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Jake Jaffe, Ph.D. - Publications

Affiliations: 
2004 Harvard University, Cambridge, MA, United States 
Area:
Computational Genetics
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23 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Mullahoo J, Zhang T, Clauser K, Carr SA, Jaffe JD, Papanastasiou M. "Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS". Methods (San Diego, Calif.). PMID 32004545 DOI: 10.1016/j.ymeth.2020.01.016  0.326
2019 Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL. Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis. Molecular & Cellular Proteomics : McP. 18: 1-2. PMID 30602589 DOI: 10.1074/mcp.E118.001286  0.347
2018 Malioutov D, Chen T, Airoldi E, Jaffe J, Budnik B, Slavov N. Quantifying Homologous Proteins and Proteoforms. Molecular & Cellular Proteomics : McP. 18: 162-168. PMID 30282776 DOI: 10.1074/Mcp.Tir118.000947  0.449
2018 Peckner R, Myers SA, Jacome ASV, Egertson JD, Abelin JG, MacCoss MJ, Carr SA, Jaffe JD. Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics. Nature Methods. PMID 29608554 DOI: 10.1038/Nmeth.4643  0.383
2016 Jaffe JD, Feeney CM, Patel J, Lu X, Mani DR. Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms. Journal of the American Society For Mass Spectrometry. PMID 27562500 DOI: 10.1007/s13361-016-1465-2  0.307
2016 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, ... ... Jaffe JD, et al. Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced phenotypes. Molecular & Cellular Proteomics : McP. PMID 26912667 DOI: 10.1074/Mcp.M116.058354  0.312
2016 Dimitrakopoulos L, Prassas I, Diamandis EP, Nesvizhskii A, Kislinger T, Jaffe J, Drabovich A. Proteogenomics: Opportunities and Caveats. Clinical Chemistry. 62: 551-7. PMID 26817480 DOI: 10.1373/Clinchem.2015.247858  0.327
2015 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, et al. Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics. 15: 3361-9. PMID 26152395 DOI: 10.1002/Pmic.201400142  0.356
2015 Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA. Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies and an optimized proteomic workflow. Molecular & Cellular Proteomics : McP. PMID 25953088 DOI: 10.1074/Mcp.O114.047555  0.33
2015 Creech AL, Taylor JE, Maier VK, Wu X, Feeney CM, Udeshi ND, Peach SE, Boehm JS, Lee JT, Carr SA, Jaffe JD. Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry. Methods (San Diego, Calif.). 72: 57-64. PMID 25448295 DOI: 10.1016/J.Ymeth.2014.10.033  0.308
2012 Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Molecular & Cellular Proteomics : McP. 11: M111.014423. PMID 22210691 DOI: 10.1074/Mcp.M111.014423  0.33
2011 Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, et al. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Research. 21: 147-63. PMID 21177972 DOI: 10.1101/Gr.110098.110  0.504
2010 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, et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. Journal of Proteome Research. 9: 761-76. PMID 19921851 DOI: 10.1021/Pr9006365  0.475
2010 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, et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Molecular & Cellular Proteomics : McP. 9: 225-41. PMID 19837981 DOI: 10.1074/Mcp.M900223-Mcp200  0.429
2009 Rudomin EL, Carr SA, Jaffe JD. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx). Journal of Proteome Research. 8: 3154-60. PMID 19344186 DOI: 10.1021/pr801017a  0.46
2008 Jaffe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Molecular & Cellular Proteomics : McP. 7: 1952-62. PMID 18534968 DOI: 10.1074/mcp.M800218-MCP200  0.463
2007 Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature. 449: 83-6. PMID 17805294 DOI: 10.1038/Nature06130  0.378
2006 Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. PEPPeR, a platform for experimental proteomic pattern recognition. Molecular & Cellular Proteomics : McP. 5: 1927-41. PMID 16857664 DOI: 10.1074/Mcp.M600222-Mcp200  0.593
2006 Leptos KC, Sarracino DA, Jaffe JD, Krastins B, Church GM. MapQuant: open-source software for large-scale protein quantification. Proteomics. 6: 1770-82. PMID 16470651 DOI: 10.1002/Pmic.200500201  0.592
2005 Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 438: 86-9. PMID 16222247 DOI: 10.1038/Nature04111  0.369
2004 Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, et al. The complete genome and proteome of Mycoplasma mobile. Genome Research. 14: 1447-61. PMID 15289470 DOI: 10.1101/Gr.2674004  0.443
2004 Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 4: 59-77. PMID 14730672 DOI: 10.1002/Pmic.200300511  0.435
2001 Chen T, Jaffe JD, Church GM. Algorithms for identifying protein cross-links via tandem mass spectrometry. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 8: 571-83. PMID 11747613 DOI: 10.1089/106652701753307494  0.534
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