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Recent Publications


Shi L, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TR Clauss, F Heffron, RD Smith, and JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Salmonella Infection." Infection and Immunity 77(8):3227-3233.

Ansong C, H Yoon, S Porwollik, HM Mottaz-Brewer, B Petritis, N Jaitly, JN Adkins, M McClelland, F Heffron, and RD Smith. 2009. "Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: Implications for virulence and global protein translation." PLoS ONE 4(3):e4809.

Chowdhury SM, L Shi, H Yoon, C Ansong, LM Rommereim, AD Norbeck, KJ Auberry, RJ Moore, JN Adkins, F Heffron, and RD Smith. 2009. "A Method for Investigating Protein-Protein Interactions Related to Salmonella Typhimurium Pathogenesis." Journal of Proteome Research 8(3):1504-1514.

Samudrala R, F Heffron, and JE McDermott. 2009. "Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems." PLoS Pathogens 5(4):e1000375.

Yoon HJ, JE McDermott, S Porwollik, M McClelland, and F Heffron. 2009. "Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium." PloS Pathogens 5(2):1-16


Ansong C, SO Purvine, JN Adkins, MS Lipton, and RD Smith. 2008. "Proteogenomics: the needs and roles to be filled by proteomics in genome annotation." Briefings in Functional Genomics and Proteomics 7(1):50-62.

Ansong C, H Yoon, AD Norbeck, JK Gustin, JE McDermott, HM Mottaz, J Rue, JN Adkins, F Heffron, and RD Smith. 2008. "Proteomics analysis of the causative agent of Typhoid Fever." Journal of Proteome Research 7(2):546-557.

Callister SJ, LA McCue, JE Turse, ME Monroe, KJ Auberry, RD Smith, JN Adkins, and MS Lipton. 2008. "Comparative bacterial proteomics: analysis of the core genome concept." PLoS ONE 3(2):e1542.

Brewer HM, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, SW Wong, RD Estep, F Heffron, L Pasa-Tolic, and RD Smith. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19(5):285-295.

Rodland KD, JN Adkins, C Ansong, S Chowdhury, NP Manes, L Shi, H Yoon, RD Smith, F Heffron. 2008 "Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella." Future Microbiology 3(6):625-634.


Manes NP, JK Gustin, J Rue, HM Mottaz, SO Purvine, AD Norbeck, ME Monroe, JS Zimmer, TO Metz, JN Adkins, RD Smith, and F Heffron. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics MCP 6(4):717-727.

Boschek CB, TC Squier, and DJ Bigelow. 2007. "Disruption of interdomain interactions upon partial calcium occupancy of calmodulin." Biochemistry 46(15):4580-4588.

Ding S, W Qian, and RD Smith. 2007. "Quantitative proteomic approaches for studying phosphotyrosine signaling." Expert Review of Proteomics 4(1):13-23.

Ding J, CM Sorensen, Q Zhang, H Jiang, N Jaitly, EA Livesay, Y Shen, RD Smith, and T Metz. 2007. "Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling." Analytical Chemistry 79(16):6081-6093.

Jiang S, C Li, W Zhang, Y Cai, Y Yunlin, S Yang, and W Jiang. 2007. "Directed evolution and structural analysis of N-carbamoyl-D-amino acid amidohydrolase provide insights on recombinant protein solubility in Escherichia coli." Biochemical Journal 402(Pt.3):429-437.

Karagiosis SA, and NJ Karin. 2007. "Lysophosphatidic acid induces osteocyte dendrite outgrowth." Biochemical and Biophysical Research Communications 357(1):194-199.

Metz T, Q Zhang, JS Page, Y Shen, SJ Callister, JM Jacobs, and RD Smith. 2007. "The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery."Biomarkers in Medicine 1(1):159-185.

Perrine KA, BL Lamarche, DF Hopkins, SE Budge, LK Opresko, HS Wiley, and MB Sowa. 2007. "High speed method for in situ multispectral image registration." Microscopy Research and Technique 70(4):382-389.

Sanfilippo AP, C Posse, B Gopalan, RM Riensche, N Beagley, BL Baddeley, SC Tratz, and ML Gregory. 2007. "Combining hierarchical and associative gene ontology relations with textual evidence in estimating gene and gene product similarity." IEEE Transactions on NanoBioscience 6(1):51-59.

Scholten JC, DE Culley, FJ Brockman, G Wu, and W Zhang. 2007. "Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer." Biochemical and Biophysical Research Communications 352(1):48-54.

Servoss SL, CL Baird, KD Rodland, and RC Zangar. 2007. "Surface chemistries for antibody microarrays." Frontiers in Bioscience 12:3956-64.

Shah AR, M Singhal, KR Klicker, EG Stephan, HS Wiley, and KM Waters. 2007. "Enabling high-throughput data management systems biology: The Bioinformatics Resource Manager." Bioinformatics 23(7):906-909.

Shankaran H, HS Wiley, and H Resat. 2007. "Cell surface receptors for signal transduction and ligand transport - a design principles study." PLoS Computational Biology. 3(6): e101.

Singhal M and H Resat. 2007. "A domain-based approach to predict protein-protein interactions." BMC Bioinformatics 8:Art.No.199.

Stenoien DL, TV Knyushko, MP Londono, L Opresko, MU Mayer, ST Brady, TC Squier, and DJ Bigelow. 2007. "Cellular trafficking of phospholamban and formation of functional sarcoplasmic reticulum during myocyte differentiation." American Journal of Physiology Cell Physiology 292(6):C2084-2094.

Webb-Robertson BM, and WR Cannon. 2007. "Current trends in computational inference from mass spectrometry-based proteomics." Briefings in Bioinformatics.

Zhang Q, W Qian, TV Knyushko, T Clauss, SO Purvine, RJ Moore, CA Sacksteder, MH Chin, DJ Smith, DG Camp, II, DJ Bigelow, and RD Smith. 2007. "A method for selective enrichment and analysis of nitrotyrosine containing peptides in complex proteome samples." Journal of Proteome Research 6(6)(6):2257-2268.


Adkins JN, HM Mottaz, AD Norbeck, JK Gustin, J Rue, TR Clauss, SO Purvine, KD Rodland, F Heffron, and RD Smith. 2006. "Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions." Molecular & Cellular Proteomics MCP 5(8):1450-1461.

Hixson KK, JN Adkins, SE Baker, RJ Moore, BA Chromy, RD Smith, SL McCutchen-Maloney, and MS Lipton. 2006. "Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics." Journal of Proteome Research 5(11):3008-3017.

Shi L, 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, and TC Squier. 2006. "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." Journal of Biological Chemistry 281:29131-29140.

Culley DE, WP Kovacik, Jr, FJ Brockman, and W Zhang. 2006. "Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis." Journal of Microbiological Methods 67(1):36-43.

Greenwood MS, and S Ahmed. 2006. "Ultrasonic diffraction grating spectroscopy and the measurement of particle size." Ultrasonics 44(Suppl.1):e1385-e1393.

Nie L, G Wu, and W Zhang. 2006. "Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis." Genetics 174(4):2229-2243.

Taylor RC, A Shah, CC Treatman, and ML Blevins. 2006. "SEBINI: Software Environment for Biological Network Inference." Bioinformatics 22:2706-2708.

Xiong Y, L Shi, B Chen, MU Mayer, BH Lower, Y Londer, S Bose, MF Hochella, JM Zachara, JK Fredrickson, and TC Squier. 2006. "High-affinity binding and direct electron transfer to solid metals by the Shewanella oneidensis MR-1 outer membrane c-type cytochrome OmcA." Journal of the American Chemical Society 128(43):13978-13979.

Zhang W, DE Culley, MA Gritsenko, RJ Moore, L Nie, JC Scholten, K Petritis, EF Strittmatter, DG Camp, II, RD Smith, and FJ Brockman. 2006. "LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris." Biochemical and Biophysical Research Communications 349(4):1412-1419.

Systems Biology at PNNL

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