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Project Publications

Recent

  • 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 Omics.pnl.gov
  • 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 Omics.pnl.gov

2012

  • 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 Omics.pnl.gov, Metabolomics data on Omics.pnl.gov, 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 Phy.org, Proteomics data on Omics.pnl.gov
  • 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 Omics.pnl.gov
  • 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 Omics.pnl.gov
  • 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 Omics.pnl.gov, 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
    Abstract,

2011

  • 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 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
  • 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,

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
  • 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.

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