U.S. Department of Energy

Pacific Northwest National Laboratory

Stephen Callister

Stephen Callister
Professional Title: 


  • Lin F, BJ Williams, PA Thangella, A Ladak, AA Schepmoes, HJ Olivos, K Zhao, SJ Callister, and LE Bartley. 2017. "Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode." Frontiers in Plant Science 8:1134.  doi:10.3389/fpls.2017.01134


  • Otwell AE, SJ Callister, EM Zink, RD Smith, and RE Richardson. 2016. "Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-positive Sulfate- and Metal-reducing Bacterium." Frontiers in Microbiology 7:191.  doi:10.3389/fmicb.2016.00191
  • van Baren MJ, C Bachy, E Reistetter, SO Purvine, J Grimwood, S Sudek, H Yu, C Poirier, TJ Deerinck, A Kuo, IV Grigoriev, CH Wong, RD Smith, SJ Callister, CL Wei, J Schmutz, and AZ Worden. 2016. "Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants." BMC Genomics 17:Article No. 267.  doi:10.1186/s12864-016-2585-6
  • Waltman P, J Guo, E Reistetter, SO Purvine, C Ansong, MJ van Baren, CH Wong, CL Wei, RD Smith, SJ Callister, J Stuart, and AZ Worden. 2016. "Identifying Aspects of the Post-transcriptional Program Governing the Proteome of the Green Algal Micromonas pusilla." PLoS One 11(7):Article No. e0155839.  doi:10.1371/journal.pone.0155839
  • White RA, III, SJ Callister, RJ Moore, EM Baker, and JK Jansson. 2016. "The Past, Present and Future of Microbiome Analyses." Nature Protocols 11(11):2049-2053. doi:10.1038/nprot.2016.148


  • Burnet MC, A Dohnalkova, AP Neumann, MS Lipton, RD Smith, G Suen, and SJ Callister. 2015. "Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85." PLoS One 10(12):e0143809.  doi:10.1371/journal.pone.0143809
  • Li Z, DD Kim, OD Nelson, AE Otwell, RE Richardson, SJ Callister, and H Lin. 2015. "Molecular dissection of a putative iron reductase from Desulfotomaculum reducens MI-1." Biochemical and Biophysical Research Communications 467(3):503-508.  doi:10.1016/j.bbrc.2015.10.016
  • Mann BF, HM Chen, EM Herndon, RK Chu, N Tolic, E Portier, TR Chowdhury, EW Robinson, SJ Callister, SD Wullschleger, DE Graham, L Liang, and B Gu. 2015. "Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry." PLoS One 10(6):Article No. e0130557.  doi:10.1371/journal.pone.0130557
  • Otwell AE, R Sherwood, S Zhang, OD Nelson, Z Li, H Lin, SJ Callister, and RE Richardson. 2015. "Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay." Environmental Microbiology 17(3):1977-1990.  doi:10.1111/1462-2920.12673


  • Aryal UK, SJ Callister, BH McMahon, LA McCue, JN Brown, J Stockel, ML Liberton, S Mishra, X Zhang, CD Nicora, TE Angel, DW Koppenaal, RD Smith, HB Pakrasi, and LA Sherman. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13(7):3262-3276. doi:10.1021/pr5000889
  • Boaro AA, YM Kim, A Konopka, SJ Callister, and BK Ahring. 2014. "Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture." FEMS Microbiology Ecology 90(3):802-15.  doi:10.1111/1574-6941.12435
  • Boaro AA, YM Kim, AE Konopka, SJ Callister, and BK Ahring. 2014. "Integrated ‘omics Analysis for Studying the Microbial Community Response to a pH Perturbation of a Cellulose-Degrading Bioreactor Culture." FEMS Microbiology Ecology 90(3):802-815. doi:10.1111/1574-6941.12435
  • Pena-Castillo L, R Mercer, A Gurinovich, SJ Callister, AT Wright, A Westbye, JT Beatty, and AS Lang. 2014. "Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides." BMC Genomics 15:Article No. 730.  doi:10.1186/1471-2164-15-730


  • Anderson LN, DE Culley, BA Hofstad, LM Chauvigne-Hines, EM Zink, SO Purvine, RD Smith, SJ Callister, JM Magnuson, and AT Wright. 2013. "Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30." Molecular Biosystems 9(12):2992-3000.  doi:10.1039/c3mb70333a
  • Aryal UK, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, and L Sherman. 2013. "Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions Resulting in Enhanced H-2 Production." Applied and Environmental Microbiology 79(4):1070-1077.  doi:10.1128/AEM.02864-12
  • Curtis DS, AR Phillips, SJ Callister, S Conlan, and LA McCue. 2013. "SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes." Bioinformatics 29(20):2641-2642.  doi:10.1093/bioinformatics/btt454
  • Isanapong J, S Hambright, AG Willis, A Boonmee, SJ Callister, KE Burnum-Johnson, L Pasa-Tolic, CD Nicora, JT Wertz, T Schmidt, and JL Rodrigues. 2013. "Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium." The ISME Journal 7(9):1803-1813.  doi:10.1038/ismej.2013.74
  • Lamarche BL, KL Crowell, N Jaitly, VA Petyuk, AR Shah, AD Polpitiya, JD Sandoval, GR Kiebel, ME Monroe, SJ Callister, TO Metz, GA Anderson, and RD Smith. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14:Article No. 49. doi:10.1186/1471-2105-14-49
  • 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


  • Cao L, DA Bryant, AA Schepmoes, K Vogl, RD Smith, MS Lipton, and SJ Callister. 2012. "Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically." Photosynthesis Research 110(3):153-168.  doi:10.1007/s11120-011-9711-8
  • 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
  • Hugo AE, DJ Baxter, WR Cannon, A Kalyanaraman, GR Kulkarni, and SJ Callister. 2012. "Proteotyping of Microbial Communities by Optimization of Tandem Mass Spectrometry Data Interpretation." In Pacific Symposium in BioComputing 2012, January 2-7, 2012, Hawaii, vol. 17, pp. 225-234.  Stanford University, Palo Alto, CA. 


  • Cannon WR, MM Rawlins, DJ Baxter, SJ Callister, MS Lipton, and DA Bryant. 2011. "Large Improvements in MS/MS Based Peptide Identification Rates using a Hybrid Analysis." Journal of Proteome Research 10(5):2306-2317.  doi:10.1021/pr101130b
  • 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
  • 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


  • 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
  • Mercer R, SJ Callister, MS Lipton, L Pasa-Tolic, H Strnad, V Paces, JT Beatty, and AS Lang. 2010. "Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in Rhodobacter capsulatus." Journal of Bacteriology 192(11):2701-2710.  doi:10.1128/JB.00160-10
  • Turse JE, MJ Marshall, JK Fredrickson, MS Lipton, and SJ Callister. 2010. "An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences." PLoS One 5(11):Article No.: e13968.  doi:10.1371/journal.pone.0013968


  • Callister SJ, JJ Parnell, ME Pfrender, and S Hashsham. 2009. "Relating Perturbation Magnitude to Temporal Gene Expression in Biological Systems." BMC Research Notes 2:Art. No. 43. 
  • 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


  • 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.  doi:10.1371/journal.pone.0001542
  • Du X, SJ Callister, NP Manes, JN Adkins, RA Alexandridis, X Zeng, JH Roh, WE Smith, TJ Donohue, S Kaplan, RD Smith, and MS Lipton. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7(7):2595-2604.  doi:10.1021/pr0704837
  • Eraso JM, JH Roh, X Zeng, SJ Callister, MS Lipton, and S Kaplan. 2008. "Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis." Journal of Bacteriology 190(14):4831-4848.  doi:10.1128/JB.00301-08
  • 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
  • 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


  • 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. 
  • Zeng X, JH Roh, SJ Callister, C Tavano, T Donohue, MS Lipton, and S Kaplan. 2007. "Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: Identification of New Proteins." Journal of Bacteriology 189(20):7464-7474.  doi:10.1128/JB.00946-07


  • Norbeck AD, SJ Callister, ME Monroe, N Jaitly, DA Elias, MS Lipton, and RD Smith. 2006. "Proteomic approaches to bacterial differentiation ." Journal of Microbiological Methods 67(3):473-486.  doi:10.1016/j.mimet.2006.04.024 
  • Norbeck AD, SJ Callister, ME Monroe, N Jaitly, DA Elias, MS Lipton, and RD Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods 67(3):473-486. 
  • 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. 
  • Callister SJ, RC Barry, JN Adkins, ET Johnson, W Qian, BJM Webb-Robertson, RD Smith, and MS Lipton. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5(2):277-286.  doi:10.1021/pr050300l
  • 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
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