Michael J. Sweredoski, Ph.D. - Publications

Affiliations: 
2008 University of California, Irvine, Irvine, CA 

53 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
2016 Renata H, Lewis RD, Sweredoski MJ, Moradian A, Hess S, Wang ZJ, Arnold FH. Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes. Journal of the American Chemical Society. PMID 27573353 DOI: 10.1021/jacs.6b06823  1
2016 Sung MK, Porras-Yakushi TR, Reitsma JM, Huber FM, Sweredoski MJ, Hoelz A, Hess S, Deshaies RJ. A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins. Elife. 5. PMID 27552055 DOI: 10.7554/eLife.19105  1
2016 Sung MK, Reitsma JM, Sweredoski MJ, Hess S, Deshaies RJ. Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system. Molecular Biology of the Cell. PMID 27385339 DOI: 10.1091/mbc.E16-05-0290  1
2016 Liu JM, Sweredoski MJ, Hess S. Improved 6-plex TMT quantification throughput using a linear ion trap - HCD MS(3) scan. Analytical Chemistry. PMID 27377715 DOI: 10.1021/acs.analchem.6b01067  1
2016 Mosadeghi R, Reichermeier KM, Winkler M, Schreiber A, Reitsma JM, Zhang Y, Stengel F, Cao J, Kim M, Sweredoski MJ, Hess S, Leitner A, Aebersold R, Peter M, Deshaies RJ, et al. Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle. Elife. 5. PMID 27031283 DOI: 10.7554/eLife.12102  1
2016 Mahdavi A, Hamblin GD, Jindal GA, Bagert JD, Dong C, Sweredoski MJ, Hess S, Schuman EM, Tirrell DA. An engineered aminoacyl-tRNA synthetase for cell-selective analysis of mammalian protein synthesis. Journal of the American Chemical Society. PMID 26991063 DOI: 10.1021/jacs.5b08980  1
2016 Nguyen TV, Lee JE, Sweredoski MJ, Yang SJ, Jeon SJ, Harrison JS, Yim JH, Lee SG, Handa H, Kuhlman B, Jeong JS, Reitsma JM, Park CS, Hess S, Deshaies RJ. Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon. Molecular Cell. 61: 809-820. PMID 26990986 DOI: 10.1016/j.molcel.2016.02.032  1
2016 Bagert JD, van Kessel JC, Sweredoski MJ, Feng L, Hess S, Bassler BL, Tirrell DA. Time-resolved proteomic analysis of quorum sensing in Vibrio harveyi. Chemical Science (Royal Society of Chemistry : 2010). 7: 1797-1806. PMID 26925210 DOI: 10.1039/C5SC03340C  1
2016 Babin BM, Bergkessel M, Sweredoski MJ, Moradian A, Hess S, Newman DK, Tirrell DA. SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America. PMID 26787849 DOI: 10.1073/pnas.1514412113  1
2016 Kuo ML, Lee MB, Tang M, den Besten W, Hu S, Sweredoski MJ, Hess S, Chou CM, Changou CA, Su M, Jia W, Su L, Yen Y. PYCR1 and PYCR2 Interact and Collaborate with RRM2B to Protect Cells from Overt Oxidative Stress. Scientific Reports. 6: 18846. PMID 26733354 DOI: 10.1038/srep18846  1
2016 Moradian A, Porras-Yakushi TR, Sweredoski MJ, Hess S. A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses. Methods in Molecular Biology (Clifton, N.J.). 1394: 75-85. PMID 26700042 DOI: 10.1007/978-1-4939-3341-9_6  1
2015 Riestra AM, Gandhi S, Sweredoski MJ, Moradian A, Hess S, Urban S, Johnson PJ. A Trichomonas vaginalis Rhomboid Protease and Its Substrate Modulate Parasite Attachment and Cytolysis of Host Cells. Plos Pathogens. 11: e1005294. PMID 26684303 DOI: 10.1371/journal.ppat.1005294  1
2015 Ramkumar P, Lee CM, Moradian A, Sweredoski MJ, Hess S, Sharrocks AD, Haines DS, Reddy EP. JNK associated leucine zipper protein functions as a docking platform for Polo like kinase 1 and regulation of the associating transcription factor Forkhead box protein K1. The Journal of Biological Chemistry. PMID 26468278 DOI: 10.1074/jbc.M115.664649  1
2015 Li J, Olvera AI, Akbari OS, Moradian A, Sweredoski MJ, Hess S, Hay BA. Vectored antibody gene delivery mediates long-term contraception. Current Biology : Cb. 25: R820-2. PMID 26439332 DOI: 10.1016/j.cub.2015.08.002  1
2015 Sweredoski MJ, Moradian A, Raedle M, Franco C, Hess S. High resolution parallel reaction monitoring with electron transfer dissociation for middle-down proteomics. Analytical Chemistry. 87: 8360-6. PMID 26176279 DOI: 10.1021/acs.analchem.5b01542  1
2015 Porras-Yakushi TR, Sweredoski MJ, Hess S. ETD Outperforms CID and HCD in the Analysis of the Ubiquitylated Proteome. Journal of the American Society For Mass Spectrometry. 26: 1580-7. PMID 25994767 DOI: 10.1007/s13361-015-1168-0  1
2015 McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 521: 232-6. PMID 25915022 DOI: 10.1038/nature14443  1
2015 Walkup WG, Washburn L, Sweredoski MJ, Carlisle HJ, Graham RL, Hess S, Kennedy MB. Phosphorylation of synaptic GTPase-activating protein (synGAP) by Ca2+/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5) alters the ratio of its GAP activity toward Ras and Rap GTPases. The Journal of Biological Chemistry. 290: 4908-27. PMID 25533468 DOI: 10.1074/jbc.M114.614420  1
2015 Sweredoski MJ, Pekar Second T, Broeker J, Moradian A, Hess S. High resolution data-independent acquisition with electron transfer dissociation mass spectrometry: Multiplexed analysis of post-translationally modified proteins International Journal of Mass Spectrometry. 390: 155-162. DOI: 10.1016/j.ijms.2015.06.018  1
2014 Chan NC, den Besten W, Sweredoski MJ, Hess S, Deshaies RJ, Chan DC. Degradation of the deubiquitinating enzyme USP33 is mediated by p97 and the ubiquitin ligase HERC2. The Journal of Biological Chemistry. 289: 19789-98. PMID 24855649 DOI: 10.1074/jbc.M114.569392  1
2014 Bagert JD, Xie YJ, Sweredoski MJ, Qi Y, Hess S, Schuman EM, Tirrell DA. Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture. Molecular & Cellular Proteomics : McP. 13: 1352-8. PMID 24563536 DOI: 10.1074/mcp.M113.031914  1
2014 Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RL, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ. F-box protein FBXL16 binds PP2A-B55α and regulates differentiation of embryonic stem cells along the FLK1+ lineage. Molecular & Cellular Proteomics : McP. 13: 780-91. PMID 24390425 DOI: 10.1074/mcp.M113.031765  1
2014 Jang KS, Sweredoski MJ, Graham RL, Hess S, Clemons WM. Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni. Journal of Proteomics. 98: 90-8. PMID 24382552 DOI: 10.1016/j.jprot.2013.12.014  1
2014 Mahdavi A, Szychowski J, Ngo JT, Sweredoski MJ, Graham RL, Hess S, Schneewind O, Mazmanian SK, Tirrell DA. Identification of secreted bacterial proteins by noncanonical amino acid tagging. Proceedings of the National Academy of Sciences of the United States of America. 111: 433-8. PMID 24347637 DOI: 10.1073/pnas.1301740111  1
2014 Moradian A, Kalli A, Sweredoski MJ, Hess S. The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications. Proteomics. 14: 489-97. PMID 24339419 DOI: 10.1002/pmic.201300256  1
2014 Lu YY, Sweredoski MJ, Huss D, Lansford R, Hess S, Tirrell DA. Prometastatic GPCR CD97 is a direct target of tumor suppressor microRNA-126. Acs Chemical Biology. 9: 334-8. PMID 24274104 DOI: 10.1021/cb400704n  1
2014 Smith GT, Sweredoski MJ, Hess S. O-linked glycosylation sites profiling in Mycobacterium tuberculosis culture filtrate proteins. Journal of Proteomics. 97: 296-306. PMID 23702328 DOI: 10.1016/j.jprot.2013.05.011  1
2013 Kolawa N, Sweredoski MJ, Graham RL, Oania R, Hess S, Deshaies RJ. Perturbations to the ubiquitin conjugate proteome in yeast δubx mutants identify Ubx2 as a regulator of membrane lipid composition. Molecular & Cellular Proteomics : McP. 12: 2791-803. PMID 23793018 DOI: 10.1074/mcp.M113.030163  1
2013 Kurimchak A, Haines DS, Garriga J, Wu S, De Luca F, Sweredoski MJ, Deshaies RJ, Hess S, Graña X. Activation of p107 by fibroblast growth factor, which is essential for chondrocyte cell cycle exit, is mediated by the protein phosphatase 2A/B55α holoenzyme. Molecular and Cellular Biology. 33: 3330-42. PMID 23775125 DOI: 10.1128/MCB.00082-13  1
2013 Kalli A, Smith GT, Sweredoski MJ, Hess S. Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers. Journal of Proteome Research. 12: 3071-86. PMID 23642296 DOI: 10.1021/pr3011588  1
2013 Pierce NW, Lee JE, Liu X, Sweredoski MJ, Graham RL, Larimore EA, Rome M, Zheng N, Clurman BE, Hess S, Shan SO, Deshaies RJ. Cand1 promotes assembly of new SCF complexes through dynamic exchange of F box proteins. Cell. 153: 206-15. PMID 23453757 DOI: 10.1016/j.cell.2013.02.024  1
2013 Kalli A, Sweredoski MJ, Hess S. Data-dependent middle-down nano-liquid chromatography-electron capture dissociation-tandem mass spectrometry: an application for the analysis of unfractionated histones. Analytical Chemistry. 85: 3501-7. PMID 23448339 DOI: 10.1021/ac303103b  1
2013 Malerod H, Graham RL, Sweredoski MJ, Hess S. Comprehensive profiling of N-linked glycosylation sites in HeLa cells using hydrazide enrichment. Journal of Proteome Research. 12: 248-59. PMID 23205564 DOI: 10.1021/pr300859k  1
2012 Hodas JJ, Nehring A, Höche N, Sweredoski MJ, Pielot R, Hess S, Tirrell DA, Dieterich DC, Schuman EM. Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal noncanonical amino acid tagging (BONCAT). Proteomics. 12: 2464-76. PMID 22744909 DOI: 10.1002/pmic.201200112  1
2012 Sohn CH, Agnew HD, Lee JE, Sweredoski MJ, Graham RL, Smith GT, Hess S, Czerwieniec G, Loo JA, Heath JR, Deshaies RJ, Beauchamp JL. Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions. Analytical Chemistry. 84: 2662-9. PMID 22339618 DOI: 10.1021/ac202637n  1
2012 Haines DS, Lee JE, Beauparlant SL, Kyle DB, den Besten W, Sweredoski MJ, Graham RL, Hess S, Deshaies RJ. Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking. Molecular & Cellular Proteomics : McP. 11: M111.016444. PMID 22337587 DOI: 10.1074/mcp.M111.016444  1
2012 Sohn CH, Lee JE, Sweredoski MJ, Graham RL, Smith GT, Hess S, Czerwieniec G, Loo JA, Deshaies RJ, Beauchamp JL. Click chemistry facilitates formation of reporter ions and simplified synthesis of amine-reactive multiplexed isobaric tags for protein quantification. Journal of the American Chemical Society. 134: 2672-80. PMID 22225568 DOI: 10.1021/ja2099003  1
2012 Bell C, Smith GT, Sweredoski MJ, Hess S. Characterization of the Mycobacterium tuberculosis proteome by liquid chromatography mass spectrometry-based proteomics techniques: a comprehensive resource for tuberculosis research. Journal of Proteome Research. 11: 119-30. PMID 22053987 DOI: 10.1021/pr2007939  1
2012 Zhang D, Sweredoski MJ, Graham RL, Hess S, Shan SO. Novel proteomic tools reveal essential roles of SRP and importance of proper membrane protein biogenesis. Molecular & Cellular Proteomics : McP. 11: M111.011585. PMID 22030350 DOI: 10.1074/mcp.M111.011585  1
2012 Graham RLJ, Kalli A, Smith GT, Sweredoski MJ, Hess S. Avoiding pitfalls in proteomics sample preparation Biomacromolecular Mass Spectrometry: Tips From the Bench. 19-34.  1
2011 Sweredoski MJ, Smith GT, Kalli A, Graham RL, Hess S. LogViewer: a software tool to visualize quality control parameters to optimize proteomics experiments using Orbitrap and LTQ-FT mass spectrometers. Journal of Biomolecular Techniques : Jbt. 22: 122-6. PMID 22131886  1
2011 Gomez TA, Kolawa N, Gee M, Sweredoski MJ, Deshaies RJ. Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1. Bmc Biology. 9: 33. PMID 21627799 DOI: 10.1186/1741-7007-9-33  1
2011 Chan NC, Salazar AM, Pham AH, Sweredoski MJ, Kolawa NJ, Graham RL, Hess S, Chan DC. Broad activation of the ubiquitin-proteasome system by Parkin is critical for mitophagy. Human Molecular Genetics. 20: 1726-37. PMID 21296869 DOI: 10.1093/hmg/ddr048  1
2011 Lee JE, Sweredoski MJ, Graham RL, Kolawa NJ, Smith GT, Hess S, Deshaies RJ. The steady-state repertoire of human SCF ubiquitin ligase complexes does not require ongoing Nedd8 conjugation. Molecular & Cellular Proteomics : McP. 10: M110.006460. PMID 21169563 DOI: 10.1074/mcp.M110.006460  1
2011 Graham RLJ, Sweredoski MJ, Hess S. Stable isotope labeling by amino acids in cell culture (SILAC) - an introduction for biologists Current Proteomics. 8: 2-16. DOI: 10.2174/157016411794697354  1
2009 Sweredoski MJ, Baldi P. COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Engineering, Design & Selection : Peds. 22: 113-20. PMID 19074155 DOI: 10.1093/protein/gzn075  1
2008 Sweredoski M, DeRose-Wilson L, Gaut BS. A comparative computational analysis of nonautonomous helitron elements between maize and rice. Bmc Genomics. 9: 467. PMID 18842139 DOI: 10.1186/1471-2164-9-467  1
2008 Sweredoski MJ, Baldi P. PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics (Oxford, England). 24: 1459-60. PMID 18443018 DOI: 10.1093/bioinformatics/btn199  1
2008 Randall A, Cheng J, Sweredoski M, Baldi P. TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinformatics (Oxford, England). 24: 513-20. PMID 18006547 DOI: 10.1093/bioinformatics/btm548  1
2007 Sweredoski MJ, Donovan KJ, Nguyen BD, Shaka AJ, Baldi P. Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. Bioinformatics (Oxford, England). 23: 2829-35. PMID 17895278 DOI: 10.1093/bioinformatics/btm406  1
2006 Cheng J, Sweredoski MJ, Baldi P. DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks Data Mining and Knowledge Discovery. 13: 1-10. DOI: 10.1007/s10618-005-0023-5  1
2005 Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research. 33: W72-6. PMID 15980571 DOI: 10.1093/nar/gki396  1
2005 Cheng J, Sweredoski MJ, Baldi P. Accurate prediction of protein disordered regions by mining protein structure data Data Mining and Knowledge Discovery. 11: 213-222. DOI: 10.1007/s10618-005-0001-y  1
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