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Project Publications

Recent

  • P Charusanti, S Chauhan, K McAteer, JA Lerman, DR Hyduke, VL Motin, C Ansong, JN Adkins, BO Palsson. In Press. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Systems Biology
    Abstract on Pubmed, Genome Scale Metabolic Reconstruction
  • C Ansong, N Tolic, SO Purvine, S Porwollik, M Jones, H Yoon, SH Payne, JL Martin, MC Burnet, ME Monroe, P Venepally, RD Smith, SN Peterson, F Heffron, M McClellend, JN Adkins. 2011. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. BMC Genomics
    Abstract on Pubmed, Proteomics data on Omics.pnl.gov
  • Y-M Kim, TO Metz, Z Hu, SD Wiedner, J-S Kim, RD Smith, WF Morgan, Q Zhang. 2011. Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics. Rapid Communications in Mass Spectrometry
    Abstract on Pubmed
  • J Schellenberger, R Que, RM Fleming, I Thiele, JD Orth, AM Feist, DC Zielinski, A Bordbar, NE Lewis, S Rahmanian, J Kang, DR Hyduke, BO Palsson. 2011. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols
    Abstract on Pubmed, Related resources
  • JR Stanley, JN Adkins, GW Slysz, ME Monroe, SO Purvine, YV Karpievitch, GA Anderson, RD Smith, AR Dabney. 2011. A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics. Analytical Chemistry
    Abstract on Pubmed
  • H Yoon, C Ansong, JE McDermott, M Gritsenko, RD Smith, F Heffron, JN Adkins. 2011. Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella. BMC Systems Biology
    Abstract on Pubmed Designated as Highly Accessed by the journal & highlighted by PNNL, Proteomics and transcriptomics data on Omics.pnl.gov
  • JE McDermott, H Yoon, ES Nakayasu, TO Metz, DR Hyduke, AS Kidwai, BO Palsson, JN Adkins, F Heffron. 2011. Technologies and approaches to elucidate and model the virulence program of Salmonella. Frontiers in Microbiology
    Abstract on Pubmed
  • H Yoon, C Ansong, JN Adkins, F Heffron. 2011. "Discovery of Salmonella virulence factors translocated via outer membrane vesicles to murine macrophages." Infection and Immunity
    Abstract on Pubmed
  • JE McDermott, M Archuleta, BD Thrall, JN Adkins, KM Waters. 2011. "Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation." PLoS One
    Abstract on Pubmed Genes part of the repsonse network
  • N Arpaia, J Godec, L Lau, KE Sivick, LM McLaughlin, MB Jones, T Dracheva, SN Peterson, DM Monack, GM Barton. 2011. "TLR Signaling Is Required for Salmonella typhimurium Virulence." Cell
    Abstract on Pubmed, Highlighted here in Cell Host & Microbe.
  • I Thiele, DR Hyduke, B Steeb, G Fankam, DK Allen, S Bazzani, P Charusanti, FC Chen, RM Fleming, CA Hsiung, SC De Keersmaecker, YC Liao, K Marchal, ML Mo, E Ozdemir, A Raghunathan, JL Reed, SI Shin, S Sigurbjörnsdóttir, J Steinmann, S Sudarsan, N Swainston, IM Thijs, K Zengler, BO Palsson, JN Adkins, D Bumann. 2011. "A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2." BMC Systems Biology
    Abstract on PubMed,Designated as Highly Accessed by the journal, Genome Scale Metabolic Reconstruction
  • JE McDermott, A Corrigan, E Peterson, C Oehmen, G Niemann, ED Cambronne, D Sharp, JN Adkins, R Samudrala, F Heffron. 2011. "Computational prediction of type III and IV secreted effectors in gram-negative bacteria." Infection and Immunity
    Abstract on PubMed, SIEVE Server
  • GS Niemann, RN Brown, JK Gustin, A Stufkens, AS Shaikh-Kidwai, J Li, JE McDermott, HM Brewer, A Schepmoes, RD Smith, JN Adkins, F Heffron. 2011. "Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants." Infection and Immunity
    Abstract on PubMed, Related data on Omics.pnl.gov
  • A Aderem, JN Adkins, C Ansong, J Galagan, S Kaiser, MJ Korth, GL Law, JE McDermott, SC Proll, C Rosenberger, G Schoolnik, MG Katze. 2011. "A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm." MBio
    Abstract on PubMed

2010

  • GW Buchko, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, JE McDermott. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular BioSystems
    Abstract on PubMed, Abstract on RSC Publishing
  • Bordbar A, NE Lewis, J Schellenberger, BØ Palsson, N. Jamshidi. 2010. "Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions." Molecular Systems Biology
    Abstract on PubMed, Genome Scale Metabolic Reconstructions
  • 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
  • JN Brown, RD Estep, D Lopez-Ferrer, HM Brewer, TR Clauss, NP Manes, M O'Connor, H Li, JN Adkins, SW Wong, RD Smith. 2010. "Characterization of Macaque Pulmonary Fluid Proteome during Monkeypox Infection: Dynamics of Host Response." Molecular and Cellular Proteomics
    Abstract on PubMed, Related data 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
    Abstract on PubMed, 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, Data 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, Data 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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