| 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 |
0.325 |
|
| 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 |
0.346 |
|
| 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 |
0.715 |
|
| 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 |
0.589 |
|
| 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 |
0.561 |
|
| 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 |
0.723 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2012 |
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. Journal of the American Chemical Society. 134: 19017-25. PMID 23088519 DOI: 10.1021/Ja306035V |
0.297 |
|
| 2023 |
Cakir Z, Lord SJ, Zhou Y, Jang GM, Polacco BJ, Eckhardt M, Jimenez-Morales D, Newton BW, Orr AL, Johnson JR, da Cruz A, Mullins RD, Krogan NJ, Mahley RW, Swaney DL. Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin-regulating protein VASP. Molecular & Cellular Proteomics : McP. 100541. PMID 37019383 DOI: 10.1016/j.mcpro.2023.100541 |
0.289 |
|
| 2018 |
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, ... ... Swaney DL, et al. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biology Open. 7. PMID 30037883 DOI: 10.1242/Bio.036103 |
0.288 |
|
| 2011 |
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. The Embo Journal. 30: 2843-52. PMID 21642955 DOI: 10.1038/Emboj.2011.181 |
0.285 |
|
| 2020 |
Zheng F, Ono K, Silva E, Swaney D, Kim M, Shangguan J, Pratt D, Nan X, Krogan N, Ideker T. Abstract PR14: A multiscale map of recurrently mutated systems in cancer Cancer Research. 80. DOI: 10.1158/1538-7445.Camodels2020-Pr14 |
0.282 |
|
| 2023 |
Fossati A, Mozumdar D, Kokontis C, Nieweglowska E, Mendez M, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping. Biorxiv : the Preprint Server For Biology. PMID 36711836 DOI: 10.1101/2023.01.13.523954 |
0.277 |
|
| 2018 |
Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B. Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits. Cell Metabolism. 27: 616-629.e4. PMID 29514069 DOI: 10.1016/J.Cmet.2018.01.018 |
0.27 |
|
| 2024 |
Ostacolo K, López García de Lomana A, Larat C, Hjaltalin V, Holm KY, Hlynsdóttir SS, Soucheray M, Sooman L, Rolfsson O, Krogan NJ, Steingrimsson E, Swaney DL, Ogmundsdottir MH. ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism. Traffic (Copenhagen, Denmark). 25: e12933. PMID 38600522 DOI: 10.1111/tra.12933 |
0.269 |
|
| 2019 |
Orr AL, Kim C, Jimenez-Morales D, Newton BW, Johnson JR, Krogan NJ, Swaney DL, Mahley RW. Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function. Journal of Alzheimer's Disease : Jad. PMID 30883359 DOI: 10.3233/Jad-181184 |
0.264 |
|
| 2013 |
Ranjitkar P, Perera BGK, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ. Correction to “Affinity-Based Probes Based on Type II Kinase Inhibitors” Journal of the American Chemical Society. 135: 948-948. DOI: 10.1021/Ja3120967 |
0.262 |
|
| 2023 |
Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping. Nature Communications. 14: 5156. PMID 37620325 DOI: 10.1038/s41467-023-40724-w |
0.258 |
|
| 2021 |
Verba K, Gupta M, Azumaya C, Moritz M, Pourmal S, Diallo A, Merz G, Jang G, Bouhaddou M, Fossati A, Brilot A, Diwanji D, Hernandez E, Herrera N, Kratochvil H, ... ... Swaney D, et al. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Research Square. PMID 34031651 DOI: 10.21203/rs.3.rs-515215/v1 |
0.255 |
|
| 2021 |
Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, ... ... Swaney DL, et al. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Biorxiv : the Preprint Server For Biology. PMID 34013269 DOI: 10.1101/2021.05.10.443524 |
0.255 |
|
| 2023 |
Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Biorxiv : the Preprint Server For Biology. PMID 37961561 DOI: 10.1101/2023.10.28.564055 |
0.254 |
|
| 2023 |
Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, et al. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. Elife. 12. PMID 36692000 DOI: 10.7554/eLife.69521 |
0.25 |
|
| 2020 |
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, et al. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. Biorxiv : the Preprint Server For Biology. PMID 32511329 DOI: 10.1101/2020.03.22.002386 |
0.247 |
|
| 2021 |
Wilburn DB, Richards AL, Swaney DL, Searle BC. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. Journal of Proteome Research. PMID 33729787 DOI: 10.1021/acs.jproteome.0c00964 |
0.246 |
|
| 2020 |
Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, Kane J, Xu J, Guo JZ, Stevenson E, Swaney DL, Franks-Skiba K, Verschueren E, Shales M, Crosby DC, Frankel AD, et al. A Quantitative Genetic Interaction Map of HIV Infection. Molecular Cell. PMID 32084337 DOI: 10.1016/J.Molcel.2020.02.004 |
0.243 |
|
| 2023 |
Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, et al. A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nature Cell Biology. PMID 37857833 DOI: 10.1038/s41556-023-01248-z |
0.242 |
|
| 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. Author response: Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages Elife. DOI: 10.7554/Elife.51461.Sa2 |
0.23 |
|
| 2017 |
Kim M, Kim K, Soucheray M, Swaney D, Krogan N. Abstract P1-05-31: Studying the interactome of breast cancer: The cancer cell map initiative Cancer Research. 77. DOI: 10.1158/1538-7445.Sabcs16-P1-05-31 |
0.229 |
|
| 2023 |
Krause GJ, Kirchner P, Stiller B, Morozova K, Diaz A, Chen KH, Krogan NJ, Agullo-Pascual E, Clement CC, Lindenau K, Swaney DL, Dilipkumar S, Bravo-Cordero JJ, Santambrogio L, Cuervo AM. Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy. Cell Reports. 42: 113529. PMID 38060380 DOI: 10.1016/j.celrep.2023.113529 |
0.228 |
|
| 2021 |
Perica T, Mathy CJP, Xu J, Jang GΜ, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. Systems-level effects of allosteric perturbations to a model molecular switch. Nature. PMID 34646016 DOI: 10.1038/s41586-021-03982-6 |
0.226 |
|
| 2017 |
Brand TM, Hartmann S, Bhola NE, Li H, Zeng Y, O'Keefe R, Ranall MV, Bandyopadhyay S, Soucheray M, Swaney DL, Krogan N, Kemp C, Duvvuri U, Johnson DE, Ozbun MA, et al. Abstract PR04: HER3 crosstalk with HPV16-E6E7 is a feedback resistance mechanism to PI3K-targeted therapies in head and neck cancer Clinical Cancer Research. 23. DOI: 10.1158/1557-3265.Aacrahns17-Pr04 |
0.226 |
|
| 2023 |
Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, ... ... Swaney DL, et al. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nature Communications. 14: 6030. PMID 37758692 DOI: 10.1038/s41467-023-41442-z |
0.221 |
|
| 2020 |
Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, ... ... Swaney DL, et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.). PMID 33060197 DOI: 10.1126/science.abe9403 |
0.201 |
|
| 2023 |
Wilburn DB, Shannon AE, Spicer V, Richards AL, Yeung D, Swaney DL, Krokhin OV, Searle BC. Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications. Biorxiv : the Preprint Server For Biology. PMID 37398395 DOI: 10.1101/2023.05.30.542978 |
0.198 |
|
| 2021 |
Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, et al. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nature Microbiology. PMID 34556855 DOI: 10.1038/s41564-021-00964-2 |
0.19 |
|
| 2022 |
Stormo AED, Shavarebi F, FitzGibbon M, Earley EM, Ahrendt H, Lum LS, Verschueren E, Swaney DL, Skibinski G, Ravisankar A, van Haren J, Davis EJ, Johnson JR, Von Dollen J, Balen C, et al. The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity. The Journal of Cell Biology. 221. PMID 35266954 DOI: 10.1083/jcb.202010065 |
0.189 |
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| 2022 |
Tracy TE, Madero-Pérez J, Swaney DL, Chang TS, Moritz M, Konrad C, Ward ME, Stevenson E, Hüttenhain R, Kauwe G, Mercedes M, Sweetland-Martin L, Chen X, Mok SA, Wong MY, et al. Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration. Cell. PMID 35063084 DOI: 10.1016/j.cell.2021.12.041 |
0.188 |
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| 2023 |
Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, ... ... Swaney DL, et al. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. PMID 37738970 DOI: 10.1016/j.cell.2023.08.026 |
0.185 |
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| 2022 |
Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, ... ... Swaney DL, et al. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Biorxiv : the Preprint Server For Biology. PMID 36299428 DOI: 10.1101/2022.10.18.512708 |
0.183 |
|
| 2024 |
Herrera CM, McMahon E, Swaney DL, Sherry J, Pha K, Adams-Boone K, Johnson JR, Krogan NJ, Stevers M, Solomon D, Elwell C, Engel J. The Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners. Biorxiv : the Preprint Server For Biology. PMID 38464023 DOI: 10.1101/2024.02.26.581999 |
0.182 |
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| 2023 |
Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen . Biorxiv : the Preprint Server For Biology. PMID 37577546 DOI: 10.1101/2023.08.03.551750 |
0.179 |
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| 2022 |
Krause GJ, Diaz A, Jafari M, Khawaja RR, Agullo-Pascual E, Santiago-Fernández O, Richards AL, Chen KH, Dmitriev P, Sun Y, See SK, Abdelmohsen K, Mazan-Mamczarz K, Krogan NJ, Gorospe M, ... Swaney DL, et al. Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion. Aging Cell. e13713. PMID 36116133 DOI: 10.1111/acel.13713 |
0.174 |
|
| 2021 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, ... ... Swaney DL, et al. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 34942634 DOI: 10.1038/s41586-021-04352-y |
0.168 |
|
| 2021 |
Bouhaddou M, Lee RH, Li H, Bhola NE, O'Keefe RA, Naser M, Zhu TR, Nwachuku K, Duvvuri U, Olshen AB, Roy R, Hechmer A, Bolen J, Keysar SB, Jimeno A, ... ... Swaney DL, et al. Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer. Jci Insight. PMID 34546978 DOI: 10.1172/jci.insight.151982 |
0.163 |
|
| 2023 |
Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, ... ... Swaney DL, et al. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host & Microbe. PMID 37738983 DOI: 10.1016/j.chom.2023.08.003 |
0.16 |
|
| 2023 |
Steinbach A, Bhadkamkar V, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen . Molecular Biology of the Cell. mbcE23060260. PMID 38117589 DOI: 10.1091/mbc.E23-06-0260 |
0.16 |
|
| 2023 |
Krogsaeter EK, McKetney J, Marquez A, Cakir Z, Stevenson E, Jang GM, Rao A, Zhou A, Huang Y, Krogan NJ, Swaney DL. Lysosomal proteomics reveals mechanisms of neuronal apoE4-associated lysosomal dysfunction. Biorxiv : the Preprint Server For Biology. PMID 37873080 DOI: 10.1101/2023.10.02.560519 |
0.158 |
|
| 2021 |
Paulo E, Zhang Y, Masand R, Huynh TL, Seo Y, Swaney DL, Soucheray M, Stevenson E, Jimenez-Morales D, Krogan NJ, Wang B. Brown adipocyte ATF4 activation improves thermoregulation and systemic metabolism. Cell Reports. 36: 109742. PMID 34551310 DOI: 10.1016/j.celrep.2021.109742 |
0.15 |
|
| 2021 |
Kumar D, Rains A, Herranz-Pérez V, Lu Q, Shi X, Swaney DL, Stevenson E, Krogan NJ, Huang B, Westlake C, Garcia-Verdugo JM, Yoder BK, Reiter JF. A ciliopathy complex builds distal appendages to initiate ciliogenesis. The Journal of Cell Biology. 220. PMID 34241634 DOI: 10.1083/jcb.202011133 |
0.149 |
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| 2023 |
Arang N, Lubrano S, Ceribelli M, Rigiracciolo DC, Saddawi-Konefka R, Faraji F, Ramirez SI, Kim D, Tosto FA, Stevenson E, Zhou Y, Wang Z, Bogomolovas J, Molinolo AA, Swaney DL, et al. High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma. Cell Reports. Medicine. 101244. PMID 37858338 DOI: 10.1016/j.xcrm.2023.101244 |
0.149 |
|
| 2023 |
Samelson AJ, Ariqat N, McKetney J, Rohanitazangi G, Parra Bravo C, Goodness D, Tian R, Grosjean P, Abskharon R, Eisenberg D, Kanaan NM, Gan L, Condello C, Swaney DL, Kampmann M. CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis. Biorxiv : the Preprint Server For Biology. PMID 37398204 DOI: 10.1101/2023.06.16.545386 |
0.148 |
|
| 2021 |
Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, ... ... Swaney DL, et al. Interpretation of cancer mutations using a multiscale map of protein systems. Science (New York, N.Y.). 374: eabf3067. PMID 34591613 DOI: 10.1126/science.abf3067 |
0.147 |
|
| 2021 |
Chaikovsky AC, Li C, Jeng EE, Loebell S, Lee MC, Murray CW, Cheng R, Demeter J, Swaney DL, Chen SH, Newton BW, Johnson JR, Drainas AP, Shue YT, Seoane JA, et al. The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D. Nature. PMID 33854239 DOI: 10.1038/s41586-021-03474-7 |
0.146 |
|
| 2023 |
Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, et al. In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response. Science Advances. 9: eadj4884. PMID 38064566 DOI: 10.1126/sciadv.adj4884 |
0.146 |
|
| 2020 |
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Zimanyi M, Deshpande I, Liang J, Anand AA, Dobzinski N, Zha BS, Barsi-Rhyne B, ... ... Swaney DL, et al. An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation. Biorxiv : the Preprint Server For Biology. PMID 32817938 DOI: 10.1101/2020.08.08.238469 |
0.137 |
|
| 2020 |
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, ... ... Swaney DL, et al. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science (New York, N.Y.). PMID 33154106 DOI: 10.1126/science.abe3255 |
0.134 |
|
| 2021 |
Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O'Keefe R, Jin N, VanLandingham NK, et al. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science (New York, N.Y.). 374: eabf2911. PMID 34591642 DOI: 10.1126/science.abf2911 |
0.134 |
|
| 2023 |
Eaton C, Avalos L, Liu SJ, Casey-Clyde T, Bisignano P, Lucas CH, Stevenson E, Choudhury A, Vasudevan H, Magill S, Krogan N, Villanueva-Meyer J, Swaney D, Raleigh D. MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features. Research Square. PMID 36993679 DOI: 10.21203/rs.3.rs-2577844/v1 |
0.132 |
|
| 2021 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Ummadi M, Rojc A, Turner J, Obernier K, Braberg H, Soucheray M, Richards A, ... ... Swaney DL, et al. Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant. Biorxiv : the Preprint Server For Biology. PMID 34127972 DOI: 10.1101/2021.06.06.446826 |
0.131 |
|
| 2021 |
Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, ... ... Swaney DL, et al. A protein interaction landscape of breast cancer. Science (New York, N.Y.). 374: eabf3066. PMID 34591612 DOI: 10.1126/science.abf3066 |
0.131 |
|
| 2022 |
O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, et al. Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2. Cancer Research. OF1-OF12. PMID 36273492 DOI: 10.1158/0008-5472.CAN-21-4335 |
0.126 |
|
| 2021 |
Tharp KM, Higuchi-Sanabria R, Timblin GA, Ford B, Garzon-Coral C, Schneider C, Muncie JM, Stashko C, Daniele JR, Moore AS, Frankino PA, Homentcovschi S, Manoli SS, Shao H, Richards AL, ... ... Swaney DL, et al. Adhesion-mediated mechanosignaling forces mitohormesis. Cell Metabolism. PMID 34019840 DOI: 10.1016/j.cmet.2021.04.017 |
0.125 |
|
| 2024 |
Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, et al. Epigenetic reprogramming shapes the cellular landscape of schwannoma. Nature Communications. 15: 476. PMID 38216587 DOI: 10.1038/s41467-023-40408-5 |
0.118 |
|
| 2022 |
Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, ... ... Swaney DL, et al. Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Nature Genetics. PMID 35534562 DOI: 10.1038/s41588-022-01061-8 |
0.117 |
|
| 2024 |
Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, et al. CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells. Mbio. e0222223. PMID 38411080 DOI: 10.1128/mbio.02222-23 |
0.113 |
|
| 2021 |
Bourdenx M, Martín-Segura A, Scrivo A, Rodriguez-Navarro JA, Kaushik S, Tasset I, Diaz A, Storm NJ, Xin Q, Juste YR, Stevenson E, Luengo E, Clement CC, Choi SJ, Krogan NJ, ... ... Swaney DL, et al. Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome. Cell. PMID 33891876 DOI: 10.1016/j.cell.2021.03.048 |
0.11 |
|
| 2021 |
Reuschl AK, Thorne L, Zuliani Alvarez L, Bouhaddou M, Obernier K, Soucheray M, Turner J, Fabius J, Nguyen GT, Swaney D, Rosales R, White KM, Aviles P, Kirby IT, Melnyk JE, et al. Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. Biorxiv : the Preprint Server For Biology. PMID 33501437 DOI: 10.1101/2021.01.24.427991 |
0.108 |
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| 2021 |
Reuschl AK, Thorne L, Zuliani Alvarez L, Bouhaddou M, Obernier K, Soucheray M, Turner J, Fabius J, Nguyen GT, Swaney D, Rosales R, White KM, Aviles P, Kirby IT, Melnyk JE, et al. Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. Biorxiv : the Preprint Server For Biology. PMID 33501437 DOI: 10.1101/2021.01.24.427991 |
0.108 |
|
| 2024 |
Patino R, Kühn MJ, Macmillan H, Inclan YF, Chavez I, Von Dollen J, Johnson JR, Swaney DL, Krogan NJ, Persat A, Engel JN. Spatial control of sensory adaptation modulates mechanosensing in . Biorxiv : the Preprint Server For Biology. PMID 38464290 DOI: 10.1101/2024.02.27.582188 |
0.08 |
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| 2021 |
Jin N, Keam B, Cho J, Lee MJ, Kim HR, Torosyan H, Jura N, Ng PK, Mills GB, Li H, Zeng Y, Barbash Z, Tarcic G, Kang H, Bauman JE, ... ... Swaney DL, et al. Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma. The Journal of Clinical Investigation. 131. PMID 34779417 DOI: 10.1172/JCI150335 |
0.076 |
|
| 2022 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, ... ... Swaney DL, et al. Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 35332335 DOI: 10.1038/s41586-022-04653-w |
0.039 |
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