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Biological Sciences Staff information

Carrie Nicora

Omic, Inst, Infra & Inform
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352
509/371-6573

PNNL Publications

2014

  • Shi T, Y Gao, SI Quek, TL Fillmore, CD Nicora, D Su, R Zhao, KD Rodland, T Liu, RD Smith, DW Chan, DG Camp, II, AY Liu, and W Qian. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13(2):875-882.  doi:10.1021/pr400912c

2013

  • Aylward FO, KE Burnum-Johnson, SG Tringe, C Teiling, D Tremmel, J Moeller, JJ Scott, KW Barry, PD Piehowski, CD Nicora, S Malfatti, ME Monroe, SO Purvine, LA Goodwin, RD Smith, G Weinstock, N Gerardo, G Suen, MS Lipton, and CR Currie. 2013. "Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens." Applied and Environmental Microbiology 79(12):3770-3778.  doi:10.1128/AEM.03833-12
  • D'haeseleer P, JM Gladden, M Allgaier, P Chain, SG Tringe, S Malfatti, JT Aldrich, CD Nicora, EW Robinson, L Pasa-Tolic, P Hugenholtz, BA Simmons, and SW Singer. 2013. "Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass." PLoS One 8(7):e68465.  doi:10.1371/journal.pone.0068465
  • DeAngelis KM, D Sharma, R Varney, BA Simmons, NG Isern, LM Markillie, CD Nicora, AD Norbeck, RC Taylor, JT Aldrich, and EW Robinson. 2013. "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1." Frontiers in Microbiology 4:Article No. 280. 
  • Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ." Proteomics 13(18-19):2776-2785.  doi:10.1002/pmic.201300003
  • Robidart JC, SJ Callister, PF Song, CD Nicora, CG Wheat, and PR Girguis. 2013. "Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers." Environmental Science & Technology 47(9):4399-4407.  doi:10.1021/es3037302
  • Wilkins MJ, KC Wrighton, CD Nicora, KH Williams, LA McCue, KM Handley, CS Miller, L Giloteaux, AP Montgomery, DR Lovley, JF Banfield, PE Long, and MS Lipton. 2013. "Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface ." PLoS One 8(3):e57819.  doi:10.1371/journal.pone.0057819
  • Zhou J, RK Krovvidi, Y Gao, H Gao, BO Petritis, A De, C Miller-Graziano, PE Bankey, VA Petyuk, CD Nicora, TRW Clauss, RJ Moore, T Shi, JN Brown, A Kaushal, W Xiao, RW Davis, RV Maier, RG Tompkins, W Qian, DG Camp, II, and RD Smith. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7(7-8):571-583.  doi:10.1002/prca.201200109

2012

  • 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
  • Aylward FO, KE Burnum, JJ Scott, G Suen, SG Tringe, SM Adams, KW Barry, CD Nicora, PD Piehowski, SO Purvine, GJ Starrett, LA Goodwin, RD Smith, MS Lipton, and CR Currie. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6(9):1688-1701.  doi:10.1038/ismej.2012.10
  • Chauvigne-Hines LM, LN Anderson, HM Weaver, JN Brown, PK Koech, CD Nicora, BA Hofstad, RD Smith, MJ Wilkins, SJ Callister, and AT Wright. 2012. "Suite of Activity-Based Probes for Cellulose-Degrading Enzymes." Journal of the American Chemical Society 134(50):20521-20532.  doi:10.1021/ja309790w
  • Chauvin T, F Xie, T Liu, CD Nicora, F Yang, DG Camp, II, RD Smith, and KP Roberts. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87(6):Article No. 141.  doi:10.1095/biolreprod.112.104208
  • Haag JR, TS Ream, M Marasco, CD Nicora, AD Norbeck, L Pasa-Tolic, and CS Pikaard. 2012. "In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing." Molecular Cell 48(5):811-8.  doi:10.1016/j.molcel.2012.09.027
  • Zhou J, GP Dann, T Shi, L Wang, X Gao, D Su, CD Nicora, AK Shukla, RJ Moore, T Liu, DG Camp, II, RD Smith, and W Qian. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84(6):2862-2867.  doi:10.1021/ac203394r

2011

  • Burnum KE, SJ Callister, CD Nicora, SO Purvine, P Hugenholtz, F Warnecke, RH Scheffrahn, RD Smith, and MS Lipton. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5(1):161-164.  doi:10.1038/ismej.2010.97
  • Parnell JJ, SJ Callister, G Rompato, CD Nicora, L Pasa-Tolic, A Williamson, and ME Pfrender. 2011. "Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock." Scientific Reports 1:Article No. 25.  doi:10.1038/srep00025
  • Qian W, BO Petritis, CD Nicora, and RD Smith. 2011. "Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics." Chapter 3 in Gel-Free Proteomics, Methods and Protocols: Methods in Molecular Biology, vol. 753, ed. K Gevaert and J Vandekerckhove, pp. 43-54.  Humana Press Inc., Totowa, NJ. 
  • 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
  • Wilkins MJ, SJ Callister, M Miletto, KH Williams, CD Nicora, DR Lovely, PE Long, and MS Lipton. 2011. "Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)." Microbial Biotechnology 4(1):55-63.  doi:10.1111/j.1751-7915.2010.00194.x

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
  • Callister SJ, MJ Wilkins, CD Nicora, KH Williams, JF Banfield, N VerBerkmoes, RL Hettich, AL N'Guessan, P Mouser, H Elifantz, RD Smith, DR Lovley, MS Lipton, and PE Long. 2010. "Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles." Environmental Science & Technology 44(23):8897-8903.  doi:10.1021/es101029f
  • Smith DP, JB Kitner, AD Norbeck, TRW Clauss, MS Lipton, MS Schwalbach, L Steindler, CD Nicora, RD Smith, and SJ Giovannoni. 2010. "Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique." PLoS One 5(5):Article Number: e10487. 

2009

  • Henne KL, JE Turse, CD Nicora, MS Lipton, SL Tollaksen, C Lindberg, G Babbnig, CS Giometti, CN Nakatsu, DK Thompson, and A Konopka. 2009. "Global Proteomic Analysis of the Chromate Response in Arthrobacter sp strain FB24." Journal of Proteome Research 8(4)(Sp.Iss.SI):1704-16.  doi:10.1021/Pr800705f
  • Kim W, MW Silby, SO Purvine, JS Nicoll, KK Hixson, ME Monroe, CD Nicora, MS Lipton, and SB Levy. 2009. "Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1." PLoS One 4(12):Article Number: e8455.  doi:10.1371/journal.pone.0008455
  • Ream TS, JR Haag, AT Wierzbicki, CD Nicora, AD Norbeck, JK Zhu, G Hagen, TJ Guilfoyle, L Pasa-Tolic, and CS Pikaard. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II ." Molecular Cell 33(2):192-203.  doi:doi:10.1016/j.molcel.2008.12.015
  • Ream TS, JR Haag, AT Wierzbicki, CD Nicora, AD Norbeck, JK Zhu, G Hagen, TJ Guilfoyle, L Pasa-Tolic, and CS Pikaard. 2009. "Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II." Molecular Cell 33(2):192-203.  doi:10.1016/j.molcel.2008.12.015
  • Sowell SM, L Wilhelm, AD Norbeck, MS Lipton, CD Nicora, DF Barofsky, C carlson, RD Smith, and SJ Giovannoni. 2009. " Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3(1):93-105. 
  • Wilkins MJ, NC VerBerkmoes, KH Williams, SJ Callister, P Mouser, H Elifantz, AL N'Guessan, BC Thomas, CD Nicora, MB Shah, P Abraham, MS Lipton, DR Lovely, RL Hettich, PE Long, and JF Banfield. 2009. "Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation." Applied and Environmental Microbiology 75(20):6591-6599.  doi:10.1128/AEM.01064-09

2008

  • Sowell SM, AD Norbeck, MS Lipton, CD Nicora, SJ Callister, RD Smith, DF Barofsky, and SJ Giovannoni. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74(13):4091-4100.  doi:10.1128/AEM.00599-08

2006

  • Callister SJ, CD Nicora, X Zeng, JH Roh, M Dominguez, C Tavano, ME Monroe, S Kaplan, T Donohue, RD Smith, and MS Lipton. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes." Journal of Microbiological Methods 67(3):424-436.  doi:10.1016/j.mimet.2006.04.021
  • Callister SJ, M Dominguez, CD Nicora, X Zeng, C Tavano, S Kaplan, T Donohue, RD Smith, and MS Lipton. 2006. "Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1 Aerobic and Photosynthetic Cell Cultures." Journal of Proteome Research 5(8):1940-1947. 
  • Fang R, DA Elias, ME Monroe, Y Shen, M McIntosh, P Wang, CD Goddard, SJ Callister, RJ Moore, YA Gorby, JN Adkins, JK Fredrickson, MS Lipton, and RD Smith. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5(4):714-725.  doi:10.1074/mcp.M500301-MCP200
  • Yang F, DL Stenoien, EF Strittmatter, JH Wang, L Ding, MS Lipton, ME Monroe, CD Nicora, MA Gritsenko, K Tang, R Fang, JN Adkins, DG Camp, II, DJ Chen, and RD Smith. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation ." Journal of Proteome Research 5(5):1252-1260. 

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