| Year |
Citation |
Score |
| 2024 |
Bakhtina AA, Wippel HH, Chavez JD, Bruce JE. Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines. Biorxiv : the Preprint Server For Biology. PMID 38915502 DOI: 10.1101/2024.06.12.598691 |
0.431 |
|
| 2022 |
Caudal A, Tang X, Chavez JD, Keller A, Mohr JP, Bakhtina AA, Villet O, Chen H, Zhou B, Walker MA, Tian R, Bruce JE. Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart. Nature Cardiovascular Research. 1: 855-866. PMID 36405497 DOI: 10.1038/s44161-022-00127-4 |
0.382 |
|
| 2022 |
Bartolec TK, Hamey JJ, Keller A, Chavez JD, Bruce JE, Wilkins MR. Differential proteome and interactome analysis reveal the basis of pleiotropy associated with the histidine methyltransferase Hpm1p. Molecular & Cellular Proteomics : McP. 100249. PMID 35609787 DOI: 10.1016/j.mcpro.2022.100249 |
0.446 |
|
| 2022 |
Wippel HH, Chavez JD, Keller AD, Bruce JE. Multiplexed Isobaric Quantitative Cross-Linking Reveals Drug-Induced Interactome Changes in Breast Cancer Cells. Analytical Chemistry. 94: 2713-2722. PMID 35107270 DOI: 10.1021/acs.analchem.1c02208 |
0.442 |
|
| 2021 |
Chavez JD, Keller A, Wippel HH, Mohr JP, Bruce JE. Multiplexed Cross-Linking with Isobaric Quantitative Protein Interaction Reporter Technology. Analytical Chemistry. PMID 34882395 DOI: 10.1021/acs.analchem.1c02209 |
0.334 |
|
| 2021 |
Wippel HH, Chavez JD, Tang X, Bruce JE. Quantitative interactome analysis with chemical cross-linking and mass spectrometry. Current Opinion in Chemical Biology. PMID 34393043 DOI: 10.1016/j.cbpa.2021.06.011 |
0.426 |
|
| 2021 |
Chavez JD, Wippel HH, Tang X, Keller A, Bruce JE. In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. Chemical Reviews. PMID 34232610 DOI: 10.1021/acs.chemrev.1c00223 |
0.379 |
|
| 2021 |
Tang X, Wippel HH, Chavez JD, Bruce JE. Crosslinking mass spectrometry (XL-MS): a link between structural biology and systems biology. Protein Science : a Publication of the Protein Society. PMID 33594738 DOI: 10.1002/pro.4045 |
0.38 |
|
| 2020 |
Chavez JD, Park SG, Mohr JP, Bruce JE. Applications and advancements of FT-ICR-MS for interactome studies. Mass Spectrometry Reviews. PMID 33289940 DOI: 10.1002/mas.21675 |
0.318 |
|
| 2020 |
Keller A, Chavez JD, Tang X, Bruce JE. Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data. Journal of Proteome Research. PMID 33263396 DOI: 10.1021/acs.jproteome.0c00495 |
0.349 |
|
| 2020 |
Chavez JD, Keller A, Mohr JP, Bruce JE. Isobaric quantitative protein interaction reporter technology for comparative interactome studies. Analytical Chemistry. PMID 32969639 DOI: 10.1021/acs.analchem.0c03128 |
0.425 |
|
| 2020 |
Chavez JD, Tang X, Campbell MD, Reyes G, Kramer PA, Stuppard R, Keller A, Zhang H, Rabinovitch PS, Marcinek DJ, Bruce JE. Mitochondrial protein interaction landscape of SS-31. Proceedings of the National Academy of Sciences of the United States of America. PMID 32554501 DOI: 10.1073/Pnas.2002250117 |
0.448 |
|
| 2020 |
Ramsey JS, Chin EL, Chavez JD, Saha S, Mischuk D, Mahoney J, Mohr J, Robison FM, Mitrovic E, Xu Y, Strickler SR, Fernandez N, Zhong X, Polek M, Godfrey KE, et al. Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by 'Candidatus Liberibacter asiaticus'. Journal of Proteome Research. PMID 32338516 DOI: 10.1021/Acs.Jproteome.9B00802 |
0.3 |
|
| 2020 |
Zhong X, Wu X, Schweppe DK, Chavez JD, Mathay M, Eng JK, Keller A, Bruce JE. In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes. Journal of the American Society For Mass Spectrometry. 31: 190-195. PMID 32031408 DOI: 10.1021/Jasms.9B00021 |
0.32 |
|
| 2020 |
Caudal A, Chavez JD, Lee CF, Villet O, Zhou B, Bruce JE, Tian R. Mitochondrial protein interactome analysis reveals physical remodeling of OXPHOS machinery and intermediary metabolism network in the failing mouse heart Journal of Molecular and Cellular Cardiology. 140: 54. DOI: 10.1016/J.Yjmcc.2019.11.129 |
0.368 |
|
| 2019 |
Chin EL, Ramsey JS, Mishchuk DO, Saha S, Foster E, Chavez JD, Howe K, Zhong X, Polek M, Godfrey KE, Mueller L, Bruce JE, Heck M, Slupsky CM. Longitudinal transcriptomic, proteomic, and metabolomic analyses of Citrus sinensis (L.) Osbeck graft-inoculated with 'Candidatus Liberibacter asiaticus'. Journal of Proteome Research. PMID 31885275 DOI: 10.1021/Acs.Jproteome.9B00616 |
0.34 |
|
| 2019 |
Chavez JD, Keller A, Zhou B, Tian R, Bruce JE. Cellular Interactome Dynamics during Paclitaxel Treatment. Cell Reports. 29: 2371-2383.e5. PMID 31747606 DOI: 10.1016/J.Celrep.2019.10.063 |
0.448 |
|
| 2019 |
Chavez JD, Mohr JP, Mathay M, Zhong X, Keller A, Bruce JE. Systems structural biology measurements by in vivo cross-linking with mass spectrometry. Nature Protocols. PMID 31270507 DOI: 10.1038/S41596-019-0181-3 |
0.486 |
|
| 2019 |
Keller A, Chavez JD, Felt KC, Bruce JE. Prediction of an Upper Limit for the Fraction of Inter-Protein Cross-Links in Large-scale In Vivo Cross-Linking Studies. Journal of Proteome Research. PMID 31267744 DOI: 10.1021/Acs.Jproteome.9B00189 |
0.497 |
|
| 2019 |
Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews PC, Bernfur K, Borchers CH, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis TN, et al. The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study. Analytical Chemistry. PMID 31045356 DOI: 10.1021/Acs.Analchem.9B00658 |
0.449 |
|
| 2018 |
Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE. Tools for 3D Interactome Visualization. Journal of Proteome Research. PMID 30520642 DOI: 10.1021/Acs.Jproteome.8B00703 |
0.439 |
|
| 2018 |
Chavez JD, Bruce JE. Chemical cross-linking with mass spectrometry: a tool for systems structural biology. Current Opinion in Chemical Biology. 48: 8-18. PMID 30172868 DOI: 10.1016/J.Cbpa.2018.08.006 |
0.482 |
|
| 2018 |
Keller A, Chavez JD, Bruce JE. Increased Sensitivity with Automated Validation of XL-MS Cleavable Peptide Crosslinks. Bioinformatics (Oxford, England). PMID 30137231 DOI: 10.1093/Bioinformatics/Bty720 |
0.322 |
|
| 2018 |
Xu L, Gordon R, Farmer R, Pattanayak A, Binkowski A, Huang X, Avram M, Krishna S, Voll E, Pavese J, Chavez J, Bruce J, Mazar A, Nibbs A, Anderson W, et al. Precision therapeutic targeting of human cancer cell motility. Nature Communications. 9: 2454. PMID 29934502 DOI: 10.1038/S41467-018-04465-5 |
0.319 |
|
| 2018 |
Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE. Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification. Analytical Chemistry. PMID 29676898 DOI: 10.1021/Acs.Analchem.7B04991 |
0.436 |
|
| 2018 |
Vreven T, Schweppe DK, Chavez JD, Weisbrod CR, Shibata S, Zheng C, Bruce JE, Weng Z. Integrating cross-linking experiments with ab initio protein-protein docking. Journal of Molecular Biology. PMID 29665372 DOI: 10.1016/J.Jmb.2018.04.010 |
0.459 |
|
| 2018 |
Caudal A, Chavez JD, Lee CF, Villet O, Bruce JE, Tian R. Abstract 275: Quantification of the Mitochondrial Protein Interactome in Failing Hearts Circulation Research. 123. DOI: 10.1161/Res.123.Suppl_1.275 |
0.396 |
|
| 2017 |
Chavez JD, Lee CF, Caudal A, Keller A, Tian R, Bruce JE. Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue. Cell Systems. PMID 29199018 DOI: 10.1016/J.Cels.2017.10.017 |
0.491 |
|
| 2017 |
Alexander MM, Mohr JP, DeBlasio SL, Chavez JD, Ziegler-Graff V, Brault V, Bruce JE, Cilia M. Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry. Virus Research. PMID 28502641 DOI: 10.1016/J.Virusres.2017.05.005 |
0.418 |
|
| 2017 |
Ramsey JS, Chavez JD, Johnson R, Hosseinzadeh S, Mahoney JE, Mohr JP, Robison F, Zhong X, Hall DG, MacCoss M, Bruce J, Cilia M. Protein interaction networks at the host-microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen. Royal Society Open Science. 4: 160545. PMID 28386418 DOI: 10.1098/Rsos.160545 |
0.42 |
|
| 2017 |
Erez Z, Sorek R, Shao S, Hegde RS, Schweppe DK, Chavez JD, Bruce JE, Mizrachi E, Verbeke L, Peer YVd, Marchal K, Myburg AA, Bennett JA, Klironomos J, Payne GF, et al. Principles of Systems Biology, No. 14: Sense Codon Reassignment Boosts Protein Chemistries Cell Systems. 4: 143-143. PMID 28231445 DOI: 10.1016/J.Cels.2017.02.004 |
0.386 |
|
| 2017 |
Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE. Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers. Journal of Proteome Research. 16: 720-727. PMID 28152603 DOI: 10.1021/Acs.Jproteome.6B00752 |
0.503 |
|
| 2017 |
Schweppe DK, Chavez JD, Lee CF, Caudal A, Kruse SE, Stuppard R, Marcinek DJ, Shadel GS, Tian R, Bruce JE. Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. PMID 28130547 DOI: 10.1073/Pnas.1617220114 |
0.499 |
|
| 2016 |
Chavez JD, Eng JK, Schweppe DK, Cilia M, Rivera K, Zhong X, Wu X, Allen T, Khurgel M, Kumar A, Lampropoulos A, Larsson M, Maity S, Morozov Y, Pathmasiri W, et al. A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. Plos One. 11: e0167547. PMID 27997545 DOI: 10.1371/Journal.Pone.0167547 |
0.512 |
|
| 2016 |
Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, et al. In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. Nature Communications. 7: 13414. PMID 27834373 DOI: 10.1038/Ncomms13414 |
0.375 |
|
| 2016 |
Chavez JD, Schweppe DK, Eng JK, Bruce JE. In Vivo Conformational Dynamics of Hsp90 and Its Interactors. Cell Chemical Biology. 23: 716-26. PMID 27341434 DOI: 10.1016/J.Chembiol.2016.05.012 |
0.42 |
|
| 2016 |
Schweppe DK, Zheng C, Chavez JD, Navare AT, Wu X, Eng JK, Bruce JE. XLinkDB 2.0: Integrated, large-scale structural analysis of protein crosslinking data. Bioinformatics (Oxford, England). PMID 27153666 DOI: 10.1093/Bioinformatics/Btw232 |
0.505 |
|
| 2016 |
Schweppe DK, Chavez JD, Navare AT, Wu X, Ruiz B, Eng JK, Lam H, Bruce JE. Spectral library searching to identify crosslinked peptides. Journal of Proteome Research. PMID 27089058 DOI: 10.1021/Acs.Jproteome.6B00014 |
0.436 |
|
| 2015 |
DeBlasio SL, Chavez JD, Alexander MM, Ramsey J, Eng JK, Mahoney J, Gray SM, Bruce JE, Cilia M. Visualization of host-polerovirus interaction topologies using Protein Interaction Reporter technology. Journal of Virology. PMID 26656710 DOI: 10.1128/Jvi.01706-15 |
0.455 |
|
| 2015 |
Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE. Host-Microbe Protein Interactions during Bacterial Infection. Chemistry & Biology. PMID 26548613 DOI: 10.1016/J.Chembiol.2015.09.015 |
0.465 |
|
| 2015 |
Schweppe DK, Chavez JD, Bruce JE. XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. Bioinformatics (Oxford, England). PMID 26411867 DOI: 10.1093/Bioinformatics/Btv519 |
0.506 |
|
| 2015 |
Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE. Quantitative interactome analysis reveals a chemoresistant edgotype. Nature Communications. 6: 7928. PMID 26235782 DOI: 10.1038/Ncomms8928 |
0.501 |
|
| 2015 |
Wu X, Held K, Zheng C, Staudinger BJ, Chavez JD, Weisbrod CR, Eng JK, Singh PK, Manoil C, Bruce JE. Dynamic Proteome Response of Pseudomonas aeruginosa to Tobramycin Antibiotic Treatment. Molecular & Cellular Proteomics : McP. 14: 2126-37. PMID 26018413 DOI: 10.1074/Mcp.M115.050161 |
0.37 |
|
| 2015 |
Navare AT, Chavez JD, Zheng C, Weisbrod CR, Eng JK, Siehnel R, Singh PK, Manoil C, Bruce JE. Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry. Structure (London, England : 1993). 23: 762-73. PMID 25800553 DOI: 10.1016/J.Str.2015.01.022 |
0.504 |
|
| 2013 |
Weisbrod CR, Chavez JD, Eng JK, Yang L, Zheng C, Bruce JE. In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy. Journal of Proteome Research. 12: 1569-79. PMID 23413883 DOI: 10.1021/Pr3011638 |
0.474 |
|
| 2013 |
Zheng C, Weisbrod CR, Chavez JD, Eng JK, Sharma V, Wu X, Bruce JE. XLink-DB: Database and software tools for storing and visualizing protein interaction topology data Journal of Proteome Research. 12: 1989-1995. PMID 23413830 DOI: 10.1021/Pr301162J |
0.37 |
|
| 2013 |
Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE. Protein interactions, post-translational modifications and topologies in human cells. Molecular & Cellular Proteomics : McP. 12: 1451-67. PMID 23354917 DOI: 10.1074/Mcp.M112.024497 |
0.531 |
|
| 2012 |
Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE. Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions. Journal of Proteome Research. 11: 2968-81. PMID 22390342 DOI: 10.1021/Pr300041T |
0.402 |
|
| 2011 |
Hoopmann MR, Chavez JD, Bruce JE. SILACtor: software to enable dynamic SILAC studies. Analytical Chemistry. 83: 8403-10. PMID 21954881 DOI: 10.1021/Ac2017053 |
0.455 |
|
| 2011 |
Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE. Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells. Plos One. 6: e19892. PMID 21637840 DOI: 10.1371/Journal.Pone.0019892 |
0.41 |
|
| 2011 |
Chavez JD, Wu J, Bisson W, Maier CS. Site-specific proteomic analysis of lipoxidation adducts in cardiac mitochondria reveals chemical diversity of 2-alkenal adduction. Journal of Proteomics. 74: 2417-29. PMID 21513823 DOI: 10.1016/J.Jprot.2011.03.031 |
0.629 |
|
| 2011 |
Chavez JD, Liu NL, Bruce JE. Quantification of protein-protein interactions with chemical cross-linking and mass spectrometry. Journal of Proteome Research. 10: 1528-37. PMID 21222489 DOI: 10.1021/Pr100898E |
0.517 |
|
| 2010 |
Chavez JD, Bisson WH, Maier CS. A targeted mass spectrometry-based approach for the identification and characterization of proteins containing α-aminoadipic and γ-glutamic semialdehyde residues. Analytical and Bioanalytical Chemistry. 398: 2905-14. PMID 20957471 DOI: 10.1007/S00216-010-4289-0 |
0.642 |
|
| 2010 |
Maier CS, Chavez J, Wang J, Wu J. Protein adducts of aldehydic lipid peroxidation products identification and characterization of protein adducts using an aldehyde/keto-reactive probe in combination with mass spectrometry. Methods in Enzymology. 473: 305-30. PMID 20513485 DOI: 10.1016/S0076-6879(10)73016-0 |
0.647 |
|
| 2010 |
Chavez J, Chung WG, Miranda CL, Singhal M, Stevens JF, Maier CS. Site-specific protein adducts of 4-hydroxy-2(E)-nonenal in human THP-1 monocytic cells: protein carbonylation is diminished by ascorbic acid. Chemical Research in Toxicology. 23: 37-47. PMID 20043646 DOI: 10.1021/Tx9002462 |
0.652 |
|
| 2009 |
Gómez LA, Monette JS, Chavez JD, Maier CS, Hagen TM. Supercomplexes of the mitochondrial electron transport chain decline in the aging rat heart. Archives of Biochemistry and Biophysics. 490: 30-5. PMID 19679098 DOI: 10.1016/J.Abb.2009.08.002 |
0.568 |
|
| 2006 |
Chavez J, Wu J, Han B, Chung WG, Maier CS. New role for an old probe: affinity labeling of oxylipid protein conjugates by N'-aminooxymethylcarbonylhydrazino d-biotin. Analytical Chemistry. 78: 6847-54. PMID 17007505 DOI: 10.1021/Ac0607257 |
0.624 |
|
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