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Danielle Swaney, PhD

TitleAssistant Professor
InstitutionUniversity of California San Francisco
DepartmentCellular Molecular Pharmacology
Address1700 4th Street
San Francisco CA 94158
Phone415-734-2767
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney D, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. 2018 Jul 23; 7(7). PMID: 30037883.
      View in: PubMed
    2. Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney D, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B. Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis. Sci Rep. 2018 Jul 20; 8(1):11001. PMID: 30030465.
      View in: PubMed
    3. Masand R, Paulo E, Wu D, Wang Y, Swaney D, Jimenez-Morales D, Krogan NJ, Wang B. Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits. Cell Metab. 2018 Mar 06; 27(3):616-629.e4. PMID: 29514069.
      View in: PubMed
    4. Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney D, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J. Evolution of protein phosphorylation across 18 fungal species. Science. 2016 10 14; 354(6309):229-232. PMID: 27738172.
      View in: PubMed
    5. Swaney D, Villén J. Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies. Cold Spring Harb Protoc. 2016 Mar 01; 2016(3):pdb.prot088013. PMID: 26933248.
      View in: PubMed
    6. Swaney D, Villén J. Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography. Cold Spring Harb Protoc. 2016 Mar 01; 2016(3):pdb.prot088005. PMID: 26933247.
      View in: PubMed
    7. Swaney D, Villén J. Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry. Cold Spring Harb Protoc. 2016 Mar 01; 2016(3):pdb.top077743. PMID: 26933252.
      View in: PubMed
    8. Swaney D, Rodríguez-Mias RA, Villén J. Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep. 2015 Sep; 16(9):1131-44. PMID: 26142280; PMCID: PMC4576982.
    9. Pruneda JN, Smith FD, Daurie A, Swaney D, Villén J, Scott JD, Stadnyk AW, Le Trong I, Stenkamp RE, Klevit RE, Rohde JR, Brzovic PS. E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis. EMBO J. 2014 Mar 03; 33(5):437-49. PMID: 24446487; PMCID: PMC3989626.
    10. Swaney D, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J. Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods. 2013 Jul; 10(7):676-82. PMID: 23749301; PMCID: PMC3868471.
    11. Ranjitkar P, Perera BG, Swaney DL, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ. Affinity-based probes based on type II kinase inhibitors. J Am Chem Soc. 2012 Nov 21; 134(46):19017-25. PMID: 23088519; PMCID: PMC3523701.
    12. Beltrao P, Albanèse V, Kenner LR, Swaney D, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25. PMID: 22817900; PMCID: PMC3404735.
    13. Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney D, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011 Sep 11; 8(10):821-7. PMID: 21983960; PMCID: PMC3432645.
    14. Helmlinger D, Marguerat S, Villén J, Swaney D, Gygi SP, Bähler J, Winston F. Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex. EMBO J. 2011 Jun 03; 30(14):2843-52. PMID: 21642955; PMCID: PMC3160243.
    15. Swaney D, Wenger CD, Coon JJ. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res. 2010 Mar 05; 9(3):1323-9. PMID: 20113005; PMCID: PMC2833215.
    16. Grimsrud PA, Swaney D, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the masses. ACS Chem Biol. 2010 Jan 15; 5(1):105-19. PMID: 20047291; PMCID: PMC2810156.
    17. Grimsrud PA, den Os D, Wenger CD, Swaney D, Schwartz D, Sussman MR, Ané JM, Coon JJ. Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol. 2010 Jan; 152(1):19-28. PMID: 19923235; PMCID: PMC2799343.
    18. Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney D, Russell JD, Coon JJ, Zabrouskov V. Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem. 2009 Sep 15; 81(18):7757-65. PMID: 19689114; PMCID: PMC2810160.
    19. Sadygov RG, Good DM, Swaney D, Coon JJ. A new probabilistic database search algorithm for ETD spectra. J Proteome Res. 2009 Jun; 8(6):3198-205. PMID: 19354237; PMCID: PMC2730765.
    20. McGivern JV, Swaney D, Coon JJ, Sheets MD. Toward defining the phosphoproteome of Xenopus laevis embryos. Dev Dyn. 2009 Jun; 238(6):1433-43. PMID: 19384857; PMCID: PMC2865133.
    21. Swaney D, Wenger CD, Thomson JA, Coon JJ. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2009 Jan 27; 106(4):995-1000. PMID: 19144917; PMCID: PMC2633571.
    22. Swaney D, McAlister GC, Coon JJ. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods. 2008 Nov; 5(11):959-64. PMID: 18931669; PMCID: PMC2597439.
    23. McAlister GC, Berggren WT, Griep-Raming J, Horning S, Makarov A, Phanstiel D, Stafford G, Swaney D, Syka JE, Zabrouskov V, Coon JJ. A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res. 2008 Aug; 7(8):3127-36. PMID: 18613715; PMCID: PMC2601597.
    24. Lecchi S, Nelson CJ, Allen KE, Swaney D, Thompson KL, Coon JJ, Sussman MR, Slayman CW. Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation. J Biol Chem. 2007 Dec 07; 282(49):35471-81. PMID: 17932035.
      View in: PubMed
    25. Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney D, Rexach JE, Sun YE, Coon JJ, Peters EC, Hsieh-Wilson LC. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nat Chem Biol. 2007 Jun; 3(6):339-48. PMID: 17496889.
      View in: PubMed
    26. Swaney D, McAlister GC, Wirtala M, Schwartz JC, Syka JE, Coon JJ. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal Chem. 2007 Jan 15; 79(2):477-85. PMID: 17222010; PMCID: PMC2522365.