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Items: 27

1.

Multiple Routes to Oncogenesis are Promoted by the Human Papillomavirus-Host Protein Network.

Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ.

Cancer Discov. 2018 Sep 12. pii: CD-17-1018. doi: 10.1158/2159-8290.CD-17-1018. [Epub ahead of print]

PMID:
30209081
2.

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.

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 DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS.

Biol Open. 2018 Jul 23;7(7). pii: bio036103. doi: 10.1242/bio.036103.

3.

Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.

Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B.

Sci Rep. 2018 Jul 20;8(1):11001. doi: 10.1038/s41598-018-29333-6.

4.

Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.

Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B.

Cell Metab. 2018 Mar 6;27(3):616-629.e4. doi: 10.1016/j.cmet.2018.01.018.

5.

Evolution of protein phosphorylation across 18 fungal species.

Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J.

Science. 2016 Oct 14;354(6309):229-232.

PMID:
27738172
6.

Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry.

Swaney DL, Villén J.

Cold Spring Harb Protoc. 2016 Mar 1;2016(3):pdb.top077743. doi: 10.1101/pdb.top077743.

PMID:
26933252
7.

Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies.

Swaney DL, Villén J.

Cold Spring Harb Protoc. 2016 Mar 1;2016(3):pdb.prot088013. doi: 10.1101/pdb.prot088013.

PMID:
26933248
8.

Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography.

Swaney DL, Villén J.

Cold Spring Harb Protoc. 2016 Mar 1;2016(3):pdb.prot088005. doi: 10.1101/pdb.prot088005.

PMID:
26933247
9.

Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover.

Swaney DL, Rodríguez-Mias RA, Villén J.

EMBO Rep. 2015 Sep;16(9):1131-44. doi: 10.15252/embr.201540298. Epub 2015 Jul 3.

10.

E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis.

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.

EMBO J. 2014 Mar 3;33(5):437-49. doi: 10.1002/embj.201386386. Epub 2014 Jan 20.

11.

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.

Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.

Nat Methods. 2013 Jul;10(7):676-82. doi: 10.1038/nmeth.2519. Epub 2013 Jun 9.

12.

Affinity-based probes based on type II kinase inhibitors.

Ranjitkar P, Perera BG, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ.

J Am Chem Soc. 2012 Nov 21;134(46):19017-25. doi: 10.1021/ja306035v. Epub 2012 Nov 6. Erratum in: J Am Chem Soc. 2013 Jan 16;135(2):948. Swaney, Daniel L [corrected to Swaney, Danielle L].

13.

Systematic functional prioritization of protein posttranslational modifications.

Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ.

Cell. 2012 Jul 20;150(2):413-25. doi: 10.1016/j.cell.2012.05.036.

14.

Proteomic and phosphoproteomic comparison of human ES and iPS cells.

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.

Nat Methods. 2011 Sep 11;8(10):821-7. doi: 10.1038/nmeth.1699.

15.

Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex.

Helmlinger D, Marguerat S, Villén J, Swaney DL, Gygi SP, Bähler J, Winston F.

EMBO J. 2011 Jun 3;30(14):2843-52. doi: 10.1038/emboj.2011.181.

16.

Value of using multiple proteases for large-scale mass spectrometry-based proteomics.

Swaney DL, Wenger CD, Coon JJ.

J Proteome Res. 2010 Mar 5;9(3):1323-9. doi: 10.1021/pr900863u.

17.

Phosphoproteomics for the masses.

Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ.

ACS Chem Biol. 2010 Jan 15;5(1):105-19. doi: 10.1021/cb900277e. Review.

18.

Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes.

Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, Ané JM, Coon JJ.

Plant Physiol. 2010 Jan;152(1):19-28. doi: 10.1104/pp.109.149625. Epub 2009 Nov 18.

19.

Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures.

Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V.

Anal Chem. 2009 Sep 15;81(18):7757-65. doi: 10.1021/ac901278y.

20.

Toward defining the phosphoproteome of Xenopus laevis embryos.

McGivern JV, Swaney DL, Coon JJ, Sheets MD.

Dev Dyn. 2009 Jun;238(6):1433-43. doi: 10.1002/dvdy.21941.

21.

A new probabilistic database search algorithm for ETD spectra.

Sadygov RG, Good DM, Swaney DL, Coon JJ.

J Proteome Res. 2009 Jun;8(6):3198-205. doi: 10.1021/pr900153b.

22.

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.

Swaney DL, Wenger CD, Thomson JA, Coon JJ.

Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):995-1000. doi: 10.1073/pnas.0811964106. Epub 2009 Jan 14.

23.

Decision tree-driven tandem mass spectrometry for shotgun proteomics.

Swaney DL, McAlister GC, Coon JJ.

Nat Methods. 2008 Nov;5(11):959-64. doi: 10.1038/nmeth.1260. Epub 2008 Oct 19.

24.

A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

McAlister GC, Berggren WT, Griep-Raming J, Horning S, Makarov A, Phanstiel D, Stafford G, Swaney DL, Syka JE, Zabrouskov V, Coon JJ.

J Proteome Res. 2008 Aug;7(8):3127-36. doi: 10.1021/pr800264t. Epub 2008 Jul 10.

25.

Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation.

Lecchi S, Nelson CJ, Allen KE, Swaney DL, Thompson KL, Coon JJ, Sussman MR, Slayman CW.

J Biol Chem. 2007 Dec 7;282(49):35471-81. Epub 2007 Oct 11.

26.

Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics.

Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, Rexach JE, Sun YE, Coon JJ, Peters EC, Hsieh-Wilson LC.

Nat Chem Biol. 2007 Jun;3(6):339-48. Epub 2007 May 13.

PMID:
17496889
27.

Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors.

Swaney DL, McAlister GC, Wirtala M, Schwartz JC, Syka JE, Coon JJ.

Anal Chem. 2007 Jan 15;79(2):477-85.

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