Sign in to see private stats on your profile page — or add photo, interests, videos, mentoring, etc.

    Danielle Swaney, PhD

    TitleAssistant Professor
    SchoolUCSF School of Medicine
    DepartmentCellular Molecular Pharmacology
    Address1700 4th Street
    San Francisco CA 94158
    vCardDownload vCard

      Collapse Bibliographic 
      Collapse Publications
      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.
      List All   |   Timeline
      1. Swaney DL, Villén J. Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography. Cold Spring Harb Protoc. 2016; 2016(3):pdb.prot088005. PMID: 26933247.
        View in: PubMed
      2. Swaney DL, Villén J. Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies. Cold Spring Harb Protoc. 2016; 2016(3):pdb.prot088013. PMID: 26933248.
        View in: PubMed
      3. Swaney DL, Villén J. Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry. Cold Spring Harb Protoc. 2016; 2016(3):pdb.top077743. PMID: 26933252.
        View in: PubMed
      4. Swaney DL, 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 [Available on 09/01/16].
      5. Pruneda JN, Smith FD, Daurie A, Swaney DL, 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 3; 33(5):437-49. PMID: 24446487; PMCID: PMC3989626.
      6. Swaney DL, 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.
      7. 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.
      8. Beltrao P, Albanèse V, Kenner LR, Swaney DL, 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.
      9. Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, 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; 8(10):821-7. PMID: 21983960; PMCID: PMC3432645.
      10. Helmlinger D, Marguerat S, Villén J, Swaney DL, Gygi SP, Bähler J, Winston F. Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex. EMBO J. 2011 Jul 20; 30(14):2843-52. PMID: 21642955; PMCID: PMC3160243.
      11. Swaney DL, Wenger CD, Coon JJ. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res. 2010 Mar 5; 9(3):1323-9. PMID: 20113005; PMCID: PMC2833215.
      12. Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the masses. ACS Chem Biol. 2010 Jan 15; 5(1):105-19. PMID: 20047291; PMCID: PMC2810156.
      13. Grimsrud PA, den Os D, Wenger CD, Swaney DL, 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.
      14. Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, 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.
      15. McGivern JV, Swaney DL, Coon JJ, Sheets MD. Toward defining the phosphoproteome of Xenopus laevis embryos. Dev Dyn. 2009 Jun; 238(6):1433-43. PMID: 19384857; PMCID: PMC2865133.
      16. Sadygov RG, Good DM, Swaney DL, Coon JJ. A new probabilistic database search algorithm for ETD spectra. J Proteome Res. 2009 Jun; 8(6):3198-205. PMID: 19354237; PMCID: PMC2730765.
      17. Swaney DL, 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.
      18. Swaney DL, 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.
      19. McAlister GC, Berggren WT, Griep-Raming J, Horning S, Makarov A, Phanstiel D, Stafford G, Swaney DL, 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.
      20. Lecchi S, Nelson CJ, Allen KE, Swaney DL, 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 7; 282(49):35471-81. PMID: 17932035.
        View in: PubMed
      21. Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, 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
      22. Swaney DL, 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.
      Danielle's Networks
      Related Concepts
      Derived automatically from this person's publications.
      People in Profiles who have published with this person.
      Related Authors
      People who share related concepts with this person.
      Back to TOP