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Peer-reviewed Manuscripts

• PDXNet Portal: Patient-Derived Xenograft Model, Data, Workflow and Tool Discovery
  Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H, Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal-Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd, Chuang JH
  PDXNet Consortium (Contributors include: Held J)
  NAR Cancer 2022 Apr 22;4(2):zcac014
• Malic Enzyme 1 Absence in Synovial Sarcoma Shifts Antioxidant System Dependence and Increases Sensitivity to Ferroptosis Induction With ACXT3102
  Brashears CB, Prudner BC, Rathore R, Caldwell KE, Dehner CA, Buchanan JL, Lange SES, Poulin N, Sehn JK, Roszik J, Spitzer D, Jones KB, O'Keefe RJ, Nielsen TO, Taylor EB, Held JM, Hawkins W, Van Tine BA
  Clin Cancer Res 2022 Apr 14:clincanres04702022; [ahead of print]
• Comprehensive Characterization of 536 Patient-Derived Xenograft Models Prioritizes Candidates For Targeted Treatment
  Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, DiPersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L
  NCI PDXNet Consortium (Contributors include: Held J)
  Nat Commun 2021 Aug 24;12(1):5086
• ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets
  Seymour RW, van der Post S, Mooradian AD, Held JM
  J Proteome Res 2021 Jul 2;20(7):3621-3628
• NOX1-Dependent Redox Signaling Potentiates Colonic Stem Cell Proliferation to Adapt to the Intestinal Microbiota by Linking EGFR and TLR Activation
  van der Post S, Birchenough GMH, Held JM
  Cell Rep 2021 Apr 6;35(1):108949
• Cancer-Associated Exportin-6 Upregulation Inhibits the Transcriptionally Repressive and Anticancer Effects of Nuclear Profilin-1
  Zhu C, Kim SJ, Mooradian A, Wang F, Li Z, Holohan S, Collins PL, Wang K, Guo Z, Hoog J, Ma CX, Oltz EM, Held JM, Shao J
  Cell Rep 2021 Feb 16;34(7):108749
• A Clickable Probe for Versatile Characterization of S-Nitrosothiols
  Clements JL, Pohl F, Muthupandi P, Rogers SC, Mao J, Doctor A, Birman VB, Held JM
  Redox Biol 2020 Oct;37:101707
• Systems Level Profiling of Arginine Starvation Reveals MYC and ERK Adaptive Metabolic Reprogramming
  Brashears CB, Barlin M, Ehrhardt WR, Rathore R, Schultze M, Tzeng SC, Van Tine BA, Held JM
  Cell Death Dis 2020 Aug 20;11(8):662
• Phospho-Ser(784)-VCP Is Required for DNA Damage Response and Is Associated With Poor Prognosis of Chemotherapy-Treated Breast Cancer
  Zhu C, Rogers A, Asleh K, Won J, Gao D, Leung S, Li S, Vij KR, Zhu J, Held JM, You Z, Nielsen TO, Shao J
  Cell Rep 2020 Jun 9;31(10):107745
• ProteoClade: A Taxonomic Toolkit for Multi-Species and Metaproteomic Analysis
  Mooradian AD, van der Post S, Naegle KM, Held JM
  PLoS Comput Biol 2020 Mar 9;16(3):e1007741
• Spatial and Temporal Alterations in Protein Structure by EGF Regulate Cryptic Cysteine Oxidation
  Behring JB, van der Post S, Mooradian AD, Egan MJ, Zimmerman MI, Clements JL, Bowman GR, Held JM
  Sci Signal 2020 Jan 21;13(615)
• Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome
  Held JM
  Antioxid Redox Signal 2020 Apr 1;32(10):659-676
• Regulated Phosphosignaling Associated With Breast Cancer Subtypes and Druggability
  Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held JM, Payne SH, Davies S, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyo D, Li S, Liu T, Carr SA, Ding L
  Mol Cell Proteomics 2019 Aug;18(8):1630-1650
• Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
  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, Fenyo D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX
  Cancer Res 2018 May 15;78(10):2732-2746
• Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate
  Mooradian AD, Held JM, Naegle KM
  Curr Protoc Bioinformatics 2017 Sep 13;59:13321-133227
• Multi-Laboratory Assessment of Reproducibility, Qualitative and Quantitative Performance of SWATH-Mass Spectrometry
  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
  Nat Commun 2017 Aug 21;8(1):291
• Breast Tumors Educate the Proteome of Stromal Tissue in an Individualized but Coordinated Manner
  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* (*corresponding author)
  Sci Signal 2017 Aug 8;10(491)
• Proteogenomic Integration Reveals Therapeutic Targets in Breast Cancer Xenografts
  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, Fenyo D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L
  Nat Commun 2017 Mar 28;8:14864
• Arginine Deprivation Inhibits the Warburg Effect and Upregulates Glutamine Anaplerosis and Serine Biosynthesis in ASS1-Deficient Cancers
  Kremer JC, Prudner BC, Lange SE, 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
  Cell Rep 2017 Jan 24;18(4):991-1004
• Synthetic Ligands of Cannabinoid Receptors Affect Dauer Formation in the Nematode Caenorhabditis Elegans
  Reis Rodrigues P, Kaul TK, Ho JH, Lucanic M, Burkewitz K, Mair WB, Held JM, Bohn LM, Gill MS
  G3 (Bethesda) 2016 Jun 1;6(6):1695-705
• Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument With Integrated Data-Dependent and Targeted Mass Spectrometric Workflows
  Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW
  Anal Chem 2015 Oct 20;87(20):10222-9
• Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma
  Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA
  Mol Cell Proteomics 2015 Sep;14(9):2357-74
• Comparative Analyses of Proteins From Haemophilus Influenzae Biofilm and Planktonic Populations Using Metabolic Labeling and Mass Spectrometry
  Post DM, Held JM, Ketterer MR, Phillips NJ, Sahu A, Apicella MA, Gibson BW
  BMC Microbiol 2014 Dec 31;14:329
• RPL24: A Potential Therapeutic Target Whose Depletion or Acetylation Inhibits Polysome Assembly and Cancer Cell Growth
  Wilson-Edell KA, Kehasse A, Scott GK, Yau C, Rothschild DE, Schilling B, Gabriel BS, Yevtushenko MA, Hanson IM, Held JM, Gibson BW, Benz CC
  Oncotarget 2014 Jul 15;5(13):5165-76
• Variation and Quantification Among a Target Set of Phosphopeptides in Human Plasma by Multiple Reaction Monitoring and SWATH-MS2 Data-Independent Acquisition
  Zawadzka AM, Schilling B, Held JM, Sahu AK, Cusack MP, Drake PM, Fisher SJ, Gibson BW
  Electrophoresis 2014 Dec;35(24):3487-3497
• Targeted Quantitation of Acetylated Lysine Peptides by Selected Reaction Monitoring Mass Spectrometry
  Rardin MJ, Held JM, Gibson BW
  Methods Mol Biol 2013;1077:121-31
• Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)
  Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA
  Mol Cell Proteomics 2013 Sep;12(9):2623-39
• Label-Free Quantitative Proteomics of the Lysine Acetylome in Mitochondria Identifies Substrates of SIRT3 in Metabolic Pathways
  Rardin MJ, Newman JC, Held JM, Cusack MP, Sorensen DJ, Li B, Schilling B, Mooney SD, Kahn CR, Verdin E, Gibson BW
  Proc Natl Acad Sci U S A 2013 Apr 16;110(16):6601-6
• Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion With Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions
  Held JM*, Schilling B, D'Souza AK, Srinivasan T, Behring JB, Sorensen DJ, Benz CC, Gibson BW (*corresponding author)
  Int J Proteomics 2013;2013:791985
• Ligand Binding Promotes CDK-Dependent Phosphorylation of ER-Alpha on Hinge Serine 294 but Inhibits Ligand-Independent Phosphorylation of Serine 305
  Held JM, Britton DJ, Scott GK, Lee EL, Schilling B, Baldwin MA, Gibson BW, Benz CC
  Mol Cancer Res 2012 Aug;10(8):1120-32
• Inhibition of Lipid Signaling Enzyme Diacylglycerol Kinase Epsilon Attenuates Mutant Huntingtin Toxicity
  Zhang N, Li B, Al-Ramahi I, Cong X, Held JM, Kim E, Botas J, Gibson BW, Ellerby LM
  J Biol Chem 2012 Jun 15;287(25):21204-13
• Lectin Chromatography/Mass Spectrometry Discovery Workflow Identifies Putative Biomarkers of Aggressive Breast Cancers
  Drake PM, Schilling B, Niles RK, Prakobphol A, Li B, Jung K, Cho W, Braten M, Inerowicz HD, Williams K, Albertolle M, Held JM, Iacovides D, Sorensen DJ, Griffith OL, Johansen E, Zawadzka AM, Cusack MP, Allen S, Gormley M, Hall SC, Witkowska HE, Gray JW, Regnier F, Gibson BW, Fisher SJ
  J Proteome Res 2012 Apr 6;11(4):2508-20
• Mass Spectrometric Identification of Novel Lysine Acetylation Sites in Huntingtin
  Cong X, Held JM, DeGiacomo F, Bonner A, Chen JM, Schilling B, Czerwieniec GA, Gibson BW, Ellerby LM
  Mol Cell Proteomics 2011 Oct;10(10):M111009829
• N-Acylethanolamine Signalling Mediates the Effect of Diet on Lifespan in Caenorhabditis Elegans
  Lucanic M, Held JM, Vantipalli MC, Klang IM, Graham JB, Gibson BW, Lithgow GJ, Gill MS
  Nature 2011 May 12;473(7346):226-9
• Confident Identification of 3-Nitrotyrosine Modifications in Mass Spectral Data Across Multiple Mass Spectrometry Platforms
  Li B, Held JM, Schilling B, Danielson SR, Gibson BW
  J Proteomics 2011 Oct 19;74(11):2510-21
• Quantitative Mapping of Reversible Mitochondrial Complex I Cysteine Oxidation in a Parkinson Disease Mouse Model
  Danielson SR, Held JM, Oo M, Riley R, Gibson BW, Andersen JK
  J Biol Chem 2011 Mar 4;286(9):7601-8
• ErbB2 Trafficking and Degradation Associated With K48 and K63 Polyubiquitination
  Marx C, Held JM, Gibson BW, Benz CC
  Cancer Res 2010 May 1;70(9):3709-17
• Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach
  Held JM, Danielson SR, Behring JB, Atsriku C, Britton DJ, Puckett RL, Schilling B, Campisi J, Benz CC, Gibson BW
  Mol Cell Proteomics 2010 Jul;9(7):1400-10
• Preferentially Increased Nitration of Alpha-Synuclein at Tyrosine-39 in a Cellular Oxidative Model of Parkinson's Disease
  Danielson SR, Held JM, Schilling B, Oo M, Gibson BW, Andersen JK
  Anal Chem 2009 Sep 15;81(18):7823-8
• Systematic Mapping of Posttranslational Modifications in Human Estrogen Receptor-Alpha With Emphasis on Novel Phosphorylation Sites
  Atsriku C*, Britton DJ*, Held JM*, Schilling B, Scott GK, Gibson BW, Benz CC, Baldwin MA (*co-first author)
  Mol Cell Proteomics 2009 Mar;8(3):467-80
• Multi-Site Assessment of the Precision and Reproducibility of Multiple Reaction Monitoring-Based Measurements of Proteins in Plasma
  Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA
  Nat Biotechnol 2009 Jul;27(7):633-41
• A Novel Serine Phosphorylation Site Detected in the N-Terminal Domain of Estrogen Receptor Isolated From Human Breast Cancer Cells
  Britton DJ, Scott GK, Schilling B, Atsriku C, Held JM, Gibson BW, Benz CC, Baldwin MA
  J Am Soc Mass Spectrom 2008 May;19(5):729-40
• DAF-12-Dependent Rescue of Dauer Formation in Caenorhabditis Elegans by (25S)-Cholestenoic Acid
  Held JM, White MP, Fisher AL, Gibson BW, Lithgow GJ, Gill MS
  Aging Cell 2006 Aug;5(4):283-91
• Vitamin K3 (Menadione)-Induced Oncosis Associated With Keratin 8 Phosphorylation and Histone H3 Arylation
  Scott GK, Atsriku C, Kaminker P, Held J, Gibson B, Baldwin MA, Benz CC
  Mol Pharmacol 2005 Sep;68(3):606-15
• Lipophilic Regulator of a Developmental Switch in Caenorhabditis Elegans
  Gill MS, Held JM, Fisher AL, Gibson BW, Lithgow GJ
  Aging Cell 2004 Dec;3(6):413-21

Invited Publications

• Informatics Solutions for Selected Reaction Monitoring
  Schilling B, Maclean B, Held JM, Gibson BW
  Proteome Informatics 2016:178-199
• Regulatory Control or Oxidative Damage? Proteomic Approaches to Interrogate the Role of Cysteine Oxidation Status in Biological Processes
  Held JM, Gibson BW
  Mol Cell Proteomics 2012 Apr;11(4):R111013037