| Year |
Citation |
Score |
| 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 |
0.526 |
|
| 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 |
0.326 |
|
| 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 |
0.319 |
|
| 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 |
0.353 |
|
| 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 |
0.395 |
|
| 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 |
0.361 |
|
| 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 |
0.335 |
|
| 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 |
0.31 |
|
| 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 |
0.362 |
|
| 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 |
0.302 |
|
| 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 |
0.338 |
|
| 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 |
0.318 |
|
| 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 |
0.335 |
|
| 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 |
0.353 |
|
| 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 |
0.335 |
|
| 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 |
0.324 |
|
| 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 |
0.346 |
|
| 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 |
0.322 |
|
| 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 |
0.437 |
|
| 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 |
0.498 |
|
| 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 |
0.389 |
|
| 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 |
0.392 |
|
| 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 |
0.335 |
|
| 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 |
0.706 |
|
| 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 |
0.761 |
|
| 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 |
0.753 |
|
| 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 |
0.753 |
|
| 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 |
0.716 |
|
| 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 |
0.6 |
|
| 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 |
0.59 |
|
| 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 |
0.764 |
|
| 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 |
0.757 |
|
| 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 |
0.755 |
|
| 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 |
0.562 |
|
| 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 |
0.525 |
|
| 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 |
0.724 |
|
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