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Submitted
Nakayasu ES, Sydor MA, Brown RN, Sobreira TJP, Slysz GW, Humphrys DR, Skarina T, Onoprienko O, Di Leo R, Deatherage BL et al..  Submitted.  Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis.
2014
Kronewitter SRyan, Marginean I, Cox JT, Zhao R, Hagler CD, Shukla AK, Carlson TS, Adkins JN, Camp DG, Moore RJ et al..  2014.  Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations and ESI-MS.. Anal Chem.
2013
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.
Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S et al..  2013.  Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.. Chem Biol. 20(1):123-33.
Nakayasu ES, Brown RN, Ansong C, Sydor MA, Imtiaz S, Mihai C, Sontag R, Hixson KK, Monroe ME, Sobreira TJP et al..  2013.  Multi-omic data integration links deleted in breast cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response.. Mol Cell Proteomics.
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.
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.
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.
Ansong C, Wu S, Meng D, Liu X, Brewer HM, Kaiser BLDeathera, Nakayasu ES, Cort JR, Pevzner P, Smith RD et al..  2013.  Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.. Proc Natl Acad Sci U S A.
2012
Brown RN, Sanford JA, Park JH, Deatherage BL, Champion BL, Smith RD, Heffron F, Adkins JN.  2012.  A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions.. Int J Proteomics. Office spreadsheet icon SubcellularProteomicSurveyOfSalmonella_SupplementaryTable2.xls (156 KB)
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.
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K et al..  2012.  In silico method for modelling metabolism and gene product expression at genome scale.. Nat Commun.
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.
2011
Niemann GS, Brown RN, Gustin JK, Stufkens A, Shaikh-Kidwai AS, Li J, McDermott JE, Brewer HM, Schepmoes A, Smith RD et al..  2011.  Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants.. Infect Immun.
Yoon H, Ansong C, McDermott JE, Gritsenko M, Smith RD, Heffron F, Adkins JN.  2011.  Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella.. BMC Syst Biol.
McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F.  2011.  Technologies and approaches to elucidate and model the virulence program of salmonella.. Front Microbiol.
2010
Brown JN, Estep RD, Lopez-Ferrer D, Brewer HM, Clauss TR, Manes NP, O'Connor M, Li H, Adkins JN, Wong SW et al..  2010.  Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response.. Mol Cell Proteomics.
Adkins JN, Mottaz H, Metz TO, Ansong C, Manes NP, Smith RD, Heffron F.  2010.  Performing comparative peptidomics analyses of Salmonella from different growth conditions.. Methods Mol Biol.
2009
Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TRW, Heffron F, Smith RD et al..  2009.  Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica.. Infect Immun.
Karpievitch Y, Stanley J, Taverner T, Huang J, Adkins JN, Ansong C, Heffron F, Metz TO, Qian W-J, Yoon H et al..  2009.  A statistical framework for protein quantitation in bottom-up MS-based proteomics.. Bioinformatics.
2008
Polpitiya AD, Qian W-J, Jaitly N, Petyuk VA, Adkins JN, Camp DG, Anderson GA, Smith RD.  2008.  DAnTE: a statistical tool for quantitative analysis of -omics data.. Bioinformatics.
Petyuk VA, Jaitly N, Moore RJ, Ding J, Metz TO, Tang K, Monroe ME, Tolmachev AV, Adkins JN, Belov ME et al..  2008.  Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content.. Anal Chem.
Monroe ME, Shaw JL, Daly DS, Adkins JN, Smith RD.  2008.  MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features.. Comput Biol Chem.
2007
Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JSD, Metz TO, Adkins JN et al..  2007.  Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics.. Mol Cell Proteomics.

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