Jake Jaffe, Ph.D. - Publications

2004 Harvard University, Cambridge, MA, United States 
Computational Genetics

42 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  0.36
2019 Barbie TU, Ritter JL, Zhu Z, Thai TC, Mahadevan NR, Mertins P, Knelson EH, Piel BP, Han S, Jaffe JD, Carr SA, Barbie DA. Phosphorylation of RAB7 by TBK1/IKKε Regulates Innate Immune Signaling in Triple Negative Breast Cancer. Cancer Research. PMID 31662325 DOI: 10.1158/0008-5472.CAN-19-1310  0.36
2019 Papanastasiou M, Mullahoo J, DeRuff KC, Bajrami B, Karageorgos I, Johnston SE, Peckner R, Myers SA, Carr SA, Jaffe JD. Chasing tails: Cathepsin-L improves structural analysis of histones by HX-MS. Molecular & Cellular Proteomics : McP. PMID 31409669 DOI: 10.1074/mcp.RA119.001325  0.36
2019 Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, ... ... Jaffe JD, et al. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nature Communications. 10: 2400. PMID 31160565 DOI: 10.1038/s41467-019-10307-9  0.36
2018 Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, et al. A curated resource for phosphosite-specific signature analysis. Molecular & Cellular Proteomics : McP. PMID 30563849 DOI: 10.1074/mcp.TIR118.000943  0.36
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  0.36
2017 Chakraborty AA, Nakamura E, Qi J, Creech A, Jaffe JD, Paulk J, Novak JS, Nagulapalli K, McBrayer SK, Cowley GS, Pineda J, Song J, Wang YE, Carr SA, Root DE, et al. HIF activation causes synthetic lethality between the VHL tumor suppressor and the EZH1 histone methyltransferase. Science Translational Medicine. 9. PMID 28701475 DOI: 10.1126/scitranslmed.aal5272  0.36
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  0.36
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  0.36
2016 Surface LE, Fields PA, Subramanian V, Behmer R, Udeshi N, Peach SE, Carr SA, Jaffe JD, Boyer LA. H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs. Cell Reports. PMID 26804911 DOI: 10.1016/j.celrep.2015.12.100  0.36
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  0.36
2015 Chou DH, Vetere A, Choudhary A, Scully SS, Schenone M, Tang A, Gomez R, Burns SM, Lundh M, Vital T, Comer E, Faloon PW, Dan?ík V, Ciarlo C, Paulk J, ... ... Jaffe J, et al. Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling. Journal of the American Chemical Society. 137: 7929-34. PMID 26042473 DOI: 10.1021/jacs.5b04284  0.36
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  0.36
2015 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, Lee JT. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Molecular & Cellular Proteomics : McP. 14: 1435-46. PMID 25680957 DOI: 10.1074/mcp.M114.044586  0.36
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  0.36
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. DOI: 10.1002/pmic.201400142  0.36
2014 Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, et al. Panorama: a targeted proteomics knowledge base. Journal of Proteome Research. 13: 4205-10. PMID 25102069 DOI: 10.1021/pr5006636  0.36
2014 Olson DE, Udeshi ND, Wolfson NA, Pitcairn CA, Sullivan ED, Jaffe JD, Svinkina T, Natoli T, Lu X, Paulk J, McCarren P, Wagner FF, Barker D, Howe E, Lazzaro F, et al. An unbiased approach to identify endogenous substrates of "histone" deacetylase 8. Acs Chemical Biology. 9: 2210-6. PMID 25089360 DOI: 10.1021/cb500492r  0.36
2014 Lassen KG, Kuballa P, Conway KL, Patel KK, Becker CE, Peloquin JM, Villablanca EJ, Norman JM, Liu TC, Heath RJ, Becker ML, Fagbami L, Horn H, Mercer J, Yilmaz OH, ... Jaffe JD, et al. Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proceedings of the National Academy of Sciences of the United States of America. 111: 7741-6. PMID 24821797 DOI: 10.1073/pnas.1407001111  0.36
2013 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, Wei L, Ma J, et al. Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia. Nature Genetics. 45: 1386-91. PMID 24076604 DOI: 10.1038/ng.2777  0.36
2013 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA. Integrated proteomic analysis of post-translational modifications by serial enrichment. Nature Methods. 10: 634-7. PMID 23749302 DOI: 10.1038/nmeth.2518  0.36
2012 Ku M, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biology. 13: R85. PMID 23034477 DOI: 10.1186/gb-2012-13-10-r85  0.36
2012 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, ... ... Jaffe JD, et al. Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. Proceedings of the National Academy of Sciences of the United States of America. 109: 14476-81. PMID 22908275 DOI: 10.1073/pnas.1203201109  0.36
2012 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Molecular & Cellular Proteomics : McP. 11: 148-59. PMID 22505724 DOI: 10.1074/mcp.M111.016857  0.36
2012 Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Molecular & Cellular Proteomics : McP. 11: 128-37. PMID 22442256 DOI: 10.1074/mcp.M111.015941  0.36
2012 Luo T, Masson K, Jaffe JD, Silkworth W, Ross NT, Scherer CA, Scholl C, Fröhling S, Carr SA, Stern AM, Schreiber SL, Golub TR. STK33 kinase inhibitor BRD-8899 has no effect on KRAS-dependent cancer cell viability. Proceedings of the National Academy of Sciences of the United States of America. 109: 2860-5. PMID 22323609 DOI: 10.1073/pnas.1120589109  0.36
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  0.36
2011 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, et al. Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation. Cell Metabolism. 14: 428-34. PMID 21907147 DOI: 10.1016/j.cmet.2011.07.010  0.36
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  0.36
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  0.36
2009 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, et al. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. Plos Biology. 7: e1000256. PMID 20016685 DOI: 10.1371/journal.pbio.1000256  0.36
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  0.36
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  0.36
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  0.6
2006 Frias MA, Thoreen CC, Jaffe JD, Schroder W, Sculley T, Carr SA, Sabatini DM. mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s. Current Biology : Cb. 16: 1865-70. PMID 16919458 DOI: 10.1016/j.cub.2006.08.001  0.36
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  0.6
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  0.6
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  0.6
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  0.6
2004 Jaffe JD, Miyata M, Berg HC. Energetics of gliding motility in Mycoplasma mobile. Journal of Bacteriology. 186: 4254-61. PMID 15205428 DOI: 10.1128/JB.186.13.4254-4261.2004  0.52
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  0.6
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  0.6
Show low-probability matches.