Staff information

PNNL Publications

2022

• Zhao Q., A.M. Thompson, S.J. Callister, M.M. Tfaily, S.L. Bell, S. Hobbie, and K.S. Hofmockel. 2022. "Dynamics of organic matter molecular composition under aerobic decomposition and their response to the nitrogen addition in grassland soils." Science of the Total Environment 806, no. Part 1:Article No. 150514. PNNL-SA-166164. doi:10.1016/j.scitotenv.2021.150514

2021

• Peterson M.J., P. Handakumbura, A.M. Thompson, Z.R. Russell, Y. Kim, S.J. Fansler, and M.L. Smith, et al. 2021. "Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil." PLoS One 16, no. 12:Art. No. e0259937. PNNL-SA-169097. doi:10.1371/journal.pone.0259937

2020

• Callister S.J., J.J. Moran, L. McCue, and L. Pasa-Tolic. 2020. Microbial Ecology of the Plant Rhizosphere (PlantMicrobe). PNNL-30791. Richland, WA: Pacific Northwest National Laboratory. Microbial Ecology of the Plant Rhizosphere (PlantMicrobe)
• Starke R.F., P. Capek, D. Morais, S.J. Callister, and N. Jehmlich. 2020. "The total microbiome function in bacteria and fungi." Journal of Proteomics 213. PNNL-SA-152540. doi:10.1016/j.jprot.2019.103623
• Zhao Q., S.J. Callister, A.M. Thompson, R.K. Kukkadapu, M. Tfaily, L.M. Bramer, and N. Qafoku, et al. 2020. "Strong mineralogic control of soil organic matter composition in response to nutrient addition across diverse grassland sites." Science of the Total Environment 736. PNNL-SA-144529. doi:10.1016/j.scitotenv.2020.137839

2019

• Christensen G.A., C.M. Gionfriddo, A.J. King, J.G. Moberly, C. Miller, A.C. Somenahally, and S.J. Callister, et al. 2019. "Determining the Reliability of Measuring Mercury Cycling Gene Abundance with Correlations with Mercury and Methylmercury Concentrations." Environmental Science & Technology 53, no. 15:8649-8663. PNNL-SA-145153. doi:10.1021/acs.est.8b06389

2018

• Callister S.J., L. McCue, A.A. Boaro, B.L. Lamarche, R.A. White, J.M. Brown, and B.K. Ahring. 2018. "Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor." PLoS One 13, no. 10:Article number e0204831. PNNL-SA-133574. doi:10.1371/journal.pone.0204831
• Callister S.J., T.L. Fillmore, C.D. Nicora, J.B. Shaw, S.O. Purvine, D.J. Orton, and R.A. White, et al. 2018. "Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage Through two-dimensional liquid chromatography." Soil Biology and Biochemistry 125. PNNL-SA-131999. doi:10.1016/j.soilbio.2018.07.018
• Guo J., S. Wilken, V. Jimenez, C.J. Choi, C.K. Ansong, R.O. Dannebaum, and L. Sudek, et al. 2018. "Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation." Nature Microbiology 3, no. 7:781-790. PNNL-SA-135227. doi:10.1038/s41564-018-0178-7
• Otwell A.E., S.J. Callister, R. Sherwood, S. Zhang, A.R. Goldman, R.D. Smith, and R.E. Richardson. 2018. "Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA." Geobiology 16, no. 5:522-539. PNNL-SA-119438. doi:10.1111/gbi.12295

2017

• Thangella P.A., A. Ladak, A.A. Schepmoes, H.J. Olivos, K. Zhao, S.J. Callister, and L.E. Bartley. 2017. "Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode." Frontiers in Plant Science 8. PNNL-SA-126832. doi:10.3389/fpls.2017.01134

2016

• Otwell A.E., S.J. Callister, E.M. Zink, R.D. Smith, and R.E. 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. PNNL-SA-115268. doi:10.3389/fmicb.2016.00191
• van Baren M.J., C. Bachy, E. Reistetter, S.O. Purvine, J. Grimwood, S. Sudek, and H. Yu, et al. 2016. "Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants." BMC Genomics 17. PNNL-SA-114561. doi:10.1186/s12864-016-2585-6
• Waltman P., J. Guo, E. Reistetter, S.O. Purvine, C. Ansong, M.J. van Baren, and C. Wong, et al. 2016. "Identifying Aspects of the Post-transcriptional Program Governing the Proteome of the Green Algal Micromonas pusilla." PLoS One 11, no. 7:Article No. e0155839. PNNL-SA-115265. doi:10.1371/journal.pone.0155839
• White R.A., S.J. Callister, R.J. Moore, E.M. Baker, and J.K. Jansson. 2016. "The Past, Present and Future of Microbiome Analyses." Nature Protocols 11, no. 11:2049-2053. PNNL-SA-119986. doi:10.1038/nprot.2016.148

2015

• Burnet M.C., A. Dohnalkova, A.P. Neumann, M.S. Lipton, R.D. Smith, G. Suen, and S.J. Callister. 2015. "Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85." PLoS One 10, no. 12:e0143809. PNNL-SA-111279. doi:10.1371/journal.pone.0143809
• Li Z., D.D. Kim, O.D. Nelson, A.E. Otwell, R.E. Richardson, S.J. Callister, and H. Lin. 2015. "Molecular dissection of a putative iron reductase from Desulfotomaculum reducens MI-1." Biochemical and Biophysical Research Communications 467, no. 3:503-508. PNNL-SA-115336. doi:10.1016/j.bbrc.2015.10.016
• Mann B.F., H. Chen, E.M. Herndon, R.K. Chu, N. Tolic, E. Portier, and T.R. Chowdhury, et al. 2015. "Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry." PLoS One 10, no. 6:Article No. e0130557. PNNL-SA-111173. doi:10.1371/journal.pone.0130557
• Otwell A.E., R. Sherwood, S. Zhang, O.D. Nelson, Z. Li, H. Lin, and S.J. Callister, et al. 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, no. 3:1977-1990. PNNL-SA-105902. doi:10.1111/1462-2920.12673

2014

• Aryal U.K., S.J. Callister, B.H. McMahon, L.A. McCue, J.N. Brown, J. Stockel, and M.L. Liberton, et al. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13, no. 7:3262-3276. PNNL-SA-102687. doi:10.1021/pr5000889
• Boaro A.A., Y. Kim, A. Konopka, S.J. Callister, and B.K. 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, no. 3:802-15. PNNL-SA-105700. doi:10.1111/1574-6941.12435
• Boaro A.A., Y. Kim, A.E. Konopka, S.J. Callister, and B.K. 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, no. 3:802-815. PNNL-SA-106822. doi:10.1111/1574-6941.12435
• Pena-Castillo L., R. Mercer, A. Gurinovich, S.J. Callister, A.T. Wright, A. Westbye, and J.T. Beatty, et al. 2014. "Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides." BMC Genomics 15. PNNL-SA-105663. doi:10.1186/1471-2164-15-730

2013

• Anderson L.N., D.E. Culley, B.A. Hofstad, L.M. Chauvigne-Hines, E.M. Zink, S.O. Purvine, and R.D. Smith, et al. 2013. "Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30." Molecular Biosystems 9, no. 12:2992-3000. PNNL-SA-97265. doi:10.1039/c3mb70333a
• Aryal U.K., S.J. Callister, S. Mishra, X. Zhang, J.I. Shutthanandan, T.E. Angel, and A.K. Shukla, et al. 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, no. 4:1070-1077. PNNL-SA-90813. doi:10.1128/AEM.02864-12
• Curtis D.S., A.R. Phillips, S.J. Callister, S. Conlan, and L.A. McCue. 2013. "SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes." Bioinformatics 29, no. 20:2641-2642. PNNL-SA-94621. doi:10.1093/bioinformatics/btt454
• Isanapong J., S. Hambright, A.G. Willis, A. Boonmee, S.J. Callister, K.E. Burnum-Johnson, and L. Pasa-Tolic, et al. 2013. "Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium." The ISME Journal 7, no. 9:1803-1813. PNNL-SA-98615. doi:10.1038/ismej.2013.74
• Lamarche B.L., K.L. Crowell, N. Jaitly, V.A. Petyuk, A.R. Shah, A.D. Polpitiya, and J.D. Sandoval, et al. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14. PNNL-SA-89778. doi:10.1186/1471-2105-14-49
• Nicora C.D., B.J. Anderson, S.J. Callister, A.D. Norbeck, S.O. Purvine, J.K. Jansson, and O.U. Mason, et al. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies." Proteomics 13, no. 18-19:2776-2785. PNNL-SA-92783. doi:10.1002/pmic.201300003
• Robidart J.C., S.J. Callister, P.F. Song, C.D. Nicora, C.G. Wheat, and P.R. Girguis. 2013. "Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers." Environmental Science & Technology 47, no. 9:4399-4407. PNNL-SA-90834. doi:10.1021/es3037302

2012

• Cao L., D.A. Bryant, A.A. Schepmoes, K. Vogl, R.D. Smith, M.S. Lipton, and S.J. Callister. 2012. "Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically." Photosynthesis Research 110, no. 3:153-168. PNNL-SA-81058. doi:10.1007/s11120-011-9711-8
• Chauvigne-Hines L.M., L.N. Anderson, H.M. Weaver, J.N. Brown, P.K. Koech, C.D. Nicora, and B.A. Hofstad, et al. 2012. "Suite of Activity-Based Probes for Cellulose-Degrading Enzymes." Journal of the American Chemical Society 134, no. 50:20521-20532. PNNL-SA-91066. doi:10.1021/ja309790w
• Hugo A.E., D.J. Baxter, W.R. Cannon, A. Kalyanaraman, G.R. Kulkarni, and S.J. 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, 17, 225-234. Palo Alto, California:Stanford University. PNNL-SA-80000.

2011

• Burnum K.E., S.J. Callister, C.D. Nicora, S.O. Purvine, P. Hugenholtz, F. Warnecke, and R.H. Scheffrahn, et al. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5, no. 1:161-164. PNNL-SA-68831. doi:10.1038/ismej.2010.97
• Cannon W.R., M.M. Rawlins, D.J. Baxter, S.J. Callister, M.S. Lipton, and D.A. Bryant. 2011. "Large Improvements in MS/MS Based Peptide Identification Rates using a Hybrid Analysis." Journal of Proteome Research 10, no. 5:2306-2317. PNNL-SA-73911. doi:10.1021/pr101130b
• Parnell J.J., S.J. Callister, G. Rompato, C.D. Nicora, L. Pasa-Tolic, A. Williamson, and M.E. Pfrender. 2011. "Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock." Scientific Reports 1. PNNL-SA-74290. doi:10.1038/srep00025
• Wilkins M.J., S.J. Callister, M. Miletto, K.H. Williams, C.D. Nicora, D.R. Lovely, and P.E. Long, et al. 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, no. 1:55-63. PNNL-SA-72264. doi:10.1111/j.1751-7915.2010.00194.x

2010

• Callister S.J., M.J. Wilkins, C.D. Nicora, K.H. Williams, J.F. Banfield, N. VerBerkmoes, and R.L. Hettich, et al. 2010. "Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles." Environmental Science & Technology 44, no. 23:8897-8903. PNNL-SA-71892. doi:10.1021/es101029f
• Mercer R., S.J. Callister, M.S. Lipton, L. Pasa-Tolic, H. Strnad, V. Paces, and J.T. Beatty, et al. 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, no. 11:2701-2710. PNNL-SA-69016. doi:10.1128/JB.00160-10
• Turse J.E., M.J. Marshall, J.K. Fredrickson, M.S. Lipton, and S.J. Callister. 2010. "An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences." PLoS One 5, no. 11:Article No.: e13968. PNNL-SA-65902. doi:10.1371/journal.pone.0013968

2009

• Callister S.J., J.J. Parnell, M.E. Pfrender, M.E. Pfrender, and S. Hashsham. 2009. "Relating Perturbation Magnitude to Temporal Gene Expression in Biological Systems." BMC Research Notes 2. PNNL-16830.
• Wilkins M.J., N.C. VerBerkmoes, K.H. Williams, S.J. Callister, P. Mouser, H. Elifantz, and A.L. N'Guessan, et al. 2009. "Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation." Applied and Environmental Microbiology 75, no. 20:6591-6599. PNNL-SA-68828. doi:10.1128/AEM.01064-09

2008

• Callister S.J., L.A. McCue, J.E. Turse, M.E. Monroe, K.J. Auberry, R.D. Smith, and J.N. Adkins, et al. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3, no. 2:e1542. PNNL-SA-58389. doi:10.1371/journal.pone.0001542
• Du X., S.J. Callister, N.P. Manes, J.N. Adkins, R.A. Alexandridis, X. Zeng, and J. Roh, et al. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7, no. 7:2595-2604. PNNL-SA-55070. doi:10.1021/pr0704837
• Eraso J.M., J. Roh, X. Zeng, S.J. Callister, M.S. 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, no. 14:4831-4848. PNNL-SA-61118. doi:10.1128/JB.00301-08
• Sowell S.M., A.D. Norbeck, M.S. Lipton, C.D. Nicora, S.J. Callister, R.D. Smith, and D.F. Barofsky, et al. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74, no. 13:4091-4100. PNNL-SA-114147. doi:10.1128/AEM.00599-08
• Sowell S.M., A.D. Norbeck, M.S. Lipton, C.D. Nicora, S.J. Callister, R.D. Smith, and D.F. Barofsky, et al. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74, no. 13:4091-4100. PNNL-SA-59403. doi:10.1128/AEM.00599-08

2007

• Metz T.O., Q. Zhang, J.S. Page, Y. Shen, S.J. Callister, J.M. Jacobs, and R.D. Smith. 2007. "The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery." Biomarkers in Medicine 1, no. 1:159-185. PNNL-SA-53806.
• Zeng X., J. Roh, S.J. Callister, C. Tavano, T. Donohue, M.S. Lipton, and S. Kaplan. 2007. "Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: Identification of New Proteins." Journal of Bacteriology 189, no. 20:7464-7474. PNNL-SA-52485. doi:10.1128/JB.00946-07

2006

• Callister S.J., C.D. Nicora, X. Zeng, J. Roh, M. Dominguez, C. Tavano, and M.E. Monroe, et al. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes." Journal of Microbiological Methods 67, no. 3:424-436. PNNL-SA-46423. doi:10.1016/j.mimet.2006.04.021
• Callister S.J., M. Dominguez, C.D. Nicora, X. Zeng, C. Tavano, S. Kaplan, and T. Donohue, et al. 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, no. 8:1940-1947. PNNL-SA-48567.
• Callister S.J., R.C. Barry, J.N. Adkins, E.T. Johnson, W. Qian, B.M. Webb-Robertson, and R.D. Smith, et al. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5, no. 2:277-286. PNNL-SA-46453. doi:10.1021/pr050300l
• Fang R., D.A. Elias, M.E. Monroe, Y. Shen, M. McIntosh, P. Wang, and C.D. Goddard, et al. 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, no. 4:714-725. PNNL-SA-47983. doi:10.1074/mcp.M500301-MCP200
• Norbeck A.D., S.J. Callister, M.E. Monroe, N. Jaitly, D.A. Elias, M.S. Lipton, and R.D. Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods 67, no. 3:473-486. PNNL-SA-46770. doi:10.1016/j.mimet.2006.04.024
• Norbeck A.D., S.J. Callister, M.E. Monroe, N. Jaitly, D.A. Elias, M.S. Lipton, and R.D. Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods 67, no. 3:473-486. PNNL-SA-47555.