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2013
Crowell KL, Slysz GW, Baker ES, LaMarche BL, Monroe ME, Ibrahim YM, Payne SH, Anderson GA, Smith RD.  2013.  LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.. Bioinformatics.
Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD et al..  2013.  Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.. Appl Environ Microbiol. File Spectra_for_fungal_CAZy_enzymes_identified_by_1_peptide.xlsx (1.21 MB)Package icon Acromyrmex_echinatior_proteomics_samples.zip (37.24 MB)Package icon Atta_cephalotes_proteomics_samples.zip (41.97 MB)Package icon Protein_FASTA_Files.zip (71.91 MB)
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.
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.
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.
Smith DP, J Thrash C, Nicora CD, Lipton MS, Burnum-Johnson KE, Carini P, Smith RD, Giovannoni SJ.  2013.  Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium.. MBio.
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.
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.
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
Shi T, Fillmore TL, Sun X, Zhao R, Schepmoes AA, Hossain M, Xie F, Wu S, Kim J-S, Jones N et al..  2012.  Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum.. Proc Natl Acad Sci U S A.
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.
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.
Chauvignè-Hines LM, Anderson LN, Weaver HM, Brown JN, Koech PK, Nicora CD, Hofstad BA, Smith RD, Wilkins MJ, Callister SJ et al..  2012.  Suite of activity-based probes for cellulose-degrading enzymes.. J Am Chem Soc.
Alfaro JF, Gong C-X, Monroe ME, Aldrich JT, Clauss TRW, Purvine SO, Wang Z, Camp DG, Shabanowitz J, Stanley P et al..  2012.  Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets.. Proc Natl Acad Sci U S A.
Burnum K.E, Hirota Y., Baker ES, Yoshie M., Ibrahim YM, Monroe ME, Anderson GA, Smith RD, Daikoku T., Dey S.K.  2012.  Uterine deletion of Trp53 compromises antioxidant responses in the mouse decidua.. Endocrinology. File Uterine deletion of Trp53 compromises antioxidant responses in the mouse decidua. Endocrinology 153 4568-4579.xlsx (2.93 MB)

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