Publications
Cysteines | Redox biology & Proteomics | Redox systems biology | Stem cells
Proteome Bioinformatics | Computational Biology | Cancer biology | Metaproteomics
Integrative 'omics | Systems Biology | Cancer signaling | Metabolomics
Chemical Biology
Protein Biochemistry & Signaling
Cysteines | Redox biology & Proteomics | Redox systems biology | Stem cells
- van der Post S, Birchenough GMH, Held JM. NOX1-dependent redox signaling potentiates colonic stem cell proliferation to adapt to the intestinal microbiota by linking EGFR and TLR activation. Cell Reports. 2021. PMID: 33826887.
- Behring JB, van der Post S, Mooradian AD, Egan MJ, Zimmerman MI, Clements JL, Bowman GR, Held JM. Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation. Science Signaling. 2020. PMID: 31964804; PMCID: PMC7263378 [PDF]
- Held JM. Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome. Antioxidants & Redox Signaling. 2020. PMID: 31368359; PMCID: PMC7047077.
- Held JM and Gibson BW. (2012) Regulatory control or oxidative damage? Proteomic approaches to interrogate the role of cysteine oxidation status in biological processes. Molecular & Cellular Proteomics 2012 11: 1-14. PMID: 22159599 [PDF]
- Danielson SR, Held JM, Oo M, Riley R, Gibson BW, Andersen JK. Quantitative mapping of reversible mitochondrial Complex I cysteine oxidation in a Parkinson disease mouse model. Journal of Biological Chemistry 2011 286: 7601-7608. PMCID: PMC3045014. [PDF]
- Held JM, Danielson SR, Behring JB, Atsriku C, Britton DJ, Puckett RL, Schilling B, Campisi J, Benz CC, Gibson BW. Targeted quantitation of site-specific cysteine oxidation in endogenous proteins using a differential alkylation and multiple reaction monitoring mass spectrometry approach. Molecular & Cellular Proteomics 2010 PMCID: PMC2938085 [PDF]
Proteome Bioinformatics | Computational Biology | Cancer biology | Metaproteomics
- Seymour RW, van der Post S, Mooradian AD, Held JM. ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets. Journal of Proteome Research. 2021. PMID: 34056901
- Mooradian AD, van der Post S, Naegle KM, Held JM. ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis. PLoS Comput Biol. 2020. PMID: 32150535; PMCID: PMC7082058.
- Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyo D, Held JM. Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner. Science Signaling 2017 10:491 1-14. PMCID: PMC5712229.
- Mooradian AD, Held JM, Naegle KM. Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate. Current Protocols in Bioinformatics. 2017 59(1):13.3211-13.21.27. PMID: 28902398.
Integrative 'omics | Systems Biology | Cancer signaling | Metabolomics
- Brashears CB, Barlin M, Ehrhardt WR, Rathore R, Schultze M, Tzeng SC, Van Tine BA, Held JM. Systems level profiling of arginine starvation reveals MYC and ERK adaptive metabolic reprogramming. Cell Death & Disease 2020 Aug 20;11(8):662. PMID: 32814773. PMCID In Process
- Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX. Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibitors in triple negative breast cancers. Cancer Research. 2018 78(10):2732-2746. PMCID: PMC5955814.
- Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MH, Ding L. Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nature Communication 2017 8:14864. PMCID: PMC5379071.
- Kremer JC, Prudner BC, Lange SES, Bean GR, Schultze MB, Brashears CB, Radyk MD, Redlich N, Tzeng SC, Kami K, Shelton L, Li A, Morgan Z, Bomalaski JS, Tsukamoto T, McConathy J, Michel LS, Held JM, Van Tine BA. Arginine Deprivation Inhibits the Warburg Effect and Upregulates Glutamine Anaplerosis and Serine Biosynthesis in ASS1-Deficient Cancers. Cell Reports 2017 18(4):991-1004.
- Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communication 2017 8(1):291.
- Held JM, Schilling B, D’Souza AK, Srinivasan T, Behring J, Sorensen DJ, Benz CC, Gibson BW. (2013) Label-free quantitation and mapping of the ErbB2 tumor receptor by multi-protease digestion with data-dependent (MS1) and data-independent (MS2) acquisitions. International Journal of Proteomics 2013; 2013:791985. PMCID: PMC3654371.
Chemical Biology
- Clements J, Pohl F, Muthupandi P, Rogers S, Mao J, Doctor A, Birman VB, Held, JM. A clickable probe for versatile characterization of S-nitrosothiols. Redox Biology. 2020 (PDF).
Protein Biochemistry & Signaling
- Held JM, Britton DJ, Scott GK, Lee E, Schilling B, Baldwin MA, Gibson BW, Benz CC. Ligand binding promotes CDK-dependent phosphorylation of ER alpha on hinge serine 294 but inhibits ligand-independent phosphorylation of serine 305. Molecular Cancer Research 2012: 10: 1120-1132. PMCID: PMC3950940.