J. Will Thompson | Scholars@Duke

J. Will Thompson
Adjunct Assistant Professor in the Department of Pharmacology & Cancer Biology

Dr. Thompson's research focuses on the development and deployment of proteomics and metabolomics mass spectrometry techniques for the analysis of biological systems. He served as the Assistant Director of the Proteomics and Metabolomics Shared Resource in the Duke School of Medicine from 2007-2021. He currently maintains collaborations in metabolomics and proteomics research at Duke, and develops new tools for chemical analysis as a Principal Scientist at 908 Devices in Carrboro, NC.

Current Appointments & Affiliations

Adjunct Assistant Professor in the Department of Pharmacology & Cancer Biology, Pharmacology & Cancer Biology, Basic Science Departments 2021

Contact Information

701 W Main St, Ste 320, Durham, NC 27701
Box 91009, 450 Research Drive, Durham, NC 27708
will.thompson@duke.edu (919) 684-5454
Proteomics and Metabolomics Shared Resource

Background
Education, Training, & Certifications
- Ph.D., University of North Carolina - Chapel Hill 2006
Previous Appointments & Affiliations
- Assistant Research Professor of Pharmacology & Cancer Biology, Pharmacology & Cancer Biology, Basic Science Departments 2014 - 2021
Research
Selected Grants
- Gender and APOE genotype interact to alter immune regulated metabolism in AD awarded by National Institutes of Health 2019 - 2024
- Identification of Novel Bioactive Lipid Metabolites for Predicting Liver-related Outcomes in Persons Co-Infected with HIV and HCV (R01) awarded by National Institutes of Health 2017 - 2023
- Proteomic Determination of APOE4-induced Neuroinflammation in the Pathogenesis of Alzheimer's Disease awarded by Ruth K. Broad Biomedical Research Foundation 2020 - 2022
- Development of an S-acylation assay for monitoring CLN1 Batten Disease clinical trials and progression of other neurological disorders awarded by Circumvent Pharmaceutical 2021 - 2022
- Abbott Diagnostics Collaborative Sponsored Research Agreement awarded by Abbott Laboratories 2016 - 2022
- Immune-based nutrient deprivation and neurodegenerative disease awarded by National Institutes of Health 2013 - 2020
- Ex vivo metabolomic profiling of statin-induced myopathy awarded by American Heart Association 2017 - 2019
- Thermo Lumos Tribrid High-Resolution Accurate-Mass Tandem Mass Spectrometer awarded by National Institutes of Health 2018 - 2019
- Gender and APOE genotype interact to alter immune regulated metabolism in AD awarded by National Institutes of Health 2017 - 2019
- Immune regulated amino acid pathways in Alzheimer's Disease awarded by National Institutes of Health 2016 - 2018
- Probing the role of Mitochondrial Short-Chain Carbon Homeostasis in the Hypertrophied and Failing Heart awarded by Sanford-Burnham Medical Research Institute 2017
- Role of SUMO Conjugation in Ischemia: Significance, Mechanisms and Pathways awarded by National Institutes of Health 2012 - 2017
- Proteomics of flavorings-induced airway disease awarded by Centers for Disease Control and Prevention 2014 - 2016
- Instrumentation for Quantitative Phosphoproteomics and Acetylomics awarded by National Institutes of Health 2014 - 2015
- S-nitrosothiol-regulated pathways in acute lung injury awarded by National Institutes of Health 2010 - 2013
- Expansion of Capacity for Quantitative and Qualitative Differential Expression - Acquisition of an Integrated System for Nanoscale Capillary LC/MS/MS Analysis Using a UPLC/NanoMate/Q-Tof with On-line and Off-line Data Acquisition Capabilities awarded by National Institutes of Health 2010 - 2011
External Relationships
- 908 Devices
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Adams, Kendra J., Joan G. Wilson, David S. Millington, M Arthur Moseley, Carol A. Colton, J Will Thompson, and W Kirby Gottschalk. “Capillary Electrophoresis-High Resolution Mass Spectrometry for Measuring In Vivo Arginine Isotope Incorporation in Alzheimer's Disease Mouse Models.” J Am Soc Mass Spectrom 32, no. 6 (June 2, 2021): 1448–58. https://doi.org/10.1021/jasms.1c00055.
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  - Langley, Raymond J., Marie E. Migaud, Lori Flores, J Will Thompson, Elizabeth A. Kean, Murphy M. Mostellar, Matthew Mowry, et al. “A metabolomic endotype of bioenergetic dysfunction predicts mortality in critically ill patients with acute respiratory failure.” Sci Rep 11, no. 1 (May 18, 2021): 10515. https://doi.org/10.1038/s41598-021-89716-0.
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  - Dutta, Punashi, Karthik M. Kodigepalli, Stephanie LaHaye, J Will Thompson, Sarah Rains, Casey Nagel, Kaitlyn Thatcher, Robert B. Hinton, and Joy Lincoln. “KPT-330 Prevents Aortic Valve Calcification via a Novel C/EBPβ Signaling Pathway.” Circ Res 128, no. 9 (April 30, 2021): 1300–1316. https://doi.org/10.1161/CIRCRESAHA.120.318503.
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  - Bryan, Jordan, Arpita Mandan, Gauri Kamat, W Kirby Gottschalk, Alexandra Badea, Kendra J. Adams, J Will Thompson, et al. “Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways.” Alzheimers Dement 17, no. 4 (April 2021): 561–73. https://doi.org/10.1002/alz.12223.
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  - MahmoudianDehkordi, Siamak, Ahmed T. Ahmed, Sudeepa Bhattacharyya, Xianlin Han, Rebecca A. Baillie, Matthias Arnold, Michelle K. Skime, et al. “Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression.” Transl Psychiatry 11, no. 1 (March 2, 2021): 153. https://doi.org/10.1038/s41398-020-01097-6.
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  - Berger, Miles, Mary Cooter, Alexander S. Roesler, Stacey Chung, John Park, Jennifer L. Modliszewski, Keith W. VanDusen, et al. “APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid.” J Alzheimers Dis 79, no. 2 (2021): 511–30. https://doi.org/10.3233/JAD-200747.
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  - VanDusen, Keith W., Yi-Ju Li, Victor Cai, Ashley Hall, Sarah Hiles, J Will Thompson, M Arthur Moseley, et al. “Cerebrospinal Fluid Proteome Changes in Older Non-Cardiac Surgical Patients with Postoperative Cognitive Dysfunction.” J Alzheimers Dis 80, no. 3 (2021): 1281–97. https://doi.org/10.3233/JAD-201544.
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  - Baloni, Priyanka, Cory C. Funk, Jingwen Yan, James T. Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken, et al. “Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease.” Cell Rep Med 1, no. 8 (November 17, 2020): 100138. https://doi.org/10.1016/j.xcrm.2020.100138.
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  - Naggie, Susanna, Sam Lusk, J Will Thompson, Meredith Mock, Cynthia Moylan, Joseph E. Lucas, Laura Dubois, Lisa St John-Williams, M Arthur Moseley, and Keyur Patel. “Metabolomic Signature as a Predictor of Liver Disease Events in Patients With HIV/HCV Coinfection.” J Infect Dis 222, no. 12 (November 13, 2020): 2012–20. https://doi.org/10.1093/infdis/jiaa316.
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  - Hannigan, Molly M., Alyson M. Hoffman, J Will Thompson, Tianli Zheng, and Christopher V. Nicchitta. “Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane.” Mol Cell Proteomics 19, no. 11 (November 2020): 1826–49. https://doi.org/10.1074/mcp.RA120.002228.
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  - Kamyszek, Reed W., Matthew W. Foster, Brooke A. Evans, Keaton Stoner, Jessica Poisson, Amudan J. Srinivasan, J Will Thompson, M Arthur Moseley, Micah J. Mooberry, and Ian J. Welsby. “The effect of pathogen inactivation on cryoprecipitate: a functional and quantitative evaluation.” Blood Transfus 18, no. 6 (November 2020): 454–64. https://doi.org/10.2450/2020.0077-20.
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  - Friede, Kevin A., Margaret M. Infeld, Ru San Tan, Holly J. Knickerbocker, Rachel A. Myers, Laura G. Dubois, J Will Thompson, et al. “Influence of Sex on Platelet Reactivity in Response to Aspirin.” J Am Heart Assoc 9, no. 14 (July 21, 2020): e014726. https://doi.org/10.1161/JAHA.119.014726.
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  - Zhao, Na, Yingxue Ren, Yu Yamazaki, Wenhui Qiao, Fuyao Li, Lindsey M. Felton, Siamak Mahmoudiandehkordi, et al. “Alzheimer's Risk Factors Age, APOE Genotype, and Sex Drive Distinct Molecular Pathways.” Neuron 106, no. 5 (June 3, 2020): 727-742.e6. https://doi.org/10.1016/j.neuron.2020.02.034.
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  - Adams, Kendra J., Brian Pratt, Neelanjan Bose, Laura G. Dubois, Lisa St John-Williams, Kevin M. Perrott, Karina Ky, et al. “Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.” J Proteome Res 19, no. 4 (April 3, 2020): 1447–58. https://doi.org/10.1021/acs.jproteome.9b00640.
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  - Arnold, Matthias, Kwangsik Nho, Alexandra Kueider-Paisley, Tyler Massaro, Kevin Huynh, Barbara Brauner, Siamak MahmoudianDehkordi, et al. “Sex and APOE ε4 genotype modify the Alzheimer's disease serum metabolome.” Nat Commun 11, no. 1 (March 2, 2020): 1148. https://doi.org/10.1038/s41467-020-14959-w.
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  - Ahmed, Ahmed T., Siamak MahmoudianDehkordi, Sudeepa Bhattacharyya, Matthias Arnold, Duan Liu, Drew Neavin, M Arthur Moseley, et al. “Acylcarnitine metabolomic profiles inform clinically-defined major depressive phenotypes.” J Affect Disord 264 (March 1, 2020): 90–97. https://doi.org/10.1016/j.jad.2019.11.122.
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  - Shuford, Christopher M., Jay S. Johnson, J Will Thompson, Patricia L. Holland, Andrew N. Hoofnagle, and Russell P. Grant. “More sensitivity is always better: Measuring sub-clinical levels of serum thyroglobulin on a µLC-MS/MS system.” Clin Mass Spectrom 15 (January 2020): 29–35. https://doi.org/10.1016/j.clinms.2020.01.001.
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  - Thompson, J Will, Kendra J. Adams, Jerzy Adamski, Yasmin Asad, David Borts, John A. Bowden, Gregory Byram, et al. “International Ring Trial of a High Resolution Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis.” Anal Chem 91, no. 22 (November 19, 2019): 14407–16. https://doi.org/10.1021/acs.analchem.9b02908.
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  - St John-Williams, Lisa, Siamak Mahmoudiandehkordi, Matthias Arnold, Tyler Massaro, Colette Blach, Gabi Kastenmüller, Gregory Louie, et al. “Bile acids targeted metabolomics and medication classification data in the ADNI1 and ADNIGO/2 cohorts.” Sci Data 6, no. 1 (October 17, 2019): 212. https://doi.org/10.1038/s41597-019-0181-8.
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  - Schaller, Teilo H., Matthew W. Foster, J Will Thompson, Ivan Spasojevic, Deimante Normantaite, M Arthur Moseley, Luis Sanchez-Perez, and John H. Sampson. “Pharmacokinetic Analysis of a Novel Human EGFRvIII:CD3 Bispecific Antibody in Plasma and Whole Blood Using a High-Resolution Targeted Mass Spectrometry Approach.” J Proteome Res 18, no. 8 (August 2, 2019): 3032–41. https://doi.org/10.1021/acs.jproteome.9b00145.
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  - Davidson, Phillip L., J Will Thompson, Matthew W. Foster, M Arthur Moseley, Maria Byrne, and Gregory A. Wray. “A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins.” Evol Dev 21, no. 4 (July 2019): 188–204. https://doi.org/10.1111/ede.12289.
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  - Brooks, Ellen R., David C. Lin, Craig B. Langman, J Will Thompson, Lisa St John-Williams, Susan L. Furth, Bradley Warady, and Shannon Haymond. “Metabolomic Patterns in Adolescents With Mild to Moderate CKD.” Kidney Int Rep 4, no. 5 (May 2019): 720–23. https://doi.org/10.1016/j.ekir.2019.01.009.
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  - Rubach, Matthew P., Haoyue Zhang, Salvatore M. Florence, Jackson P. Mukemba, Ayam R. Kalingonji, Nicholas M. Anstey, Tsin W. Yeo, et al. “Kinetic and Cross-Sectional Studies on the Genesis of Hypoargininemia in Severe Pediatric Plasmodium falciparum Malaria.” Infect Immun 87, no. 4 (April 2019). https://doi.org/10.1128/IAI.00655-18.
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  - “Erratum to “Altered bile acid profile associates with cognitive impairment in Alzheimer’s disease—An emerging role for gut microbiome” [Alzheimer’s & Dementia 2019;15:76‐92.].” Alzheimer’S &Amp; Dementia 15, no. 4 (April 2019): 604–604. https://doi.org/10.1016/j.jalz.2019.03.002.
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  - Fisher-Wellman, Kelsey H., James A. Draper, Michael T. Davidson, Ashley S. Williams, Tara M. Narowski, Dorothy H. Slentz, Olga R. Ilkayeva, et al. “Respiratory Phenomics across Multiple Models of Protein Hyperacylation in Cardiac Mitochondria Reveals a Marginal Impact on Bioenergetics.” Cell Rep 26, no. 6 (February 5, 2019): 1557-1572.e8. https://doi.org/10.1016/j.celrep.2019.01.057.
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  - Antonia, Alejandro L., Kyle D. Gibbs, Esme D. Trahair, Kelly J. Pittman, Amelia T. Martin, Benjamin H. Schott, Jeffrey S. Smith, et al. “Pathogen Evasion of Chemokine Response Through Suppression of CXCL10.” Front Cell Infect Microbiol 9 (2019): 280. https://doi.org/10.3389/fcimb.2019.00280.
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  - Harrison, Alistair, Rachael L. Hardison, Rachel M. Wallace, James Fitch, Derek R. Heimlich, Meghan O’ Bryan, Laura Dubois, et al. “Reprioritization of biofilm metabolism is associated with nutrient adaptation and long-term survival of Haemophilus influenzae.” Npj Biofilms Microbiomes 5, no. 1 (2019): 33. https://doi.org/10.1038/s41522-019-0105-6.
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  - MahmoudianDehkordi, Siamak, Matthias Arnold, Kwangsik Nho, Shahzad Ahmad, Wei Jia, Guoxiang Xie, Gregory Louie, et al. “Altered bile acid profile associates with cognitive impairment in Alzheimer's disease-An emerging role for gut microbiome.” Alzheimers Dement 15, no. 1 (January 2019): 76–92. https://doi.org/10.1016/j.jalz.2018.07.217.
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  - Hardison, Rachael L., Derek R. Heimlich, Alistair Harrison, Wandy L. Beatty, Sarah Rains, M Arthur Moseley, J Will Thompson, Sheryl S. Justice, and Kevin M. Mason. “Erratum for Hardison et al., "Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development".” Msphere 3, no. 5 (October 31, 2018). https://doi.org/10.1128/mSphere.00562-18.
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  - Mabe, Nathaniel W., Douglas B. Fox, Ryan Lupo, Amy E. Decker, Stephanie N. Phelps, J Will Thompson, and James V. Alvarez. “Epigenetic silencing of tumor suppressor Par-4 promotes chemoresistance in recurrent breast cancer.” J Clin Invest 128, no. 10 (October 1, 2018): 4413–28. https://doi.org/10.1172/JCI99481.
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  - Hardison, Rachael L., Derek R. Heimlich, Alistair Harrison, Wandy L. Beatty, Sarah Rains, M Arthur Moseley, J Will Thompson, Sheryl S. Justice, and Kevin M. Mason. “Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development.” Msphere 3, no. 5 (September 12, 2018). https://doi.org/10.1128/mSphere.00286-18.
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  - Yuan, Lifeng, Linhui Zhai, Lili Qian, De Huang, Yi Ding, Handan Xiang, Xiaojing Liu, et al. “Switching off IMMP2L signaling drives senescence via simultaneous metabolic alteration and blockage of cell death.” Cell Res 28, no. 6 (June 2018): 625–43. https://doi.org/10.1038/s41422-018-0043-5.
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  - Juvvadi, Praveen R., M Arthur Moseley, Christopher J. Hughes, Erik J. Soderblom, Sarah Lennon, Simon R. Perkins, J Will Thompson, et al. “Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs.” J Proteome Res 17, no. 2 (February 2, 2018): 780–93. https://doi.org/10.1021/acs.jproteome.7b00499.
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  - Moseley, M Arthur, Christopher J. Hughes, Praveen R. Juvvadi, Erik J. Soderblom, Sarah Lennon, Simon R. Perkins, J Will Thompson, et al. “Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization.” J Proteome Res 17, no. 2 (February 2, 2018): 770–79. https://doi.org/10.1021/acs.jproteome.7b00464.
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  - Bowden, John A., Alan Heckert, Candice Z. Ulmer, Christina M. Jones, Jeremy P. Koelmel, Laila Abdullah, Linda Ahonen, et al. “Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma.” J Lipid Res 58, no. 12 (December 2017): 2275–88. https://doi.org/10.1194/jlr.M079012.
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  - St John-Williams, Lisa, Colette Blach, Jon B. Toledo, Daniel M. Rotroff, Sungeun Kim, Kristaps Klavins, Rebecca Baillie, et al. “Targeted metabolomics and medication classification data from participants in the ADNI1 cohort.” Sci Data 4 (October 17, 2017): 170140. https://doi.org/10.1038/sdata.2017.140.
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  - Banks, Courtney J., Nathan W. Rodriguez, Kyle R. Gashler, Rushika R. Pandya, Jeffrey B. Mortenson, Matthew D. Whited, Erik J. Soderblom, et al. “Acylation of Superoxide Dismutase 1 (SOD1) at K122 Governs SOD1-Mediated Inhibition of Mitochondrial Respiration.” Mol Cell Biol 37, no. 20 (October 15, 2017). https://doi.org/10.1128/MCB.00354-17.
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  - Baek, Amy E., Yen-Rei A. Yu, Sisi He, Suzanne E. Wardell, Ching-Yi Chang, Sanghoon Kwon, Ruchita V. Pillai, et al. “The cholesterol metabolite 27 hydroxycholesterol facilitates breast cancer metastasis through its actions on immune cells.” Nat Commun 8, no. 1 (October 11, 2017): 864. https://doi.org/10.1038/s41467-017-00910-z.
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  - Toledo, Jon B., Matthias Arnold, Gabi Kastenmüller, Rui Chang, Rebecca A. Baillie, Xianlin Han, Madhav Thambisetty, et al. “Metabolic network failures in Alzheimer's disease: A biochemical road map.” Alzheimers Dement 13, no. 9 (September 2017): 965–84. https://doi.org/10.1016/j.jalz.2017.01.020.
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  - Foster, Matthew W., Zhonghui Yang, David M. Gooden, J Will Thompson, Carol H. Ball, Meredith E. Turner, Yongyong Hou, Jingbo Pi, M Arthur Moseley, and Loretta G. Que. “Correction to "Proteomic Characterization of the Cellular Response to Nitrosative Stress Mediated by S-Nitrosoglutathione Reductase Inhibition".” J Proteome Res 16, no. 7 (July 7, 2017): 2661. https://doi.org/10.1021/acs.jproteome.7b00368.
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  - Kimbung, Siker, Ching-Yi Chang, Pär-Ola Bendahl, Laura Dubois, J Will Thompson, Donald P. McDonnell, and Signe Borgquist. “Impact of 27-hydroxylase (CYP27A1) and 27-hydroxycholesterol in breast cancer.” Endocr Relat Cancer 24, no. 7 (July 2017): 339–49. https://doi.org/10.1530/ERC-16-0533.
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  - Anderson, Kristin A., Frank K. Huynh, Kelsey Fisher-Wellman, J Darren Stuart, Brett S. Peterson, Jonathan D. Douros, Gregory R. Wagner, et al. “SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion.” Cell Metab 25, no. 4 (April 4, 2017): 838-855.e15. https://doi.org/10.1016/j.cmet.2017.03.003.
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  - Wagner, Gregory R., Dhaval P. Bhatt, Thomas M. O’Connell, J Will Thompson, Laura G. Dubois, Donald S. Backos, Hao Yang, et al. “A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation.” Cell Metab 25, no. 4 (April 4, 2017): 823-837.e8. https://doi.org/10.1016/j.cmet.2017.03.006.
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  - Alfaqih, Mahmoud A., Erik R. Nelson, Wen Liu, Rachid Safi, Jeffery S. Jasper, Everardo Macias, Joseph Geradts, et al. “CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer.” Cancer Res 77, no. 7 (April 1, 2017): 1662–73. https://doi.org/10.1158/0008-5472.CAN-16-2738.
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  - Burke, Thomas W., Ricardo Henao, Erik Soderblom, Ephraim L. Tsalik, J Will Thompson, Micah T. McClain, Marshall Nichols, et al. “Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection.” Ebiomedicine 17 (March 2017): 172–81. https://doi.org/10.1016/j.ebiom.2017.02.015.
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  - Wang, Liuyang, Emily R. Ko, James J. Gilchrist, Kelly J. Pittman, Anna Rautanen, Matti Pirinen, J Will Thompson, et al. “Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis.” Sci Adv 3, no. 3 (March 2017): e1602096. https://doi.org/10.1126/sciadv.1602096.
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  - Foster, Matthew W., William M. Gwinn, Francine L. Kelly, David M. Brass, Ashlee M. Valente, M Arthur Moseley, J Will Thompson, Daniel L. Morgan, and Scott M. Palmer. “Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl.” J Proteome Res 16, no. 2 (February 3, 2017): 538–49. https://doi.org/10.1021/acs.jproteome.6b00672.
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  - Peterson, Christine Tara, Joseph Lucas, Lisa St John-Williams, J Will Thompson, M Arthur Moseley, Sheila Patel, Scott N. Peterson, et al. “Corrigendum: Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI).” Sci Rep 6 (October 10, 2016): 34678. https://doi.org/10.1038/srep34678.
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  - Feger, Bryan J., J Will Thompson, Laura G. Dubois, Reddy P. Kommaddi, Matthew W. Foster, Rajashree Mishra, Sudha K. Shenoy, et al. “Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection.” Sci Rep 6 (September 27, 2016): 34091. https://doi.org/10.1038/srep34091.
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  - Peterson, Christine Tara, Joseph Lucas, Lisa St John-Williams, J Will Thompson, M Arthur Moseley, Sheila Patel, Scott N. Peterson, et al. “Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI).” Sci Rep 6 (September 9, 2016): 32609. https://doi.org/10.1038/srep32609.
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  - Pham, Hai T., Kathrin Arnhard, Yasmin J. Asad, Lu Deng, Thomas K. Felder, Lisa St John-Williams, Volkhard Kaever, et al. “Inter-Laboratory Robustness of Next-Generation Bile Acid Study in Mice and Humans: International Ring Trial Involving 12 Laboratories.” J Appl Lab Med 1, no. 2 (September 1, 2016): 129–42. https://doi.org/10.1373/jalm.2016.020537.
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  - Alwarawrah, Yazan, Philip Hughes, David Loiselle, David A. Carlson, David B. Darr, Jamie L. Jordan, Jessie Xiong, et al. “Fasnall, a Selective FASN Inhibitor, Shows Potent Anti-tumor Activity in the MMTV-Neu Model of HER2(+) Breast Cancer.” Cell Chem Biol 23, no. 6 (June 23, 2016): 678–88. https://doi.org/10.1016/j.chembiol.2016.04.011.
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  - Michelotti, Gregory A., Anikia Tucker, Marzena Swiderska-Syn, Mariana Verdelho Machado, Steve S. Choi, Leandi Kruger, Erik Soderblom, et al. “Pleiotrophin regulates the ductular reaction by controlling the migration of cells in liver progenitor niches.” Gut 65, no. 4 (April 2016): 683–92. https://doi.org/10.1136/gutjnl-2014-308176.
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  - Harrison, Alistair, Laura G. Dubois, Lisa St John-Williams, M Arthur Moseley, Rachael L. Hardison, Derek R. Heimlich, Alexander Stoddard, et al. “Comprehensive Proteomic and Metabolomic Signatures of Nontypeable Haemophilus influenzae-Induced Acute Otitis Media Reveal Bacterial Aerobic Respiration in an Immunosuppressed Environment.” Mol Cell Proteomics 15, no. 3 (March 2016): 1117–38. https://doi.org/10.1074/mcp.M115.052498.
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  - Davies, Michael N., Lilja Kjalarsdottir, J Will Thompson, Laura G. Dubois, Robert D. Stevens, Olga R. Ilkayeva, M Julia Brosnan, Timothy P. Rolph, Paul A. Grimsrud, and Deborah M. Muoio. “The Acetyl Group Buffering Action of Carnitine Acetyltransferase Offsets Macronutrient-Induced Lysine Acetylation of Mitochondrial Proteins.” Cell Rep 14, no. 2 (January 12, 2016): 243–54. https://doi.org/10.1016/j.celrep.2015.12.030.
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  - Michelotti, Gregory A., Anikia Tucker, Marzena Swiderska-Syn, Mariana Verdelho Machado, Steve S. Choi, Leandi Kruger, Erik Soderblom, et al. “Pleiotrophin regulates the ductular reaction by controlling the migration of cells in liver progenitor niches.” Gut 65, no. 4 (2016): 683–92. https://doi.org/10.1136/gutjnl-2014-308176.
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  - Bennett, Keiryn L., Xia Wang, Cory E. Bystrom, Matthew C. Chambers, Tracy M. Andacht, Larry J. Dangott, Félix Elortza, et al. “The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.” Mol Cell Proteomics 14, no. 12 (December 2015): 3299–3309. https://doi.org/10.1074/mcp.O115.051888.
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  - Figueiredo-Freitas, Cícero, Raul A. Dulce, Matthew W. Foster, Jingsheng Liang, Aline M. S. Yamashita, Frederico L. Lima-Rosa, J Will Thompson, et al. “S-Nitrosylation of Sarcomeric Proteins Depresses Myofilament Ca2+)Sensitivity in Intact Cardiomyocytes.” Antioxid Redox Signal 23, no. 13 (November 1, 2015): 1017–34. https://doi.org/10.1089/ars.2015.6275.
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  - Vermulst, M., A. S. Denney, M. J. Lang, C. W. Hung, S. Moore, M. A. Moseley, J. W. Thompson, et al. “Erratum: Transcription errors induce proteotoxic stress and shorten cellular lifespan (Nature Communications (2015) 6:8065 DOI: 10.1038/ncomms9065).” Nature Communications 6 (October 14, 2015). https://doi.org/10.1038/ncomms9738.
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  - Vermulst, Marc, Ashley S. Denney, Michael J. Lang, Chao-Wei Hung, Stephanie Moore, M Arthur Moseley, J Will Thompson, et al. “Transcription errors induce proteotoxic stress and shorten cellular lifespan.” Nat Commun 6 (August 25, 2015): 8065. https://doi.org/10.1038/ncomms9065.
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  - Priola, Ginna M., Matthew W. Foster, Allison M. Deal, Brenna M. Richardson, J Will Thompson, and Julie Blatt. “Cerebrospinal fluid proteomics in children during induction for acute lymphoblastic leukemia: A pilot study.” Pediatr Blood Cancer 62, no. 7 (July 2015): 1190–94. https://doi.org/10.1002/pbc.25420.
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  - Mortenson, Jeffrey B., Lisa N. Heppler, Courtney J. Banks, Vajira K. Weerasekara, Matthew D. Whited, Stephen R. Piccolo, William E. Johnson, J Will Thompson, and Joshua L. Andersen. “Histone deacetylase 6 (HDAC6) promotes the pro-survival activity of 14-3-3ζ via deacetylation of lysines within the 14-3-3ζ binding pocket.” J Biol Chem 290, no. 20 (May 15, 2015): 12487–96. https://doi.org/10.1074/jbc.M114.607580.
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  - Tang, Xiaohu, Melissa M. Keenan, Jianli Wu, Chih-An Lin, Laura Dubois, J Will Thompson, Stephen J. Freedland, Susan K. Murphy, and Jen-Tsan Chi. “Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis.” Plos Genet 11, no. 4 (April 2015): e1005158. https://doi.org/10.1371/journal.pgen.1005158.
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  - Foster, Matthew W., Lake D. Morrison, Jamie L. Todd, Laurie D. Snyder, J Will Thompson, Erik J. Soderblom, Kelly Plonk, et al. “Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis.” J Proteome Res 14, no. 2 (February 6, 2015): 1238–49. https://doi.org/10.1021/pr501149m.
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  - Paglia, Giuseppe, Peggi Angel, Jonathan P. Williams, Keith Richardson, Hernando J. Olivos, J Will Thompson, Lochana Menikarachchi, et al. “Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification.” Anal Chem 87, no. 2 (January 20, 2015): 1137–44. https://doi.org/10.1021/ac503715v.
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  - Foltz, Emily, Sassan Azad, Mary Lou Everett, Zoie E. Holzknecht, Nathan L. Sanders, J Will Thompson, Laura G. Dubois, et al. “An assessment of human gastric fluid composition as a function of PPI usage.” Physiol Rep 3, no. 1 (January 1, 2015). https://doi.org/10.14814/phy2.12269.
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  - Saka, Hector Alex, J Will Thompson, Yi-Shan Chen, Laura G. Dubois, Joel T. Haas, Arthur Moseley, and Raphael H. Valdivia. “Chlamydia trachomatis Infection Leads to Defined Alterations to the Lipid Droplet Proteome in Epithelial Cells.” Plos One 10, no. 4 (2015): e0124630. https://doi.org/10.1371/journal.pone.0124630.
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  - Pfenning, Andreas R., Erina Hara, Osceola Whitney, Miriam V. Rivas, Rui Wang, Petra L. Roulhac, Jason T. Howard, et al. “Convergent transcriptional specializations in the brains of humans and song-learning birds.” Science 346, no. 6215 (December 12, 2014): 1256846. https://doi.org/10.1126/science.1256846.
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  - Weerasekara, Vajira K., David J. Panek, David G. Broadbent, Jeffrey B. Mortenson, Andrew D. Mathis, Gideon N. Logan, John T. Prince, David M. Thomson, J Will Thompson, and Joshua L. Andersen. “Metabolic-stress-induced rearrangement of the 14-3-3ζ interactome promotes autophagy via a ULK1- and AMPK-regulated 14-3-3ζ interaction with phosphorylated Atg9.” Mol Cell Biol 34, no. 24 (December 2014): 4379–88. https://doi.org/10.1128/MCB.00740-14.
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  - Mehta, K., E. J. Soderblom, J. W. Thompson, L. G. Que, H. E. Marshall, M. A. Moseley, and M. W. Foster. “Targeted proteomics for unraveling the post-translational regulation of human nitric oxide synthase 2.” Nitric Oxide 42C (November 15, 2014): 132. https://doi.org/10.1016/j.niox.2014.09.100.
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  - Jagannathan, Sujatha, Jack C-C Hsu, David W. Reid, Qiang Chen, Will J. Thompson, Arthur M. Moseley, and Christopher V. Nicchitta. “Multifunctional roles for the protein translocation machinery in RNA anchoring to the endoplasmic reticulum.” J Biol Chem 289, no. 37 (September 12, 2014): 25907–24. https://doi.org/10.1074/jbc.M114.580688.
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  - Foster, Matthew W., J Will Thompson, Julie G. Ledford, Laura G. Dubois, John W. Hollingsworth, Dave Francisco, Sasipa Tanyaratsrisakul, et al. “Identification and Quantitation of Coding Variants and Isoforms of Pulmonary Surfactant Protein A.” J Proteome Res 13, no. 8 (August 1, 2014): 3722–32. https://doi.org/10.1021/pr500307f.
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  - Paglia, Giuseppe, Jonathan P. Williams, Lochana Menikarachchi, J Will Thompson, Richard Tyldesley-Worster, Skarphédinn Halldórsson, Ottar Rolfsson, et al. “Ion mobility derived collision cross sections to support metabolomics applications.” Anal Chem 86, no. 8 (April 15, 2014): 3985–93. https://doi.org/10.1021/ac500405x.
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  - Yang, Wei, Huaxin Sheng, J Will Thompson, Shengli Zhao, Liangli Wang, Pei Miao, Xiaozhi Liu, M Arthur Moseley, and Wulf Paschen. “Small ubiquitin-like modifier 3-modified proteome regulated by brain ischemia in novel small ubiquitin-like modifier transgenic mice: putative protective proteins/pathways.” Stroke 45, no. 4 (April 2014): 1115–22. https://doi.org/10.1161/STROKEAHA.113.004315.
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  - Iwabuchi, Masahiro, Huaxin Sheng, J Will Thompson, Liangli Wang, Laura G. Dubois, David Gooden, Marthur Moseley, Wulf Paschen, and Wei Yang. “Characterization of the ubiquitin-modified proteome regulated by transient forebrain ischemia.” J Cereb Blood Flow Metab 34, no. 3 (March 2014): 425–32. https://doi.org/10.1038/jcbfm.2013.210.
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  - Little, Dianne, J Will Thompson, Laura G. Dubois, David S. Ruch, M Arthur Moseley, and Farshid Guilak. “Proteomic differences between male and female anterior cruciate ligament and patellar tendon.” Plos One 9, no. 5 (2014): e96526. https://doi.org/10.1371/journal.pone.0096526.
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  - Schechter, Matthew A., Michael K. H. Hsieh, Linda W. Njoroge, J Will Thompson, Erik J. Soderblom, Bryan J. Feger, Constantine D. Troupes, et al. “Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.” Plos One 9, no. 8 (2014): e104157. https://doi.org/10.1371/journal.pone.0104157.
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  - Benjamin, Ashlee M., J Will Thompson, Erik J. Soderblom, Scott J. Geromanos, Ricardo Henao, Virginia B. Kraus, M Arthur Moseley, and Joseph E. Lucas. “A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.” Bmc Bioinformatics 14 (December 16, 2013): 364. https://doi.org/10.1186/1471-2105-14-364.
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  - Foster, Matthew W., J Will Thompson, Michael T. Forrester, Yonggang Sha, Timothy J. McMahon, Dawn E. Bowles, M Arthur Moseley, and Harvey E. Marshall. “Proteomic analysis of the NOS2 interactome in human airway epithelial cells.” Nitric Oxide 34 (November 1, 2013): 37–46. https://doi.org/10.1016/j.niox.2013.02.079.
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  - Hoos, Michael D., Brenna M. Richardson, Matthew W. Foster, Angela Everhart, J Will Thompson, M Arthur Moseley, and Carol A. Colton. “Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase.” J Proteome Res 12, no. 10 (October 4, 2013): 4462–77. https://doi.org/10.1021/pr4005103.
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  - Thompson, J Will, Michael T. Forrester, M Arthur Moseley, and Matthew W. Foster. “Solid-phase capture for the detection and relative quantification of S-nitrosoproteins by mass spectrometry.” Methods 62, no. 2 (August 1, 2013): 130–37. https://doi.org/10.1016/j.ymeth.2012.10.001.
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  - Langley, Raymond J., Ephraim L. Tsalik, Jennifer C. van Velkinburgh, Seth W. Glickman, Brandon J. Rice, Chunping Wang, Bo Chen, et al. “An integrated clinico-metabolomic model improves prediction of death in sepsis.” Sci Transl Med 5, no. 195 (July 24, 2013): 195ra95. https://doi.org/10.1126/scitranslmed.3005893.
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  - Skiba, Nikolai P., William J. Spencer, Raquel Y. Salinas, Eric C. Lieu, J Will Thompson, and Vadim Y. Arshavsky. “Proteomic identification of unique photoreceptor disc components reveals the presence of PRCD, a protein linked to retinal degeneration.” J Proteome Res 12, no. 6 (June 7, 2013): 3010–18. https://doi.org/10.1021/pr4003678.
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  - Henao, R., J. W. Thompson, M. A. Moseley, G. S. Ginsburg, L. Carin, and J. E. Lucas. “Latent protein trees.” Annals of Applied Statistics 7, no. 2 (June 1, 2013): 691–713. https://doi.org/10.1214/13-AOAS639.
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  - Foster, Matthew W., J Will Thompson, Loretta G. Que, Ivana V. Yang, David A. Schwartz, M Arthur Moseley, and Harvey E. Marshall. “Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure.” J Proteome Res 12, no. 5 (May 3, 2013): 2194–2205. https://doi.org/10.1021/pr400066g.
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  - Richardson, Brenna McJury, Erik J. Soderblom, J Will Thompson, and M Arthur Moseley. “Automated, reproducible, titania-based phosphopeptide enrichment strategy for label-free quantitative phosphoproteomics.” J Biomol Tech 24, no. 1 (April 2013): 8–16. https://doi.org/10.7171/jbt.13-2401-002.
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  - Kummarapurugu, Apparao B., Bernard M. Fischer, Shuo Zheng, Ginger L. Milne, Andrew J. Ghio, Erin N. Potts-Kant, W Michael Foster, et al. “NADPH:quinone oxidoreductase 1 regulates host susceptibility to ozone via isoprostane generation.” J Biol Chem 288, no. 7 (February 15, 2013): 4681–91. https://doi.org/10.1074/jbc.M112.438440.
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  - Fan, Yongliang, J Will Thompson, Laura G. Dubois, M Arthur Moseley, and Jennifer J. Wernegreen. “Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes.” J Proteome Res 12, no. 2 (February 1, 2013): 704–18. https://doi.org/10.1021/pr3007842.
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  - Soderblom, Erik J., J Will Thompson, Evan A. Schwartz, Edward Chiou, Laura G. Dubois, M Arthur Moseley, and Rahima Zennadi. “Proteomic analysis of ERK1/2-mediated human sickle red blood cell membrane protein phosphorylation.” Clin Proteomics 10, no. 1 (January 3, 2013): 1. https://doi.org/10.1186/1559-0275-10-1.
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  - Foster, M. W., J. W. Thompson, L. G. Que, I. V. Yang, D. A. Schwartz, M. A. Moseley, and H. E. Marshall. “Proteomic Analysis Of Human Bronchoalveolar Lavage Fluid After Subsegmental Challenge.” American Journal of Respiratory and Critical Care Medicine 187 (2013).
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  - Thompson, J Will, Alex Robeson, and Joshua L. Andersen. “Identification of deacetylase substrates with the biotin switch approach.” Methods Mol Biol 1077 (2013): 133–48. https://doi.org/10.1007/978-1-62703-637-5_9.
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  - Chan, Mark Y., Min Lin, Joseph Lucas, Arthur Moseley, J Will Thompson, Derek Cyr, Hitoshi Ueda, Mariko Kajikawa, Thomas L. Ortel, and Richard C. Becker. “Plasma proteomics of patients with non-valvular atrial fibrillation on chronic anti-coagulation with warfarin or a direct factor Xa inhibitor.” Thromb Haemost 108, no. 6 (December 2012): 1180–91. https://doi.org/10.1160/TH12-05-0310.
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  - Thompson, J Will, Haoyue Zhang, Peter Smith, Steven Hillman, M Arthur Moseley, and David S. Millington. “Extraction and analysis of carnitine and acylcarnitines by electrospray ionization tandem mass spectrometry directly from dried blood and plasma spots using a novel autosampler.” Rapid Commun Mass Spectrom 26, no. 21 (November 15, 2012): 2548–54. https://doi.org/10.1002/rcm.6370.
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  - Thalassinos, Konstantinos, Johannes P. C. Vissers, Stefan Tenzer, Yishai Levin, J Will Thompson, David Daniel, Darrin Mann, et al. “Design and application of a data-independent precursor and product ion repository.” J Am Soc Mass Spectrom 23, no. 10 (October 2012): 1808–20. https://doi.org/10.1007/s13361-012-0416-9.
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  - Henao, R., J. W. Thompson, M. A. Moseley, G. S. Ginsburg, L. Carin, and J. E. Lucas. “Hierarchical factor modeling of proteomics data.” 2012 Ieee 2nd International Conference on Computational Advances in Bio and Medical Sciences, Iccabs 2012, May 8, 2012. https://doi.org/10.1109/ICCABS.2012.6182638.
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  - Lucas, Joseph E., J Will Thompson, Laura G. Dubois, Jeanette McCarthy, Hans Tillmann, Alexander Thompson, Norah Shire, et al. “Metaprotein expression modeling for label-free quantitative proteomics.” Bmc Bioinformatics 13 (May 4, 2012): 74. https://doi.org/10.1186/1471-2105-13-74.
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  - Petricka, Jalean J., Monica A. Schauer, Molly Megraw, Natalie W. Breakfield, J Will Thompson, Stoyan Georgiev, Erik J. Soderblom, et al. “The protein expression landscape of the Arabidopsis root.” Proc Natl Acad Sci U S A 109, no. 18 (May 1, 2012): 6811–18. https://doi.org/10.1073/pnas.1202546109.
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  - Foster, Matthew W., Zhonghui Yang, David M. Gooden, J Will Thompson, Carol H. Ball, Meredith E. Turner, Yongyong Hou, Jingbo Pi, M Arthur Moseley, and Loretta G. Que. “Proteomic characterization of the cellular response to nitrosative stress mediated by s-nitrosoglutathione reductase inhibition.” J Proteome Res 11, no. 4 (April 6, 2012): 2480–91. https://doi.org/10.1021/pr201180m.
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  - Chireau, Monique V., J Will Thompson, Brenna Richardson, Arthur Moseley, and L Kristin Newby. “Proteomics of Preeclamptic Placenta.” Reproductive Sciences 19, no. S3 (March 1, 2012): 201A-201A.
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  - Yang, Wei, J Will Thompson, Zhengfeng Wang, Liangli Wang, Huaxin Sheng, Matthew W. Foster, M Arthur Moseley, and Wulf Paschen. “Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics.” J Proteome Res 11, no. 2 (February 3, 2012): 1108–17. https://doi.org/10.1021/pr200834f.
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  - Zennadi, Rahima, Erin J. Whalen, Erik J. Soderblom, Susan C. Alexander, J Will Thompson, Laura G. Dubois, M Arthur Moseley, and Marilyn J. Telen. “Erythrocyte plasma membrane-bound ERK1/2 activation promotes ICAM-4-mediated sickle red cell adhesion to endothelium.” Blood 119, no. 5 (February 2, 2012): 1217–27. https://doi.org/10.1182/blood-2011-03-344440.
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  - Thompson, J. W., and E. J. Soderblom. “Keeping Sample Preparation Simple: Tips on How to Perform Proteomics Measurements with Consistency and Accuracy.” Genetic Engineering and Biotechnology News 31, no. 21 (December 1, 2011): 38–39. https://doi.org/10.1089/gen.31.21.17.
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  - Saka, Hector A., J Will Thompson, Yi-Shan Chen, Yadunanda Kumar, Laura G. Dubois, M Arthur Moseley, and Raphael H. Valdivia. “Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms.” Mol Microbiol 82, no. 5 (December 2011): 1185–1203. https://doi.org/10.1111/j.1365-2958.2011.07877.x.
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  - Melvin, Jeffrey A., Christine F. Murphy, Laura G. Dubois, J Will Thompson, M Arthur Moseley, and Dewey G. McCafferty. “Staphylococcus aureus sortase A contributes to the Trojan horse mechanism of immune defense evasion with its intrinsic resistance to Cys184 oxidation.” Biochemistry 50, no. 35 (September 6, 2011): 7591–99. https://doi.org/10.1021/bi200844h.
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  - Andersen, Joshua L., J Will Thompson, Kelly R. Lindblom, Erika S. Johnson, Chih-Sheng Yang, Lauren R. Lilley, Christopher D. Freel, M Arthur Moseley, and Sally Kornbluth. “A biotin switch-based proteomics approach identifies 14-3-3ζ as a target of Sirt1 in the metabolic regulation of caspase-2.” Mol Cell 43, no. 5 (September 2, 2011): 834–42. https://doi.org/10.1016/j.molcel.2011.07.028.
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  - Patel, Keyur, Joseph E. Lucas, J Will Thompson, Laura G. Dubois, Hans L. Tillmann, Alexander J. Thompson, Diane Uzarski, et al. “High predictive accuracy of an unbiased proteomic profile for sustained virologic response in chronic hepatitis C patients.” Hepatology 53, no. 6 (June 2011): 1809–18. https://doi.org/10.1002/hep.24284.
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  - Soderblom, Erik J., Melanie Philipp, J Will Thompson, Marc G. Caron, and M Arthur Moseley. “Quantitative label-free phosphoproteomics strategy for multifaceted experimental designs.” Anal Chem 83, no. 10 (May 15, 2011): 3758–64. https://doi.org/10.1021/ac200213b.
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  - Andersen, Joshua L., J Will Thompson, Marisa R. Buchakjian, M Arthur Moseley, and Sally Kornbluth. “Abstract 4697: Metabolic regulation of caspase-2.” Cancer Research 71, no. 8_Supplement (April 15, 2011): 4697–4697. https://doi.org/10.1158/1538-7445.am2011-4697.
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  - Reidel, Boris, J Will Thompson, Sina Farsiu, M Arthur Moseley, Nikolai P. Skiba, and Vadim Y. Arshavsky. “Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells.” Mol Cell Proteomics 10, no. 3 (March 2011): M110.002469. https://doi.org/10.1074/mcp.M110.002469.
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  - Forrester, Michael T., Douglas T. Hess, J Will Thompson, Rainbo Hultman, M Arthur Moseley, Jonathan S. Stamler, and Patrick J. Casey. “Site-specific analysis of protein S-acylation by resin-assisted capture.” J Lipid Res 52, no. 2 (February 2011): 393–98. https://doi.org/10.1194/jlr.D011106.
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  - Roulhac, Petra L., James M. Ward, J Will Thompson, Erik J. Soderblom, Michael Silva, M Arthur Moseley, and Erich D. Jarvis. “Microproteomics: quantitative proteomic profiling of small numbers of laser-captured cells.” Cold Spring Harb Protoc 2011, no. 2 (February 1, 2011): pdb.prot5573. https://doi.org/10.1101/pdb.prot5573.
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  - Cyr, Derek D., Joseph E. Lucas, J Will Thompson, Keyur Patel, Paul J. Clark, Alexander Thompson, Hans L. Tillmann, John G. McHutchison, M Arthur Moseley, and Jeanette J. McCarthy. “Characterization of serum proteins associated with IL28B genotype among patients with chronic hepatitis C.” Plos One 6, no. 7 (2011): e21854. https://doi.org/10.1371/journal.pone.0021854.
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  - Kozubowski, Lukasz, J Will Thompson, Maria E. Cardenas, M Arthur Moseley, and Joseph Heitman. “Association of calcineurin with the COPI protein Sec28 and the COPII protein Sec13 revealed by quantitative proteomics.” Plos One 6, no. 10 (2011): e25280. https://doi.org/10.1371/journal.pone.0025280.
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  - Lee, Anthony, Dena L. Toffaletti, Jennifer Tenor, Erik J. Soderblom, J Will Thompson, M Arthur Moseley, Michael Price, and John R. Perfect. “Survival defects of Cryptococcus neoformans mutants exposed to human cerebrospinal fluid result in attenuated virulence in an experimental model of meningitis.” Infect Immun 78, no. 10 (October 2010): 4213–25. https://doi.org/10.1128/IAI.00551-10.
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  - Benhar, Moran, J Will Thompson, M Arthur Moseley, and Jonathan S. Stamler. “Identification of S-nitrosylated targets of thioredoxin using a quantitative proteomic approach.” Biochemistry 49, no. 32 (August 17, 2010): 6963–69. https://doi.org/10.1021/bi100619k.
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  - Morris, Daniel P., Eric D. Roush, J Will Thompson, M Arthur Moseley, James W. Murphy, and Jonathan L. McMurry. “Kinetic characterization of Salmonella FliK-FlhB interactions demonstrates complexity of the Type III secretion substrate-specificity switch.” Biochemistry 49, no. 30 (August 3, 2010): 6386–93. https://doi.org/10.1021/bi100487p.
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  - West, Graham M., J Will Thompson, Erik J. Soderblom, Laura G. Dubois, Patrick D. Dearmond, M Arthur Moseley, and Michael C. Fitzgerald. “Mass spectrometry-based thermal shift assay for protein-ligand binding analysis.” Anal Chem 82, no. 13 (July 1, 2010): 5573–81. https://doi.org/10.1021/ac100465a.
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  - Xia, Wenle, Sarah Bacus, Intisar Husain, Leihua Liu, Sumin Zhao, Zuguo Liu, M Arthur Moseley, et al. “Resistance to ErbB2 tyrosine kinase inhibitors in breast cancer is mediated by calcium-dependent activation of RelA.” Mol Cancer Ther 9, no. 2 (February 2010): 292–99. https://doi.org/10.1158/1535-7163.MCT-09-1041.
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  - Thompson, J Will, Rachel A. Lieberman, and James W. Jorgenson. “Hydrodynamic chromatography for the size classification of micron and sub-micron sized packing materials.” J Chromatogr A 1216, no. 45 (November 6, 2009): 7732–38. https://doi.org/10.1016/j.chroma.2009.08.088.
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  - Andersen, Joshua L., Carrie E. Johnson, Christopher D. Freel, Amanda B. Parrish, Jennifer L. Day, Marisa R. Buchakjian, Leta K. Nutt, J Will Thompson, M Arthur Moseley, and Sally Kornbluth. “Restraint of apoptosis during mitosis through interdomain phosphorylation of caspase-2.” Embo J 28, no. 20 (October 21, 2009): 3216–27. https://doi.org/10.1038/emboj.2009.253.
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  - Forrester, Michael T., J Will Thompson, Matthew W. Foster, Leonardo Nogueira, M Arthur Moseley, and Jonathan S. Stamler. “Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture.” Nat Biotechnol 27, no. 6 (June 2009): 557–59. https://doi.org/10.1038/nbt.1545.
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  - Kaiser, T. J., J. W. Thompson, J. S. Mellors, and J. W. Jorgenson. “Capillary-based instrument for the simultaneous measurement of solution viscosity and solute diffusion coefficient at pressures up to 2000 bar and implications for ultrahigh pressure liquid chromatography.” Analytical Chemistry 81, no. 8 (April 15, 2009): 2860–68. https://doi.org/10.1021/ac802467k.
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  - Thompson, J Will, Theodore J. Kaiser, and James W. Jorgenson. “Viscosity measurements of methanol-water and acetonitrile-water mixtures at pressures up to 3500 bar using a novel capillary time-of-flight viscometer.” J Chromatogr A 1134, no. 1–2 (November 17, 2006): 201–9. https://doi.org/10.1016/j.chroma.2006.09.006.
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  - Thompson, J. W., J. S. Mellors, J. W. Eschelbach, and J. W. Jorgenson. “Recent advances in ultrahigh-pressure liquid chromatography.” Lcgc North America 24, no. 4 SUPPL. (January 1, 2006): 16–20.
  - Jerkovich, A. D., J. S. Mellors, J. W. Thompson, and J. W. Jorgenson. “Linear velocity surge caused by mobile-phase compression as a source of band broadening in isocratic ultrahigh-pressure liquid chromatography.” Analytical Chemistry 77, no. 19 (October 1, 2005): 6292–99. https://doi.org/10.1021/ac0504924.
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  - Thompson, J. W., J. W. Eschelbach, R. T. Wilburn, and J. W. Jorgenson. “Investigation of electrospray ionization and electrostatic focusing devices using a three-dimensional electrospray current density profiler.” Journal of the American Society for Mass Spectrometry 16, no. 3 (March 1, 2005): 312–23. https://doi.org/10.1016/j.jasms.2004.11.012.
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- Book Sections
  - Thompson, J. W., M. Jiang, and W. Yang. “Proteomic analysis of SUMOylation in the post-ischemic brain.” In Neuromethods, 127:207–24, 2017. https://doi.org/10.1007/978-1-4939-7119-0_13.
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  - Millington, D. S., H. Zhang, M. Arthur Moseley, J. Will Thompson, and P. Smith. “Direct Solvent Extraction and Analysis of Biomarkers in Dried Blood Spots Using a Flow-Through Autosampler.” In Dried Blood Spots: Applications and Techniques, 9781118054697:314–24, 2014. https://doi.org/10.1002/9781118890837.ch24.
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- Conference Papers
  - West, Erin E., Simon Freeley, Marcin M. Kaminski, Sharon Veenbergen, Duck-Yeon Lee, Lisa St John-Williams, J Will Thompson, et al. “You are what you eat: CD46 regulated amino acid usage dictates T cell function.” In Journal of Immunology, Vol. 202. AMER ASSOC IMMUNOLOGISTS, 2019.
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  - Naagie, Susanna, Sam Lusk, J Will Thompson, Meredith Mock, Joseph Lucas, Laura Dubois, Lisa St John-Williams, Arthur Moseley, and Keyur Patel. “Lipidomic Signature As a Predictor of Liver Disease Events in HIV/HCV Co-Infectedpatients.” In Hepatology, 68:919A-919A. WILEY, 2018.
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  - Todd, J. L., V. Venkat, R. Henao, C. Brinkley, F. L. Kelly, C. W. Frankel, A. Frear, et al. “Bronchoalveolar Lavage Fluid Proteome in Chronic Lung Allograft Dysfunction.” In The Journal of Heart and Lung Transplantation, 37:S204–S204. Elsevier BV, 2018. https://doi.org/10.1016/j.healun.2018.01.496.
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  - Lin, Chao-Chieh, Mayumi Kitagawa, Xiaohu Tang, Ming-Hsin Hou, Jianli Wu, Dan Chen Qu, Vinayaka Srinivas, et al. “CoA synthase regulates mitotic fidelity via CBP-mediated acetylation.” In Nat Commun, 9:1039, 2018. https://doi.org/10.1038/s41467-018-03422-6.
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  - Kazi, Zoheb B., Ankit K. Desai, Mari Mori, Karanjeet Dua, J Will Thompson, Joseph Lucas, Arthur Moseley, and Priya S. Kishnani. “Differentially expressed proteins in infantile Pompe disease: prediction of patients likely to mount an immune response to enzyme replacement therapy.” In Molecular Genetics and Metabolism, 117:S66–S66. Elsevier BV, 2016. https://doi.org/10.1016/j.ymgme.2015.12.316.
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  - Foster, M. W., J. W. Thompson, D. M. Brass, M. A. Moseley, D. L. Morgan, and S. M. Palmer. “Plasma Metabolomics Analysis Identifies Candidate Biomarkers Of Flavoring-Induced Bronchiolitis Obliterans.” In American Journal of Respiratory and Critical Care Medicine, Vol. 193. AMER THORACIC SOC, 2016.
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  - Foster, M. W., W. M. Gwinn, F. L. Kelly, D. M. Brass, J. W. Thompson, M. A. Moseley, D. L. Morgan, and S. M. Palmer. “Proteomic Analysis Reveals Significant Epithelial Remodeling After In Vitro Exposure To Diacetyl Vapor.” In American Journal of Respiratory and Critical Care Medicine, Vol. 193. AMER THORACIC SOC, 2016.
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  - Kazi, Zoheb, Katie Berrier, Cheng Lu, Deeksha Bali, J. Will Thompson, M. Arthur Moseley, and Priya Kishnani. “Proteomics to identify signature proteins in patients likely to mount an immune response to enzyme replacement therapy in infantile Pompe disease.” In Molecular Genetics and Metabolism, 114:S61–S61. Elsevier BV, 2015. https://doi.org/10.1016/j.ymgme.2014.12.128.
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  - Figueiredo-Freitas, Cicero, Michael W. Foster, Leonardo Nogueira, Jingsheng Liang, Aline Yamashita, Raul Dulce, J Will Thompson, et al. “S-Nitrosylation Decreases Ca2+ Sensitivity and Actomyosin ATPase Activity of Contractile Proteins in Cardiac Myofibrils.” In Biophysical Journal, 104:451a-451a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.2498.
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  - Naggie, Susanna, Anu Osinusi, Tiffany Himmel, Joseph Lucas, J. W. Thompson, Laura G. Dubois, Martin A. Moseley, Paul J. Clark, Shyam Kottilil, and Keyur Patel. “Targeted proteomics signature identifies corticosteroid binding globulin peptides as highly predictive of treatment response in IL28B unfavorable genotype patients.” In Hepatology, 56:999A-1000A. WILEY-BLACKWELL, 2012.
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  - Foster, Matthew, J Will Thompson, Michael Forrester, Yonggang Sha, Dawn Bowles, M Arthur Moseley, and Harvey Marshall. “Quantitative proteomics of the cytokine-modulated NOS2 interactome in airway epithelial cells.” In Nitric Oxide, 27:S13–S13. Elsevier BV, 2012. https://doi.org/10.1016/j.niox.2012.04.047.
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  - Philipp, M., E. J. Soderblom, J. W. Thompson, M. G. Caron, and M. A. Moseley. “A Label-free Quantitative Phosphoproteomic Platform To Assess The Phosphorylation State Of A Complex Sample.” In Naunyn Schmiedebergs Archives of Pharmacology, 383:69–69. SPRINGER, 2011.
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  - Foster, M. W., Z. Yang, J. W. Thompson, C. H. Ball, M. Turner, M. A. Moseley, and L. G. Que. “A Proteomic Investigation Of GSNOR-Regulated Pathways In Cytokine-Stimulated Mouse Alveolar Macrophages.” In American Journal of Respiratory and Critical Care Medicine, Vol. 183. AMER THORACIC SOC, 2011.
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  - Piacentino III, P., J. W. Thompson, E. J. Soderblom, M. Foster, V. A. Burns, J. G. Rogers, C. A. Milano, M. A. Moseley, and D. E. Bowles. “Ischemic Human Heart Failure is Associated With Decreased Phosphorylation of Pyruvate Dehydrogenase and Triosephosphate Isomerase: Proteomic Evidence Supporting Carbohydrate Utilization Preference in the End-Stage Failing Ischemic Heart.” In Circulation, Vol. 122, 2010.
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  - Tutaeva, Victoria, J Will Thompson, Matthew W. Foster, M Arthur Moseley, Stephen P. Holly, Martha Delahunty, Leslie V. Parise, and Marilyn J. Telen. “S-Nitrosylation of Rap1and Relationship to Rap1 Activity and Disease Status In SCD.” In Blood, 116:1098–1098. AMER SOC HEMATOLOGY, 2010.
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  - Patel, Keyur, Joseph Lucas, J. W. Thompson, Martin A. Moseley, Diane M. Uzarski, Hans L. Tillmann, Robert M. Califf, Jeanette McCarthy, and John G. McHutchison. “HIGH PREDICTIVE ACCURACY OF AN UNBIASED PROTEOMIC PROFILE TO PREDICT SUSTAINED VIROLOGIC RESPONSE IN GENOTYPE 1 CHRONIC HEPATITIS C PATIENTS.” In Hepatology, 48:403A-403A. JOHN WILEY & SONS INC, 2008.
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