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Submitted
Matzke MM, Datta S, Payne SH, Nicora CD, Shukla AK, Metz TO, Smith RD, Tardiff MF, Waters KM, McDermott JE et al..  Submitted.  Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Experiments. Molecular & Cellular Proteomics. File MCP_Bayesian_Proteoform_Dilution_All_Raw_Intensity.xlsx (15.74 MB)File MCP_Bayesian_Proteoform_Dilution_Normalized.xlsx (8.9 MB)
2014
Webb-Robertson B-J, Kim Y-M, Zink EM, Hallaian KA, Zhang Q, Madupu R, Waters KM, Metz TO.  2014.  A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry.. Metabolomics.
Merkley ED, Metz TO, Smith RD, Baynes JW, Frizzell N.  2014.  The succinated proteome.. Mass Spectrom Rev.
2013
Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE et al..  2013.  A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.. Proteomics.
Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR.  2013.  GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.. Bioinformatics.
Gralinski LE, Bankhead A, Jeng S, Menachery VD, Proll S, Belisle SE, Matzke M, Webb-Robertson B-JM, Luna ML, Shukla AK et al..  2013.  Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury.. MBio.
LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ et al..  2013.  MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.. BMC Bioinformatics.
Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim Y-M, McAteer K, Kaiser BLDeathera, Dubois JL, Brewer HM et al..  2013.  A multi-omic systems approach to elucidating Yersinia virulence mechanisms.. Mol Biosyst.
Kaiser BLDeathera, Li J, Sanford JA, Kim Y-M, Kronewitter SR, Jones MB, Peterson CT, Peterson SN, Frank BC, Purvine SO et al..  2013.  A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection.. PLoS One.
Mitchell HD, Eisfeld AJ, Sims AC, McDermott JE, Matzke MM, Webb-Robertson B-JM, Tilton SC, Tchitchek N, Josset L, Li C et al..  2013.  A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses.. PLoS One.
Sims AC, Tilton SC, Menachery VD, Gralinski LE, Schäfer A, Matzke MM, Webb-Robertson B-JM, Chang J, Luna ML, Long CE et al..  2013.  Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells.. J Virol.
Kim Y-M, Schmidt BJ, Kidwai AS, Jones MB, Kaiser BLDeathera, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F et al..  2013.  Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.. Mol Biosyst.
Webb-Robertson B-JM, Matzke MM, Metz TO, McDermott JE, Walker H, Rodland KD, Pounds JG, Waters KM.  2013.  Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies.. Biotechniques.
Zhang Q, Fillmore TL, Schepmoes AA, Clauss TRW, Gritsenko MA, Mueller PW, Rewers M, Atkinson MA, Smith RD, Metz TO.  2013.  Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes.. J Exp Med.
Tchitchek N, Eisfeld AJ, Tisoncik-Go J, Josset L, Gralinski LE, Bécavin C, Tilton SC, Webb-Robertson B-J, Ferris MT, Totura AL et al..  2013.  Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice.. BMC Syst Biol.
Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim Y-M, Nakayasu ES et al..  2013.  Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.. Curr Top Microbiol Immunol.
2012
Nagai R, Murray DB, Metz TO, Baynes JW.  2012.  Chelation: a fundamental mechanism of action of AGE inhibitors, AGE breakers, and other inhibitors of diabetes complications.. Diabetes.
Perera R, Riley C, Isaac G, Hopf-Jannasch AS, Moore RJ, Weitz KW, Pasa-Tolic L, Metz TO, Adamec J, Kuhn RJ.  2012.  Dengue virus infection perturbs lipid homeostasis in infected mosquito cells.. PLoS Pathog.
Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO.  2012.  Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics.. J Proteome Res.
Kangas LJ, Metz TO, Isaac G, Schrom BT, Ginovska-Pangovska B, Wang L, Tan L, Lewis RR, Miller JH.  2012.  In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids.. Bioinformatics.
Hu Z-P, Kim Y-M, Sowa MB, R Robinson J, Gao X, Metz TO, Morgan WF, Zhang Q.  2012.  Metabolomic response of human skin tissue to low dose ionizing radiation.. Mol Biosyst.
Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim Y-M, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN et al..  2012.  Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.. Mol Syst Biol.
Gao X, Zhang Q, Meng D, Isaac G, Zhao R, Fillmore TL, Chu RK, Zhou J, Tang K, Hu Z et al..  2012.  A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling.. Anal Bioanal Chem.
2011
Zhang Q, Monroe ME, Schepmoes AA, Clauss TRW, Gritsenko MA, Meng D, Petyuk VA, Smith RD, Metz TO.  2011.  Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects.. J Proteome Res.
Gonzalez RM, Zhang Q, Zangar RC, Smith RD, Metz TO.  2011.  Development of a fibrinogen-specific sandwich enzyme-linked immunosorbent assay microarray assay for distinguishing between blood plasma and serum samples.. Anal Biochem.

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