissman JS, Carr SA, Hacohen N., and Regev A. Science (New York, N.Y.), 2015/03/06, Volume 347, Issue 6226, p.1259038, (2015) Read More / View Supplemental Materials
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Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.Creech, AL, Taylor JE, Maier VK, Wu X., Feeney CM, Udeshi ND, Peach SE, Boehm JS, Lee JT, Carr SA, and Jaffe JD Methods (San Diego, Calif.), 2015/01/15, Volume 72, p.57-64, (2015) Read More / View Supplemental Materials
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Antibody-based capture of target peptides in multiple reaction monitoring experiments.De Marchi, T., Kuhn E., Carr SA, and Umar A. Methods in molecular biology (Clifton, N.J.), 2015/01/01, Volume 1293, p.123-35, (2015) Read More / View Supplemental Materials
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Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer.Theurillat, JP, Udeshi ND, Errington WJ, Svinkina T., Baca SC, Pop M., Wild PJ, Blattner M., Groner AC, Rubin MA, Moch H., Privé GG, Carr SA, and Garraway LA Science (New York, N.Y.), 2014/10/03, Volume 346, Issue 6205, p.85-9, (2014) Read More / View Supplemental Materials
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Proteogenomic characterization of human colon and rectal cancer.Zhang, B., Wang J., Wang X., Zhu J., Liu Q., Shi Z., Chambers MC, Zimmerman LJ, Shaddox KF, Kim S., Davies SR, Wang S., Wang P., Kinsinger CR, Rivers RC, Rodriguez H., Townsend RR, Ellis MJ, Carr SA, Tabb DL, et al. Nature, 2014/09/18, Volume 513, Issue 7518, p.382-7, (2014) Read More / View Supplemental Materials
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Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver.Naba, A., Clauser KR, Whittaker CA, Carr SA, Tanabe KK, and Hynes R. O. BMC cancer, 2014/07/18, Volume 14, p.518, (2014) Read More / View Supplemental Materials
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Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.Hung, V., Zou P., Rhee HW, Udeshi ND, Cracan V., Svinkina T., Carr SA, Mootha VK, and Ting AY Molecular cell, 2014/07/17, Volume 55, Issue 2, p.332-41, (2014) Read More / View Supplemental Materials
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CPTAC Assay Portal: a repository of targeted proteomic assays.Whiteaker, JR, Halusa GN, Hoofnagle AN, Sharma V., Maclean B., Yan P., Wrobel JA, Kennedy J., Mani D. R., Zimmerman LJ, Meyer MR, Mesri M., Rodriguez H., Clinical Proteomic Tumor Analysis Consortium(CPTAC), and Paulovich AG Nature methods, 2014/06/27, Volume 11, Issue 7, p.703-4, (2014) Read More / View Supplemental Materials
A framework for installable external tools in Skyline.Broudy, D., Killeen T., Choi M., Shulman N., Mani D. R., Abbatiello SE, Mani D., Ahmad R., Sahu AK, Schilling B., Tamura K., Boss Y., Sharma V., Gibson BW, Carr SA, Vitek O., Maccoss MJ, and Maclean B. Bioinformatics (Oxford, England), 2014/05/09, (2014) Read More / View Supplemental Materials
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Mycobacterial esx-3 requires multiple components for iron acquisition.Siegrist, MS, Steigedal M., Ahmad R., Mehra A., Dragset MS, Schuster BM, Philips JA, Carr SA, and Rubin EJ mBio, 2014/05/06, Volume 5, Issue 3, (2014) Read More / View Supplemental Materials
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Simplified and Efficient Quantification of Low-abundance Proteins at Very High Multiplex via Targeted Mass Spectrometry.Burgess, MW, Keshishian H., Mani D. R., Gillette MA, and Carr SA Molecular & cellular proteomics : MCP, 2014/04/01, Volume 13, Issue 4, p.1137-49, (2014) Read More / View Supplemental Materials
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Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters.Naba, A., Clauser KR, Lamar JM, Carr SA, and Hynes R. O. eLife, 2014/03/11, Volume 3, p.e01308, (2014) Read More / View Supplemental Materials
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Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach.Carr, SA, Abbatiello SE, Ackermann BL, Borchers C., Domon B., Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R., Koomen JM, Liebler DC, Liu T., Maclean B., Mani D., Mansfield E., Neubert H., Paulovich AG, Reiter L., Vitek O., Aebersold R., et al. Molecular & cellular proteomics : MCP, 2014/03/01, Volume 13, Issue 3, p.907-17, (2014) Read More / View Supplemental Materials
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Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.Kennedy, JJ, Abbatiello SE, Kim K., Yan P., Whiteaker JR, Lin C., Kim JS, Zhang Y., Wang X., Ivey RG, Zhao L., Min H., Lee Y., Yu MH, Yang EG, Lee C., Wang P., Rodriguez H., Kim Y., Carr SA, et al. Nature methods, 2014/02/01, Volume 11, Issue 2, p.149-55, (2014) Read More / View Supplemental Materials
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Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells.Krönke, J., Udeshi ND, Narla A., Grauman P., Hurst SN, McConkey M., Svinkina T., Heckl D., Comer E., Li X., Ciarlo C., Hartman E., Munshi N., Schenone M., Schreiber SL, Carr SA, and Ebert BL Science (New York, N.Y.), 2014/01/17, Volume 343, Issue 6168, p.301-5, (2014) Read More / View Supplemental Materials
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Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defenseKG, Lassen, P Kuballa, KL Conway, KK Patel, CE Becker, JM Peloquin, EJ Villablanca, JM Norman, T Liu, RJ Heath, ML Becker, L Fagbami, H Horn, J Mercer, OH Yilmaz, JJ Jaffe, AF Shamji, AK Bhan, SA Carr, MJ Daly, et al. Molecular & cellular proteomics : MCP, (2014) Read More / View Supplemental Materials
EMRE is an essential component of the mitochondrial calcium uniporter complex.Sancak, Y., Markhard AL, Kitami T., Kovács-Bogdán E., Kamer KJ, Udeshi ND, Carr SA, Chaudhuri D., Clapham DE, Li AA, Calvo SE, Goldberger O., and Mootha VK Science (New York, N.Y.), 2013/12/13, Volume 342, Issue 6164, p.1379-82, (2013) Read More / View Supplemental Materials
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Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies.Skates, SJ, Gillette MA, LaBaer J., Carr SA, Anderson L., Liebler DC, Ransohoff D., Rifai N., Kondratovich M., Težak Ž., Mansfield E., Oberg AL, Wright I., Barnes G., Gail M., Mesri M., Kinsinger CR, Rodriguez H., and Boja ES Journal of proteome research, 2013/12/06, Volume 12, Issue 12, p.5383-94, (2013) Read More / View Supplemental Materials
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High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.Schwartz, S., Agarwala SD, Mumbach MR, Jovanovic M., Mertins P., Shishkin A., Tabach Y., Mikkelsen TS, Satija R., Ruvkun G., Carr SA, Lander E. S., Fink GR, and Regev A. Cell, 2013/12/05, Volume 155, Issue 6, p.1409-21, (2013) Read More / View Supplemental Materials
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Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia.Jaffe, JD, Wang Y., Chan HM, Zhang J., Huether R., Kryukov GV, Bhang HE, Taylor JE, Hu M., Englund NP, Yan F., Wang Z., Robert McDonald E 3rd, Wei L., Ma J., Easton J., Yu Z., Debeaumount R., Gibaja V., Venkatesan K., et al. Nature genetics, 2013/11/01, Volume 45, Issue 11, p.1386-91, (2013) Read More / View Supplemental Materials
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Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium.Ellis, MJ, Gillette M., Carr SA, Paulovich AG, Smith RD, Rodland KK, Townsend RR, Kinsinger C., Mesri M., Rodriguez H., Liebler DC, and Clinical Proteomic Tumor Analysis Consortium(CPTAC) Cancer discovery, 2013/10/01, Volume 3, Issue 10, p.1108-12, (2013) Read More / View Supplemental Materials
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Large-scale identification of ubiquitination sites by mass spectrometry.Udeshi, ND, Mertins P., Svinkina T., and Carr SA Nature protocols, 2013/10/01, Volume 8, Issue 10, p.1950-60, (2013) Read More / View Supplemental Materials
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High reliability in respiratory rate assessment in children with respiratory symptomatology in a rural area in MozambiqueLanaspa, M., Valim C., Acacio S., Almendinger K., Ahmad R., Wiegand R., and Bassat Q. Journal of Tropical Pediatrics, 2013/09/25, (2013) Read More / View Supplemental Materials
Integrated proteomic analysis of post-translational modifications by serial enrichment.Mertins, P., Qiao JW, Patel J., Udeshi ND, Clauser KR, Mani D. R., Burgess MW, Gillette MA, Jaffe JD, and Carr SA Nature methods, 2013/07/01, Volume 10, Issue 7, p.634-7, (2013) Read More / View Supplemental Materials
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Design, Implementation, and Multi-Site Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in LC-MRM-MS.Abbatiello, SE, Mani D. R., Schilling B., Maclean B., Zimmerman LJ, Feng X., Cusack MP, Sedransk N., Hall SC, Addona T., Allen S., Dodder NG, Ghosh M., Held JM, Hedrick V., Inerowicz HD, Jackson A., Keshishian H., Kim JW, Lyssand JS, et al. Molecular & cellular proteomics : MCP, 2013/05/20, (2013) Read More / View Supplemental Materials
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Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.Rhee, HW, Zou P., Udeshi ND, Martell JD, Mootha VK, Carr SA, and Ting AY Science (New York, N.Y.), 2013/03/15, Volume 339, Issue 6125, p.1328-31, (2013) Read More / View Supplemental Materials
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Complementary RNA and Protein Profiling Identifies Iron as a Key Regulator of Mitochondrial Biogenesis.Rensvold, JW, Ong SE, Jeevananthan A., Carr SA, Mootha VK, and Pagliarini DJ Cell reports, 2013/01/09, (2013) Read More / View Supplemental Materials
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Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry.Gillette, MA, and Carr SA Nature methods, 2013/01/01, Volume 10, Issue 1, p.28-34, (2013) Read More / View Supplemental Materials
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Magnetic barcode assay for genetic detection of pathogens.Liong, M., Hoang AN, Chung J., Gural N., Ford CB, Min C., Shah RR, Ahmad R., Fernandez-Suarez M., Fortune SM, Toner M., Lee H., and Weissleder R. Nature communications, 2013/01/01, Volume 4, p.1752, (2013) Read More / View Supplemental Materials
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Identification of Trypanosome proteins in plasma from African sleeping sickness patients infected with T. b. rhodesiense.Eyford, BA, Ahmad R., Enyaru JC, Carr SA, and Pearson TW PloS one, 2013/01/01, Volume 8, Issue 8, p.e71463, (2013) Read More / View Supplemental Materials
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Refined Preparation and Use of Anti-K- epsilon -GG Antibody Enables Routine Quantification of 10,000s of Ubiquitination Sites in Single Proteomics Experiments.Udeshi, ND, Svinkina T., Mertins P., Kuhn E., Mani D. R., Qiao JW, and Carr SA Molecular & cellular proteomics : MCP, 2012/12/24, (2012) Read More / View Supplemental Materials
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Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach.Lee, MN, Roy M., Ong SE, Mertins P., Villani AC, Li W., Dotiwala F., Sen J., Doench JG, Orzalli MH, Kramnik I., Knipe DM, Lieberman J., Carr SA, and Hacohen N. Nature immunology, 2012/12/23, Volume 14, Issue 2, p.179-85, (2012) Read More / View Supplemental Materials
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H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions.Ku, M., Jaffe JD, Koche RP, Rheinbay E., Endoh M., Koseki H., Carr SA, and Bernstein BE Genome biology, 2012/10/03, Volume 13, Issue 10, p.R85, (2012) Read More / View Supplemental Materials
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Shotgun protein sequencing with meta-contig assembly.Guthals, A., Clauser KR, and Bandeira N. Molecular & cellular proteomics : MCP, 2012/10/01, Volume 11, Issue 10, p.1084-96, (2012) Read More / View Supplemental Materials
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Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.Greulich, H., Kaplan B., Mertins P., Chen TH, Tanaka KE, Yun CH, Zhang X., Lee SH, Cho J., Ambrogio L., Liao R., Imielinski M., Banerji S., Berger AH, Lawrence MS, Zhang J., Pho NH, Walker SR, Winckler W., Getz G., et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/09/04, Volume 109, Issue 36, p.14476-81, (2012) Read More / View Supplemental Materials
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ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.Abdel-Wahab, O., Adli M., LaFave LM, Gao J., Hricik T., Shih AH, Pandey S., Patel JP, Chung YR, Koche R., Perna F., Zhao X., Taylor JE, Park CY, Carroll M., Melnick A., Nimer SD, Jaffe JD, Aifantis I., Bernstein BE, et al. Cancer cell, 2012/08/14, Volume 22, Issue 2, p.180-93, (2012) Read More / View Supplemental Materials
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Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.Wen, Q., Goldenson B., Silver SJ, Schenone M., Dancik V., Huang Z., Wang LZ, Lewis TA, An WF, Li X., Bray MA, Thiollier C., Diebold L., Gilles L., Vokes MS, Moore CB, Bliss-Moreau M., VerPlank L., Tolliday NJ, Mishra R., et al. Cell, 2012/08/03, Volume 150, Issue 3, p.575-89, (2012) Read More / View Supplemental Materials
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Modification site localization scoring: strategies and performance.Chalkley, RJ, and Clauser KR Molecular & cellular proteomics : MCP, 2012/05/01, Volume 11, Issue 5, p.3-14, (2012) Read More / View Supplemental Materials
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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
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Quantitative assessment of ChIP-grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.Peach, SE, Rudomin EL, Udeshi ND, Carr SA, and Jaffe JD Molecular & cellular proteomics : MCP, 2012/03/23, (2012) Read More / View Supplemental Materials
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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.), 2012/01/01, Volume 803, p.129-40, (2012) Read More / View Supplemental Materials
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Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.Mani, D. R., Abbatiello SE, and Carr SA BMC bioinformatics, 2012/01/01, Volume 13 Suppl 16, p.S9, (2012) Read More / View Supplemental Materials
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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, (2012) Read More / View Supplemental Materials
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Quantitative assessment of ChIP-grade antbodies directed against histone modifications reveals patterns of co-occurring marks on histone protein moleculesPeach, Sally E., Rudomin Emily L., Udeshi Namrata D., Carr Steven A., and Jaffe Jacob D. Molecular & Cellular Proteomics, (2012) Read More / View Supplemental Materials
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Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma.Kuhn, E., Whiteaker JR, Mani D. R., Jackson AM, Zhao L., Pope ME, Smith D., Rivera KD, Anderson NL, Skates SJ, Pearson TW, Paulovich AG, and Carr SA Molecular & cellular proteomics : MCP, 2011/12/22, (2011) Read More / View Supplemental Materials
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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
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Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers.Burgener, A., Rahman S., Ahmad R., Lajoie J., Ramdahin S., Mesa C., Brunet S., Wachihi C., Kimani J., Fowke K., Carr S., Plummer F., and Ball TB Journal of proteome research, 2011/11/04, Volume 10, Issue 11, p.5139-49, (2011) Read More / View Supplemental Materials
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A face in the crowd: recognizing peptides through database search.Eng, JK, Searle BC, Clauser KR, and Tabb DL Molecular & cellular proteomics : MCP, 2011/11/01, Volume 10, Issue 11, p.R111.009522, (2011) Read More / View Supplemental Materials
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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
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STK33 kinase activity is nonessential in KRAS-dependent cancer cells.Babij, C., Zhang Y., Kurzeja RJ, Munzli A., Shehabeldin A., Fernando M., Quon K., Kassner PD, Ruefli-Brasse AA, Watson VJ, Fajardo F., Jackson A., Zondlo J., Sun Y., Ellison AR, Plewa CA, San MT, Robinson J., McCarter J., Schwandner R., et al. Cancer research, 2011/09/01, Volume 71, Issue 17, p.5818-26, (2011) Read More / View Supplemental Materials
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The genome of the green anole lizard and a comparative analysis with birds and mammals.Alföldi, J., Di Palma F., Grabherr M., Williams C., Kong L., Mauceli E., Russell P., Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S., Shedlock AM, Botka C., Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D., et al. Nature, 2011/08/31, Volume 477, Issue 7366, p.587-91, (2011) Read More / View Supplemental Materials
Abstract
Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis.Frühwirth, R., Mani D. R., and Pyne S. BMC bioinformatics, 2011/08/31, Volume 12, p.358, (2011) Read More / View Supplemental Materials
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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
Abstract
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
Abstract
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
Abstract
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
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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
Abstract
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
Abstract
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
Abstract
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
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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
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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
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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
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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
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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
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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
Abstract
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
Abstract
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
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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
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
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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
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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
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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
Abstract
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
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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
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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
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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
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