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Biological Sciences Staff information

Jon Jacobs

Integrative Omics
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352
509/371-6570

PNNL Publications

2013

  • Price RW, J Peterson, D Fuchs, TE Angel, H Zetterberg, L Hagberg, SS Spudich, RD Smith, JM Jacobs, JN Brown, and M Gisslen. 2013. "Approach to Cerebrospinal Fluid (CSF) Biomarker Discovery and Evaluation in HIV Infection." Journal of Neuroimmune Pharmacology 8(5):1147-1158.  doi:10.1007/s11481-013-9491-3

2012

  • Angel TE, JM Jacobs, RP Smith, MS Pasternack, S Elias, MA Gritsenko, AK Shukla, EC Gilmore, C McCarthy, DG Camp, II, and RD Smith. 2012. "Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease." Journal of Proteome Research 11(10):4814-4822.  doi:10.1021/pr300577p
  • Angel TE, JM Jacobs, SS Spudich, MA Gritsenko, D Fuchs, T Liegler, H Zetterberg, DG Camp, II, RW Price, and RD Smith. 2012. "The cerebrospinal fluid proteome in HIV infection: change associated with disease severity." Clinical Proteomics 9:Article No. 3.  doi:10.1186/1559-0275-9-3
  • Aryal UK, J Stockel, EA Welsh, MA Gritsenko, CD Nicora, DW Koppenaal, RD Smith, HB Pakrasi, and JM Jacobs. 2012. "Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light." Journal of Proteome Research 11(2):609-619.  doi:10.1021/pr200959x
  • Brown JN, GM Ortiz, TE Angel, JM Jacobs, MA Gritsenko, EY Chan, DE Purdy, RD Murnane, K Larsen, RE Palermo, AK Shukla, TRW Clauss, MG Katze, JM McCune, and RD Smith. 2012. "Morphine Produces Immunosuppressive Effects in Non-human Primates at the Proteomic and Cellular Levels." Molecular & Cellular Proteomics. MCP 11(9):605-618.  doi:10.1074/mcp.M111.016121
  • Diamond DL, A Krasnoselski, KE Burnum, ME Monroe, BJM Webb-Robertson, JE McDermott, MM Yeh, JF Golib-Dzib, N Susnow, S Strom , S Proll, S Belisle, DE Purdy, A Rasmussen, KA Walters, JM Jacobs, MA Gritsenko, DG Camp, II, R Bhattacharya, JD Perkins, RL Carithers, IW Liou, AM Larson, A Benecke, KM Waters, RD Smith, and MG Katze. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 53(1):28-38.  doi:10.1002/hep.25649

2011

  • Aryal UK, J Stockel, RK Krovvidi, MA Gritsenko, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, HB Pakrasi, and JM Jacobs. 2011. "Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles." BMC Systems Biology 5:Article No. 194.  doi:10.1186/1752-0509-5-194
  • Dresang LR, JR Teuton, H Feng, JM Jacobs, DG Camp, II, SO Purvine, MA Gritsenko, Z Li, RD Smith, B Sugden, PS Moore, and Y Chang. 2011. "Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes." BMC Genomics 12:Article No. 625.  doi:10.1186/1471-2164-12-625
  • Matzke MM, KM Waters, TO Metz, JM Jacobs, A Sims, R Baric, JG Pounds, and BJM Webb-Robertson. 2011. "Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data." Bioinformatics 27(20):2866-2872. 
  • Stockel J, JM Jacobs, TR Elvitigala, ML Liberton, EA Welsh, AD Polpitiya, MA Gritsenko, CD Nicora, DW Koppenaal, RD Smith, and HB Pakrasi. 2011. "Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142." PLoS One 6(2):Article No.: e16680.  doi:10.1371/journal.pone.0016680
  • Teeguarden JG, BJM Webb-Robertson, KM Waters, A Murray, E Kisin, SM Varnum, JM Jacobs, JG Pounds, RC Zangar, and A Shvedova. 2011. "Comparative Proteomics and Pulmonary Toxicity of Instilled Single Walled Carbon Nanotubes, Crocidolite Asbestos and Ultrafine Carbon Black in Mice." Toxicological Sciences 120(1):123-135.  doi:10.1093/toxsci/kfq363
  • Wang Y, F Yang, Y Fu, X Huang, W Wang, X Jiang, MA Gritsenko, R Zhao, ME Monroe, OC Pertz, SO Purvine, DJ Orton, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286(20):18190-18201. 
  • Waters KM, JM Jacobs, MA Gritsenko, and NJ Karin. 2011. "Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth." Bone 48(6):1328-35.  doi:10.1016/j.bone.2011.02.020
  • Webb-Robertson BJM, MM Matzke, JM Jacobs, JG Pounds, and KM Waters. 2011. "A Statistical Selection Strategy for Normalization Procedures in LC-MS Proteomics Experiments through Dataset Dependent Ranking of Normalization Scaling Factors." Proteomics 11(24):4736-4741.  doi: 10.1002/pmic.201100078

2010

  • Angel TE, BJ Luft, X Yang, CD Nicora, DG Camp, II, JM Jacobs, and RD Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5(11):Article No.: e13800.  doi:10.1371/journal.pone.0013800
  • Brown JN, R Palermo, CR Baskin, MA Gritsenko, PJ Sabourin, JP Long, CL Sabourin, H Bielefeldt-Ohmann, A Garcia-Sastre, R Albrecht, TM Tumpey, JM Jacobs, RD Smith, and MG Katze. 2010. "Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections." Journal of Virology 84(22):12058-12068. 
  • Diamond DL, AJ Syder, JM Jacobs, CM Sorensen, KA Walters, S Proll, JE McDermott, MA Gritsenko, Q Zhang, R Zhao, TO Metz, DG Camp, II, KM Waters, RD Smith, CM Rice, and MG Katze. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics ." PLoS Pathogens 6(1):Art. No. e1000719.  doi:10.1371/journal.ppat.1000719
  • Webb-Robertson BJM, LA McCue, KM Waters, MM Matzke, JM Jacobs, TO Metz, SM Varnum, and JG Pounds. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9(11):5748-5756. 
  • Wegener KM, AK Singh, JM Jacobs, TR Elvitigala, EA Welsh, NS Keren, MA Gritsenko, BK Ghosh, DG Camp, II, RD Smith, and HB Pakrasi. 2010. "Global Proteomics Reveal An Atypical Strategy for Carbon/Nitrogen Assimilation by a Cyanobacterium Under Diverse Environmental Perturbations." Molecular & Cellular Proteomics. MCP 9(12):2678-89.  doi:10.1074/mcp.M110.000109
  • Zhang X, ME Monroe, B Chen, MH Chin, TH Heibeck, AA Schepmoes, F Yang, BO Petritis, DG Camp, II, JG Pounds, JM Jacobs, DJ Smith, DJ Bigelow, RD Smith, and W Qian. 2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9(6):1199-1208. 

2009

  • Chan EY, JN Sutton, JM Jacobs, A Bondarenko, RD Smith, and MG Katze. 2009. "Dynamic Host Energetics and Cytoskeletal Proteomes in HIV-1 -Infected Human Primary CD4 Cells: Analysis by Multiplexed Label-free Mass Spectrometry." Journal of Virology 83(18):9283-9295. 

2008

  • Jacobs JM, KM Waters, LE Kathmann, DG Camp, II, HS Wiley, RD Smith, and BD Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7(2):558-569.  doi:10.1021/pr0704377
  • Ding SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD Smith. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step 8O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7(10):4215-24.  doi:10.1021/pr7007785
  • Dumortier J, DN Streblow, AV Moses, JM Jacobs, CN Kreklywich, DG Camp, II, RD Smith, SL Orloff, and J Nelson. 2008. "Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing." Journal of Virology 82(13):6524-6535.  doi:doi:10.1128/JVI.00502-08
  • Metz TO, W Qian, JM Jacobs, MA Gritsenko, RJ Moore, AD Polpitiya, ME Monroe, DG Camp, II, PW mueller, and RD Smith. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset ." Journal of Proteome Research 7(2):698-707.  doi:10.1021/pr700606w
  • Pasa-Tolic L, JM Jacobs, W Qian, and RD Smith. 2008. "Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry." Chapter 7 in Clinical Proteomics: From Diagnosis to Therapy, ed. JE Van Eyk and MJ Dunn, pp. 89-100.  Wiley-VCH, Weinheim, Germany. 
  • Wegener KM, EA Welsh, LE Thornton, NS Keren, JM Jacobs, KK Hixson, ME Monroe, DG Camp, II, RD Smith, and HB Pakrasi. 2008. "High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex." Journal of Biological Chemistry 283(41):27829-27837.  doi:10.1074/jbc.M803918200
  • Welsh EA, ML Liberton, J Stockel, T Loh, TR Elvitigala, C Wang, A Wollam, RS Fulton, SW Clifton, JM Jacobs, R Aurora, BK Ghosh, LA Sherman, RD Smith, RK Wilson, and HB Pakrasi. 2008. "The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle." Proceedings of the National Academy of Sciences of the United States of America 105(39):15094-15099.  doi:10.1073/pnas.0805418105

2007

  • Diamond DL, JM Jacobs, B Paeper, S Proll, MA Gritsenko, RL Carithers, Jr., AM Larson , MM Yeh, DG Camp, II, RD Smith, and MG Katze. 2007. "Proteomic Profiling of Human Liver Biopsies: Hepatitis C Virus-Induced Fibrosis and Mitochondrial Dysfunction." Hepatology 46(3):649-657.  doi:10.1002/hep.21751
  • Dutta D, SK Sundaram, JG Teeguarden, BJ Riley, LS Fifield, JM Jacobs, RS Addleman, GA Kaysen, BM Moudgil, and TJ Weber. 2007. "Adsorbed Proteins Influence the Biological Activity and Molecular Targeting of Nanomaterials." Toxicological Sciences 100(1):303-315.  doi:10.1093/toxsci/kfm217
  • Metz TO, Q Zhang, JS Page, Y Shen, SJ Callister, JM Jacobs, and RD Smith. 2007. "The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery." Biomarkers in Medicine 1(1):159-185. 
  • Wang Y, SJ Ding, W Wang, JM Jacobs, W Qian, RJ Moore, F Yang, DG Camp, II, RD Smith, and RL Klemke. 2007. "Profiling Signaling Polarity in Chemotactic Cells." Proceedings of the National Academy of Sciences of the United States of America 104(20):8328-8333.  doi:10.1073/pnas.0701103104
  • Wang Y, SJ Ding, W Wang, F Yang, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2007. "Methods for Pseudopodia Purification and Proteomic Analysis." Sciences STKE Signal Transduction Knowledge Environment 2007(400):p14. 

2006

  • Jacobs JM, and RD Smith. 2006. "Proteomic Analyses Using High-Efficiency Separations and Accurate Mass Measurements." Chapter 20 in Separation Methods in Proteomics, ed. GB Smejkal and A Lazareu, pp. 363-385.  CRC Taylor & Francis, Boca Raton, FL. 
  • Jacobs JM, and RD Smith. 2006. "Proteomic Analyses using High-Efficiency Separations and Accurate Mass Measurements." Chapter 20 in Separations in Proteomics , ed. Smejkal, GB and A Lazareu, pp. 363-385.  CRC Taylor and Francis Group, New York, NY. 
  • Baas T, CR Baskin, DL Diamond, A Garcia-Sastre, H Bielefeldt-Ohmann, TM Tumpey, MJ Thomas, VS Carter, TH Teal, N Van Hoven, S Proll, JM Jacobs, Z Caldwell, MA Gritsenko, R Hukkanen, DG Camp, II, RD Smith, and MG Katze. 2006. "Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics." Journal of Virology 80(21):10813 (16 pages).  doi:10.1128/JVI.00851-06
  • Diamond DL, S Proll, JM Jacobs, EY Chan, DG Camp, II, RD Smith, and MG Katze. 2006. "HepatoProteomics: Applying Proteomic Technologies to the Study of Liver Function and Disease." Hepatology 44(2):299-308. 
  • Metz TO, JM Jacobs, MA Gritsenko, G Fontes, W Qian, DG Camp, II, VJ Poitout, and RD Smith. 2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5(12):3345-3354.  doi: 10.1021/pr060322n
  • Qian W, JM Jacobs, T Liu, DG Camp, II, and RD Smith. 2006. "Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications." Molecular & Cellular Proteomics. MCP 5(10):1727-1744.  doi:10.1074/mcp.M600162-MCP200

2005

  • Jacobs JM, DL Diamond, EY Chan, MA Gritsenko, W Qian, M Stastna, T Baas, DG Camp, II, RL Carithers, Jr., RD Smith, and MG Katze. 2005. "Proteome Analysis of Liver Cells Expressing a Full- Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients." Journal of Virology 79(12):7558-7569. 
  • Jacobs JM, JN Adkins, W Qian, T Liu, Y Shen, DG Camp, II, and RD Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4(4):1073-1085.  doi:10.1021/pr0500657
  • Jacobs JM, ME Monroe, W Qian, Y Shen, GA Anderson, and RD Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240(3):195-212. 
  • Jacobs JM, X Yang, BJ Luft, JJ Dunn, DG Camp, II, and RD Smith. 2005. "Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia burgdorferi." Proteomics 5(5):1446-1453. 
  • Adkins JN, ME Monroe, KJ Auberry, Y Shen, JM Jacobs, DG Camp, II, F Vitzthum, KD Rodland, RC Zangar, RD Smith, and JG Pounds. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy." Proteomics 5(13):3454-3466.  doi:10.1002/pmic.200401333
  • Liu T, W Qian, WNU Chen, JM Jacobs, RJ Moore, DJ Anderson, MA Gritsenko, ME Monroe, BD Thrall, DG Camp, II, and RD Smith. 2005. "Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome." Proteomics 5(5):1263-1273. 
  • Qian W, JM Jacobs, DG Camp, II, ME Monroe, RJ Moore, MA Gritsenko, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, and RD Smith. 2005. "Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry." Proteomics 5(2):572-584.  doi:10.1002/pmic.200400942
  • Qian W, JM Jacobs, DG Camp, II, ME Monroe, RJ Moore, MA Gritsenko, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, and RD Smith. 2005. "Comparative Proteome Analyses of Human Plasma Following in vivo Lipopolysaccharide Administration Using Multidimensional Separations Coupled with Tandem Mass Spectrometry." Proteomics 5(2):572-584. 
  • Qian W, ME Monroe, T Liu, JM Jacobs, GA Anderson, Y Shen, RJ Moore, DJ Anderson, R Zhang, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 4(5):700-709. 
  • Qian W, T Liu, ME Monroe, EF Strittmatter, JM Jacobs, LJ Kangas, K Petritis, DG Camp, II, and RD Smith. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research 4(1):53-62. 
  • Shen Y, J Kim, EF Strittmatter, JM Jacobs, DG Camp, II, R Fang, N Tolic, RJ Moore, and RD Smith. 2005. "Characterization of the human blood plasma proteome." Proteomics 5(15):4034-4045. 

2004

  • Jacobs JM, HM Mottaz, LR Yu, DJ Anderson, RJ Moore, WNU Chen, KJ Auberry, EF Strittmatter, ME Monroe, BD Thrall, DG Camp, II, and RD Smith. 2004. "Multidimensional Proteome Analysis of Human Mammary Epithelial Cells." Journal of Proteome Research 3(1):68-75. 
  • Shen Y, JM Jacobs, DG Camp, II, R Fang, RJ Moore, RD Smith, W Xiao, RW Davis, and RG Tompkins. 2004. "Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome." Analytical Chemistry 76(4):1134-1144. 
  • Strittmatter EF, LJ Kangas, K Petritis, HM Mottaz, GA Anderson, Y Shen, JM Jacobs, DG Camp, II, and RD Smith. 2004. "Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry." Journal of Proteome Research 3(4):760-769. 

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