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Items: 35

1.

Tools for 3D Interactome Visualization.

Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE.

J Proteome Res. 2019 Feb 1;18(2):753-758. doi: 10.1021/acs.jproteome.8b00703. Epub 2018 Dec 18.

PMID:
30520642
2.

Chemical cross-linking with mass spectrometry: a tool for systems structural biology.

Chavez JD, Bruce JE.

Curr Opin Chem Biol. 2019 Feb;48:8-18. doi: 10.1016/j.cbpa.2018.08.006. Epub 2018 Aug 30. Review.

PMID:
30172868
3.

Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.

Keller A, Chavez JD, Bruce JE.

Bioinformatics. 2019 Mar 1;35(5):895-897. doi: 10.1093/bioinformatics/bty720.

PMID:
30137231
4.

Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification.

Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE.

Anal Chem. 2018 May 15;90(10):6028-6034. doi: 10.1021/acs.analchem.7b04991. Epub 2018 Apr 27.

PMID:
29676898
5.

Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.

Vreven T, Schweppe DK, Chavez JD, Weisbrod CR, Shibata S, Zheng C, Bruce JE, Weng Z.

J Mol Biol. 2018 Jun 8;430(12):1814-1828. doi: 10.1016/j.jmb.2018.04.010. Epub 2018 Apr 14.

PMID:
29665372
6.

Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue.

Chavez JD, Lee CF, Caudal A, Keller A, Tian R, Bruce JE.

Cell Syst. 2018 Jan 24;6(1):136-141.e5. doi: 10.1016/j.cels.2017.10.017. Epub 2017 Nov 29.

7.

Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry.

Alexander MM, Mohr JP, DeBlasio SL, Chavez JD, Ziegler-Graff V, Brault V, Bruce JE, Heck MC.

Virus Res. 2017 Sep 15;241:42-52. doi: 10.1016/j.virusres.2017.05.005. Epub 2017 May 11.

PMID:
28502641
8.

Protein interaction networks at the host-microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen.

Ramsey JS, Chavez JD, Johnson R, Hosseinzadeh S, Mahoney JE, Mohr JP, Robison F, Zhong X, Hall DG, MacCoss M, Bruce J, Cilia M.

R Soc Open Sci. 2017 Feb 8;4(2):160545. doi: 10.1098/rsos.160545. eCollection 2017 Feb.

9.

Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers.

Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE.

J Proteome Res. 2017 Feb 3;16(2):720-727. doi: 10.1021/acs.jproteome.6b00752. Epub 2016 Nov 30.

10.

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.

Schweppe DK, Chavez JD, Lee CF, Caudal A, Kruse SE, Stuppard R, Marcinek DJ, Shadel GS, Tian R, Bruce JE.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1732-1737. doi: 10.1073/pnas.1617220114. Epub 2017 Jan 27.

11.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

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, Perez-Neut M, Pineyro-Ruiz C, Polina E, Post S, Rider M, Tokmina-Roszyk D, Tyson K, Vieira Parrine Sant'Ana D, Bruce JE.

PLoS One. 2016 Dec 20;11(12):e0167547. doi: 10.1371/journal.pone.0167547. eCollection 2016.

12.

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075.

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, Singh PK, Manoil C, Bruce JE.

Nat Commun. 2016 Nov 11;7:13414. doi: 10.1038/ncomms13414.

13.

Normalization of NAD+ Redox Balance as a Therapy for Heart Failure.

Lee CF, Chavez JD, Garcia-Menendez L, Choi Y, Roe ND, Chiao YA, Edgar JS, Goo YA, Goodlett DR, Bruce JE, Tian R.

Circulation. 2016 Sep 20;134(12):883-94. doi: 10.1161/CIRCULATIONAHA.116.022495. Epub 2016 Aug 3.

14.

In Vivo Conformational Dynamics of Hsp90 and Its Interactors.

Chavez JD, Schweppe DK, Eng JK, Bruce JE.

Cell Chem Biol. 2016 Jun 23;23(6):716-26. doi: 10.1016/j.chembiol.2016.05.012.

15.

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data.

Schweppe DK, Zheng C, Chavez JD, Navare AT, Wu X, Eng JK, Bruce JE.

Bioinformatics. 2016 Sep 1;32(17):2716-8. doi: 10.1093/bioinformatics/btw232. Epub 2016 Apr 29.

16.

Spectral Library Searching To Identify Cross-Linked Peptides.

Schweppe DK, Chavez JD, Navare AT, Wu X, Ruiz B, Eng JK, Lam H, Bruce JE.

J Proteome Res. 2016 May 6;15(5):1725-31. doi: 10.1021/acs.jproteome.6b00014. Epub 2016 Apr 28.

17.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

DeBlasio SL, Chavez JD, Alexander MM, Ramsey J, Eng JK, Mahoney J, Gray SM, Bruce JE, Cilia M.

J Virol. 2015 Dec 9;90(4):1973-87. doi: 10.1128/JVI.01706-15. Print 2016 Feb 15.

18.

Host-Microbe Protein Interactions during Bacterial Infection.

Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE.

Chem Biol. 2015 Nov 19;22(11):1521-1530. doi: 10.1016/j.chembiol.2015.09.015. Epub 2015 Nov 5.

19.

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Schweppe DK, Chavez JD, Bruce JE.

Bioinformatics. 2016 Jan 15;32(2):306-8. doi: 10.1093/bioinformatics/btv519. Epub 2015 Sep 26.

20.

Quantitative interactome analysis reveals a chemoresistant edgotype.

Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE.

Nat Commun. 2015 Aug 3;6:7928. doi: 10.1038/ncomms8928.

21.

Differential proteomic analysis reveals that EGCG inhibits HDGF and activates apoptosis to increase the sensitivity of non-small cells lung cancer to chemotherapy.

Flores-Pérez A, Marchat LA, Sánchez LL, Romero-Zamora D, Arechaga-Ocampo E, Ramírez-Torres N, Chávez JD, Carlos-Reyes Á, Astudillo-de la Vega H, Ruiz-García E, González-Pérez A, López-Camarillo C.

Proteomics Clin Appl. 2016 Feb;10(2):172-82. doi: 10.1002/prca.201500008. Epub 2015 Sep 14.

PMID:
26175166
22.

Dynamic Proteome Response of Pseudomonas aeruginosa to Tobramycin Antibiotic Treatment.

Wu X, Held K, Zheng C, Staudinger BJ, Chavez JD, Weisbrod CR, Eng JK, Singh PK, Manoil C, Bruce JE.

Mol Cell Proteomics. 2015 Aug;14(8):2126-37. doi: 10.1074/mcp.M115.050161. Epub 2015 May 27.

23.

Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry.

Navare AT, Chavez JD, Zheng C, Weisbrod CR, Eng JK, Siehnel R, Singh PK, Manoil C, Bruce JE.

Structure. 2015 Apr 7;23(4):762-73. doi: 10.1016/j.str.2015.01.022. Epub 2015 Mar 19.

24.

Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.

O'Loughlin JL, Eucker TP, Chavez JD, Samuelson DR, Neal-McKinney J, Gourley CR, Bruce JE, Konkel ME.

PLoS One. 2015 Feb 19;10(2):e0118533. doi: 10.1371/journal.pone.0118533. eCollection 2015.

25.

In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy.

Weisbrod CR, Chavez JD, Eng JK, Yang L, Zheng C, Bruce JE.

J Proteome Res. 2013 Apr 5;12(4):1569-79. doi: 10.1021/pr3011638. Epub 2013 Feb 28.

26.

XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

Zheng C, Weisbrod CR, Chavez JD, Eng JK, Sharma V, Wu X, Bruce JE.

J Proteome Res. 2013 Apr 5;12(4):1989-95. doi: 10.1021/pr301162j. Epub 2013 Mar 5.

27.

Protein interactions, post-translational modifications and topologies in human cells.

Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE.

Mol Cell Proteomics. 2013 May;12(5):1451-67. doi: 10.1074/mcp.M112.024497. Epub 2013 Jan 25.

28.

Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions.

Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE.

J Proteome Res. 2012 May 4;11(5):2968-81. doi: 10.1021/pr300041t. Epub 2012 Mar 30.

29.

SILACtor: software to enable dynamic SILAC studies.

Hoopmann MR, Chavez JD, Bruce JE.

Anal Chem. 2011 Nov 15;83(22):8403-10. doi: 10.1021/ac2017053. Epub 2011 Oct 27.

30.

Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells.

Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE.

PLoS One. 2011;6(5):e19892. doi: 10.1371/journal.pone.0019892. Epub 2011 May 26.

31.

Site-specific proteomic analysis of lipoxidation adducts in cardiac mitochondria reveals chemical diversity of 2-alkenal adduction.

Chavez JD, Wu J, Bisson W, Maier CS.

J Proteomics. 2011 Oct 19;74(11):2417-29. doi: 10.1016/j.jprot.2011.03.031. Epub 2011 Apr 13.

32.

Quantification of protein-protein interactions with chemical cross-linking and mass spectrometry.

Chavez JD, Liu NL, Bruce JE.

J Proteome Res. 2011 Apr 1;10(4):1528-37. doi: 10.1021/pr100898e. Epub 2011 Feb 18.

33.

A targeted mass spectrometry-based approach for the identification and characterization of proteins containing α-aminoadipic and γ-glutamic semialdehyde residues.

Chavez JD, Bisson WH, Maier CS.

Anal Bioanal Chem. 2010 Dec;398(7-8):2905-14. doi: 10.1007/s00216-010-4289-0. Epub 2010 Oct 19.

34.

Supercomplexes of the mitochondrial electron transport chain decline in the aging rat heart.

Gómez LA, Monette JS, Chavez JD, Maier CS, Hagen TM.

Arch Biochem Biophys. 2009 Oct 1;490(1):30-5. doi: 10.1016/j.abb.2009.08.002. Epub 2009 Aug 11.

35.

Latinos en Extasis.

Betancourt T, Chavez JD.

Focus. 1998 May;13(6):5-6.

PMID:
11365418

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