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Project Publications


  • BJ Schmidt, A Ebrahim, TO Metz, JN Adkins, BO Palsson, DR Hyduke. 2013. "GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data." Bioinformatics
    Abstract on Pubmed
  • ES Nakayasu, R Tempel, XA Cambronne, VA Petyuk, MB Jones, MA Gritsenko, F Yang, RD Smith, JN Adkins, F Heffron. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Mol Cell Proteomics
    Abstract on Pubmed
  • C Ansong, S Wu, D Meng, X Liu, HM Brewer, BL Deatherage Kaiser, ES Nakayasu, JR Cort, P Pevzner, RD Smith, F Heffron, JN Adkins, L Pasa-Tolic. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions." PNAS
    Abstract on Pubmed, Related news release,
  • BL Deatherage Kaiser, J Li, JA Sanford, YM Kim, SR Kronewitter, MB Jones, CT Peterson, SN Peterson, BC Frank, SO Purvine, JN Brown, TO Metz, RD Smith, F Heffron, JN Adkins. 2013. "A Multi-omic view of host-pathogen-commensal interplay in Salmonella-mediated intestinal infection." PLOS ONE
    Abstract on Pubmed, Related Scientific American story
  • KM Hovis, S Mojica, JE McDermott, L Pedersen, C Simhi, RG Rank, GS Myers, J Ravel, RC Hsia, PM Bavoil. 2013. "Genus-optimized strategy for the identification of chlamydial type III secretion substrates." Pathog Dis
    Abstract on Pubmed
  • ES Nakayasu, C Ansong, JN Brown, F Yang, D Lopez-Ferrer, WJ Qian, RD Smith, JN Adkins. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." J Am Soc Mass Spectrom
    Abstract on Pubmed
  • A Ebrahim, JA Lerman, BO Palsson, DR Hyduke. 2013. "COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Systems Biology
    Abstract on Pubmed
  • ES Nakayasu, RN Brown, C Ansong, MA Sydor, S Imtiaz, C Mihai, R Sontag, KK Hixson, ME Monroe, TJ Sobreira, G Orr, VA Petyuk, F Yang, RD Smith, JN Adkins. 2013. "Multi-omic Data Integration Links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Mol Cell Proteomics
    Abstract on Pubmed
  • DR Hyduke,NE Lewis, BO Palsson. 2013. "Analysis of omics data with genome-scale models of metabolism." Molecular BioSystems
    Abstract on Pubmed
  • YM Kim, BJ Schmidt, AS Kidwai, MB Jones, BL Deatherage Kaiser, HM Brewer, HD Mitchell, BO Palsson, JE McDermott, F Heffron, RD Smith, SN Peterson, C Ansong, DR Hyduke, TO Metz, JN Adkins. 2013. "Salmonella modulates metabolism during growth under conditions that induce expression of virulence gene." Molecular BioSystems
    Abstract on Pubmed
  • ED Merkley, ES Baker, KL Crowell, DJ Orton, T Taverner, C Ansong, YM Ibrahim, MC Burnet, JR Cort, GA Anderson, RD Smith, JN Adkins. 2013. "Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking." J Am Soc Mass Spectrom
    Abstract on Pubmed
  • GS Niemann, RN Brown, IT Mushamiri, NT Nguyen, R Taiwo, A Stufkens, RD Smith, JN Adkins, JE McDermott, and F Heffron. 2013. "RNA Type III Secretion Signals that require Hfq." J Bacteriol
    Abstract on Pubmed Highlighted J. Bac. commentary
  • C Ansong, C Ortega, SH Payne, DH Haft, LM Chauvigne-Hines, MP Lewis, SO Purvine, AK Shukla, S Fortuin, RD Smith, JN Adkins, C Grundner, and AT Wright. 2013. "Identification of Widespread Adenosine Nucleotide-Binding in Mycobacterium." Chemistry & Biology
    Abstract on Chemistry & Biology, Proteomics data on
  • PD Piehowski, VA Petyuk, DJ Orton, F Xie, RJ Moore, M Ramirez-Restrepo, A Engel, AP Lieberman, RL Albin, DG Camp, RD Smith, AJ Myers. 2013. "Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis." J Proteome Res
    Abstract on Pubmed
  • DR Hyduke, NE Lewis, BO Palsson. 2013. "Analysis of omics data with genome-scale models of metabolism." Molecular Biosystems
    Abstract on Pubmed
  • C Ansong, AC Schrimpe-Rutledge, HD Mitchell, S Chauhan, MB Jones, YM Kim, K McAteer, BL Deatherage Kaiser, JL Dubois, HM Brewer, BC Frank, JE McDermott, TO Metz, SN Peterson, RD Smith, VL Motin, JN Adkins. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems
    Abstract on Pubmed, Highlighted as Journal Cover, Related data on


  • X Wang, GA Anderson, RD Smith, AR Dabney. 2012. "A hybrid approach to protein differential expression in mass spectrometry-based proteomics." Bioinformatics
    Abstract on Pubmed
  • CK Ansong, BL Deatherage, D Hyduke, B Schmidt, JE McDermott, S Chauhan, P Charusanti, YM Kim, ES Nakayasu, J Li, A Kidwai, G Niemann, RN Brown, TO Metz, K McAteer, F Heffron, SN Peterson, V Motin, BO Palsson, RD Smith, JN Adkins. 2012. "Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated 'Omics and Moding." Current Topics in Microbiology and Immunology
    Abstract on PubMed
  • A Bordbar, ES Nakayasu, AC Schrimpe-Rutledge, YM Kim, TO Metz, MB Jones, BC Frank, RD Smith, SN Peterson, DR Hyduke, JN Adkins and BO Palsson. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology
    Abstract onPubMed, Highlighted by PNNL, Proteomics data on, Metabolomics data on, Metabolomics data at MetaboLights
  • JA Lerman, DR Hyduke, H Latif, VA Portnoy, NE Lewis, JD Orth, AC Schrimpe-Rutledge, RD Smith, JN Adkins, K Zengler and BO Palsson. 2012. "In silico method for modelling metabolism and gene product expression at genome scale." Nature Communications
    Paper on Nature Communications, Highlighted by, Proteomics data on
  • R Brown, J Sanford, J Park, B Deatherage, B Champion, RD Smith, F Heffron and JN Adkins. 2012. "A comprehensive subcellular proteomic survey of Salmonella grown under phagosome-mimicking vs. standard laboratory conditions." International Journal of Proteomics
    Abstract on Pubmed, Proteomics data on
  • AC Schrimpe-Rutledge, G Fontes, MA Gritsenko, AD Norbeck, KM Waters, JN Adkins, RD Smith, V Poitout and TO Metz. 2012. "Discovery of Novel Glucose-Regulated Proteins in Isolated Human Pancreatic Islets Using LC-MS/MS-Based Proteomics." Journal of Proteome Research
    Abstract on PubMed, Proteomics data on
  • ES Peterson, LA McCue, AC Schrimpe-Rutledge, JL Jensen, H Walker, MA Kobold, SR Webb, SH Payne, CK Ansong, JN Adkins, WR Cannon, BJ Webb-Robertson. 2012. "VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data." BMC Genomics
    Paper on BMC Genomics, Software available
  • AC Schrimpe-Rutledge, MB Jones, S Chauhan, SO Purvine, JA Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, SN Peterson, VL Motin, JN Adkins. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS ONE
    Paper on PLoS ONE, Related data on, Highlighted by PNNL
  • JE McDermott, P Braun, R Bonneau, DR Hyduke. 2012. "Modeling Host-Pathogen Interactions: Computational Biology and Bioinformatics for Infectious Disease Research." Pacific Symposium on Biocomputing Proceedings


  • P Charusanti, S Chauhan, K McAteer, JA Lerman, DR Hyduke, VL Motin, C Ansong, JN Adkins, BO Palsson. 2011. "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
  • 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
  • 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
  • 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


  • 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
  • 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
  • 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. " A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information.Journal of Proteomics & Bioinformatics
    Abstract on PubMed
  • Singal M, Shah AR, Adkins JN, Brown RN. 2010. "Using support vector machine for improving protein-protein interaction prediction utilizing domain interactions." Proceed First ACM Inter Conf Bioinf and Comp Bio
    Abstract on Here,


  • 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
  • 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
  • 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).
  • 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.
  • 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.

Systems Biology



Fundamental & Computational Sciences