☰

Danielle L. Swaney, Ph.D. - Publications

Affiliations: 
2009 University of Wisconsin, Madison, Madison, WI 
Area:
Bioanalytical Chemistry, Mass Spectrometry & Proteomics
Tree Info Similar researchers PubMed Report error

47 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
2024 Kaushal P, Ummadi MR, Jang GM, Delgado Y, Makanani SK, Alba K, Winters DM, Blanc SF, Xu J, Polacco B, Zhou Y, Stevenson E, Eckhardt M, Zuliani-Alvarez L, Kaake R, ... Swaney DL, et al. Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry. Star Protocols. 5: 103286. PMID 39488835 DOI: 10.1016/j.xpro.2024.103286  0.345
2024 Kaushal P, Ummadi MR, Jang GM, Delgado Y, Makanani SK, Blanc SF, Winters DM, Xu J, Polacco B, Zhou Y, Stevenson E, Eckhardt M, Zuliani-Alvarez L, Kaake R, Swaney DL, et al. Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry. Arxiv. PMID 38800652  0.347
2023 Tharp K, Park S, Timblin G, Richards A, Twells N, Riley N, Peltan E, Shon J, Stevenson E, Tsui K, Palomba F, Lefebvre A, Soens R, Ayad N, Hoeve-Scott JT, ... ... Swaney D, et al. The microenvironment dictates glycocalyx construction and immune surveillance. Research Square. PMID 37645943 DOI: 10.21203/rs.3.rs-3164966/v1  0.522
2022 Richards AL, Chen KH, Wilburn DB, Stevenson E, Polacco BJ, Searle BC, Swaney DL. Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes. Journal of Proteome Research. PMID 35234472 DOI: 10.1021/acs.jproteome.1c00960  0.325
2021 Fossati A, Richards AL, Chen KH, Jaganath D, Cattamanchi A, Ernst JD, Swaney DL. Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion. Journal of Proteome Research. PMID 34319755 DOI: 10.1021/acs.jproteome.1c00357  0.318
2020 Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, ... ... Swaney DL, et al. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. PMID 32645325 DOI: 10.1016/J.Cell.2020.06.034  0.354
2020 Alme EB, Stevenson E, Krogan NJ, Swaney DL, Toczyski DP. The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae. Plos Genetics. 16: e1008840. PMID 32579556 DOI: 10.1371/Journal.Pgen.1008840  0.397
2020 Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, ... ... Swaney DL, et al. Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Cancer Cell. PMID 32531271 DOI: 10.1016/J.Ccell.2020.05.003  0.395
2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. PMID 32353859 DOI: 10.1038/S41586-020-2286-9  0.362
2020 Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. Dynamic post-translational modification profiling of -infected primary macrophages. Elife. 9. PMID 31951200 DOI: 10.7554/Elife.51461  0.336
2020 Humtsoe JO, Kim H, Soucheray M, Swaney D, Ha PK. Abstract A27: Differential protein-interactome of MYB-NF1B fusion in adenoid cystic carcinoma Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Aacrahns19-A27  0.323
2020 Hwang Y, Swaney DL, Bardeesy N, Gordan JD. Abstract 6572: Integrative network propagation to uncover potential drug resistance mechanisms in FGFR2 fusion-positive cholangiocarcinoma Cancer Research. 80: 6572-6572. DOI: 10.1158/1538-7445.Am2020-6572  0.311
2020 Gordan JD, Pitea A, Eckhardt M, Jang G, Turnham RE, Choi ALM, Dollen JV, Lim HC, Thayer EF, Kelley RK, Swaney DL, Zhang W, Theis FJ, Ideker T, Krogan NJ. Abstract 4891: Hepatitis B virus remodels host protein interaction networks to generate distinct cellular dependencies Cancer Research. 80: 4891-4891. DOI: 10.1158/1538-7445.Am2020-4891  0.325
2020 Chan GKL, Maisel SM, Hwang YC, Wolber R, Swaney DL, Bardeesy N, Gordan JD. Abstract 309: Mapping oncogenic signal transduction in PKA-driven cancers Cancer Research. 80: 309-309. DOI: 10.1158/1538-7445.Am2020-309  0.363
2019 Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, et al. The functional landscape of the human phosphoproteome. Nature Biotechnology. PMID 31819260 DOI: 10.1038/S41587-019-0344-3  0.442
2019 Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC. Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen. Cell Host & Microbe. PMID 31540829 DOI: 10.1016/J.Chom.2019.08.017  0.303
2019 Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell. PMID 31474367 DOI: 10.1016/J.Cell.2019.07.046  0.339
2019 Lou K, Steri V, Ge AY, Hwang YC, Yogodzinski CH, Shkedi AR, Choi ALM, Mitchell DC, Swaney DL, Hann B, Gordan JD, Shokat KM, Gilbert LA. KRAS inhibition produces a driver-limited state revealing collateral dependencies. Science Signaling. 12. PMID 31138768 DOI: 10.1126/Scisignal.Aaw9450  0.319
2019 Perez-Bermejo JA, Judge LM, Wu K, Jensen CL, Kaake RM, Swaney D, So P, Krogan NJ, Conklin BR. Abstract 934: Physical and Genetic Interaction Analyses in Human Pluripotent Stem Cell-Derived Cardiomyocytes to Study Protein Quality Control Disease in the Heart Circulation Research. 125. DOI: 10.1161/Res.125.Suppl_1.934  0.336
2019 Kim M, Kim K, Tutuncuoglu B, Soucheray M, Swaney D, Zheng F, Park J, O'Leary P, Coppé J, Veer Lv', Ashworth A, Ideker T, Krogan N. Abstract P6-06-01: Analyzing the physical and functional protein interaction landscape of breast cancer Cancer Research. 79. DOI: 10.1158/1538-7445.Sabcs18-P6-06-01  0.354
2019 John Liu S, Vasudevan H, Pekmezci M, Choudhury A, Lien B, Breshears J, Swaney D, Magill S, Lang U, Chen W, Gopinath C, Castro M, Villanueva-Meyer J, Braunstein S, Sneed P, et al. GENE-37. VESTIBULAR SCHWANNOMA IS COMPRISED OF NEURAL CREST AND IMMUNE SUBGROUPS Neuro-Oncology. 21: vi105-vi105. DOI: 10.1093/Neuonc/Noz175.439  0.334
2018 Weinman LM, Running KLD, Carey NS, Stevenson EJ, Swaney DL, Chow BY, Krogan NJ, Krogan NT. TCO, a Putative Transcriptional Regulator in , Is a Target of the Protein Kinase CK2. International Journal of Molecular Sciences. 20. PMID 30597831 DOI: 10.3390/Ijms20010099  0.336
2018 Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, et al. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell. 175: 1931-1945.e18. PMID 30550790 DOI: 10.1016/J.Cell.2018.11.028  0.325
2018 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, et al. Multiple Routes to Oncogenesis are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discovery. PMID 30209081 DOI: 10.1158/2159-8290.Cd-17-1018  0.347
2018 Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, 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. Scientific Reports. 8: 11001. PMID 30030465 DOI: 10.1038/S41598-018-29333-6  0.345
2018 Kim M, Kim K, Soucheray M, Swaney D, Krogan N. Abstract B45: Studying the interactome of breast cancer: The cancer cell map initiative Molecular Cancer Research. 16. DOI: 10.1158/1557-3125.Advbc17-B45  0.323
2016 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. Evolution of protein phosphorylation across 18 fungal species. Science (New York, N.Y.). 354: 229-232. PMID 27738172 DOI: 10.1126/Science.Aaf2144  0.438
2016 Swaney DL, Villén J. Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry. Cold Spring Harbor Protocols. 2016: pdb.top077743. PMID 26933252 DOI: 10.1101/Pdb.Top077743  0.497
2016 Swaney DL, Villén J. Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies. Cold Spring Harbor Protocols. 2016: pdb.prot088013. PMID 26933248 DOI: 10.1101/Pdb.Prot088013  0.388
2016 Swaney DL, Villén J. Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography. Cold Spring Harbor Protocols. 2016: pdb.prot088005. PMID 26933247 DOI: 10.1101/Pdb.Prot088005  0.39
2015 Swaney DL, Rodríguez-Mias RA, Villén J. Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. Embo Reports. 16: 1131-44. PMID 26142280 DOI: 10.15252/Embr.201540298  0.397
2014 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. The Embo Journal. 33: 437-49. PMID 24446487 DOI: 10.1002/Embj.201386386  0.336
2013 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. Nature Methods. 10: 676-82. PMID 23749301 DOI: 10.1038/Nmeth.2519  0.458
2012 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. 150: 413-25. PMID 22817900 DOI: 10.1016/J.Cell.2012.05.036  0.419
2011 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. Nature Methods. 8: 821-7. PMID 21983960 DOI: 10.1038/Nmeth.1699  0.707
2010 Swaney DL, Wenger CD, Coon JJ. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. Journal of Proteome Research. 9: 1323-9. PMID 20113005 DOI: 10.1021/Pr900863U  0.76
2010 Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the masses. Acs Chemical Biology. 5: 105-19. PMID 20047291 DOI: 10.1021/Cb900277E  0.752
2010 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 Physiology. 152: 19-28. PMID 19923235 DOI: 10.1104/Pp.109.149625  0.752
2009 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. Analytical Chemistry. 81: 7757-65. PMID 19689114 DOI: 10.1021/Ac901278Y  0.713
2009 McGivern JV, Swaney DL, Coon JJ, Sheets MD. Toward defining the phosphoproteome of Xenopus laevis embryos. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 238: 1433-43. PMID 19384857 DOI: 10.1002/Dvdy.21941  0.598
2009 Sadygov RG, Good DM, Swaney DL, Coon JJ. A new probabilistic database search algorithm for ETD spectra. Journal of Proteome Research. 8: 3198-205. PMID 19354237 DOI: 10.1021/Pr900153B  0.586
2009 Swaney DL, Wenger CD, Thomson JA, Coon JJ. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 106: 995-1000. PMID 19144917 DOI: 10.1073/Pnas.0811964106  0.763
2008 Swaney DL, McAlister GC, Coon JJ. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nature Methods. 5: 959-64. PMID 18931669 DOI: 10.1038/Nmeth.1260  0.752
2008 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. Journal of Proteome Research. 7: 3127-36. PMID 18613715 DOI: 10.1021/Pr800264T  0.757
2007 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. The Journal of Biological Chemistry. 282: 35471-81. PMID 17932035 DOI: 10.1074/Jbc.M706094200  0.559
2007 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. Nature Chemical Biology. 3: 339-48. PMID 17496889 DOI: 10.1038/Nchembio881  0.523
2007 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. Analytical Chemistry. 79: 477-85. PMID 17222010 DOI: 10.1021/Ac061457F  0.718
Show low-probability matches.