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Project Publications

Recent

  • NE Lewis, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, JN Adkins, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, R Eils, R König, RD Smith, BØ Palsson. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology
    Abstract on PubMed/ Details on Omics.pnl.gov
  • DR Hyduke, BO Palsson. 2010. "Towards genome-scale signalling-network reconstructions." Nature Reviews Genetics
    Abstract on PubMed
  • JN Adkins, H Mottaz, TO Metz, C Ansong, NP Manes, RD Smith, F Heffron. 2010. "Performing comparative peptidomics analyses of Salmonella from different growth conditions." Methods in Molecular Biology
    Abstract on PubMed
  • KJ Auberry, GR Kiebel, ME Monroe, JN Adkins, GA Anderson, RD Smith. 2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics & Bioinformatics
    Omics.pnl.gov

2009

  • L Shi, C Ansong, HS Smallwood, L Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, JN Adkins. 2009. "Proteome of Salmonella enterica Serotype Typhimurium Grown in a Low Mg2+/pH Medium." J. Proteomics and Bionformatics
    Abstract on PubMed / Details on Omics.pnl.gov
  • L Shi, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TR Clauss, F Heffron, RD Smith, JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Salmonella Infection." Infection and Immunity
    Abstract on PubMed / Details on Omics.pnl.gov
  • JN Adkins, HM Mottaz-Brewer, TO Metz, C Ansong, NP Manes, RD Smith, F Heffron, in M. Soloviev (Ed.), Peptidomics, Methods in Molecular Biology. The Humana Press Inc., Totowa, NJ, USA, In press.
  • C Ansong, H Yoon, S Porwollik, HM Mottaz-Brewer, B Petritis, N Jaitly, JN Adkins, M McClelland, F Heffron, RD Smith. Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella:Implications for virulence and global protein translation. PLoS ONE (2009).
  • SM Chowdhury, L Shi, H Yoon, C Ansong, LM Rommereim, AD Norbeck, KJ Auberry, RJ Moore, JN Adkins, F Heffron, RD Smith. A Method for Investigating Protein-Protein Interactions Related to Salmonella Typhimurium Pathogenesis. J Proteome Res (2009).
  • AM Feist, MJ Herrgard, I Thiele, JL Reed, BO Palsson. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7 (2009) 129-43.
  • A Raghunathan, J Reed, S Shin, B Palsson, S Daefler. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst Biol 3 (2009) 38.
    SIEVE Server
  • R Samudrala, F Heffron, JE McDermott. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog 5 (2009) e1000375.
  • I Thiele, N Jamshidi, RM Fleming, BO Palsson. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 5 (2009) e1000312.
  • HJ Yoon, JE McDermott, S Porwollik, M McClelland, F Heffron. Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium. Plos Pathogens 5 (2009).
  • C Ansong, SO Purvine, JN Adkins, MS Lipton, RD Smith. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct Genomic Proteomic 7 (2008) 50-62.
  • C Ansong, H Yoon, AD Norbeck, JK Gustin, JE McDermott, HM Mottaz, J Rue, JN Adkins, F Heffron, RD Smith. Proteomics analysis of the causative agent of typhoid Fever. J Proteome Res 7 (2008) 546-57.
  • SJ Callister, LA McCue, JE Turse, ME Monroe, KJ Auberry, RD Smith, JN Adkins, MS Lipton. Comparative bacterial proteomics: analysis of the core genome concept. PLoS ONE 3 (2008) e1542.
  • AM Feist, BO Palsson. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26 (2008) 659-67.
  • HM Mottaz-Brewer, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, SW Wong, RD Estep, F Heffron, L Pasa-Tolic, RD Smith. Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems. J Biomol Tech 19 (2008) 285-95.
  • R Pieper, ST Huang, DJ Clark, JM Robinson, PP Parmar, H Alami, CL Bunai, RD Perry, RD Fleischmann, SN Peterson. Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change. Proteomics 8 (2008) 1442-58.
  • KD Rodland, JN Adkins, C Ansong, S Chowdhury, NP Manes, L Shi, H Yoon, RD Smith, F Heffron. Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella. Future Microbiol 3 (2008) 625-34.
  • NP Manes, JK Gustin, J Rue, HM Mottaz, SO Purvine, AD Norbeck, ME Monroe, JS Zimmer, TO Metz, JN Adkins, RD Smith, F Heffron. Targeted Protein Degradation by Salmonella under Phagosome-mimicking Culture Conditions Investigated Using Comparative Peptidomics. Mol Cell Proteomics 6 (2007) 717-27.
  • JN Adkins, HM Mottaz, AD Norbeck, JK Gustin, J Rue, TR Clauss, SO Purvine, KD Rodland, F Heffron, RD Smith. Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Mol Cell Proteomics 5 (2006) 1450-61.
  • KK Hixson, JN Adkins, SE Baker, RJ Moore, BA Chromy, RD Smith, SL McCutchen-Maloney, MS Lipton. Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res 5 (2006) 3008-17.
  • L Shi, JN Adkins, JR Coleman, AA Schepmoes, A Dohnkova, HM Mottaz, AD Norbeck, SO Purvine, NP Manes, HS Smallwood, H Wang, J Forbes, P Gros, S Uzzau, KD Rodland, F Heffron, RD Smith, TC Squier. Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. J Biol Chem 281 (2006) 29131-40.
  • PS Chain, E Carniel, FW Larimer, J Lamerdin, PO Stoutland, WM Regala, AM Georgescu, LM Vergez, ML Land, VL Motin, RR Brubaker, J Fowler, J Hinnebusch, M Marceau, C Medigue, M Simonet, V Chenal-Francisque, B Souza, D Dacheux, JM Elliott, A Derbise, LJ Hauser, E Garcia. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 101 (2004) 13826-31.
  • CM Fraser, J Eisen, RD Fleischmann, KA Ketchum, S Peterson. Comparative genomics and understanding of microbial biology. Emerg Infect Dis 6 (2000) 505-12.

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