Publications
2023
Ni, Z., Arevalo Jr, R., Bardyn, A., Willhite, L., Ray, S., Southard, A., ... & Nunn, B. L. (2023). Detection of Short Peptides as Putative Biosignatures of Psychrophiles via Laser Desorption Mass Spectrometry. Astrobiology, 23(6), 657-669.
Gomes, K. M., Nunn, B. L., Chappell, P. D., & Jenkins, B. D. (2023). Subcellular proteomics for determining iron‐limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta). Journal of Phycology, 59(5), 1085-1099.
Jaffe, M. D., Padilla-Gamino, J. L., Nunn, B. L., & Rodrigues, L. J. Coral trophic pathways impact the allocation of carbon and nitrogen for egg development after bleaching. Frontiers in Ecology and Evolution, 11, 1251220.
2022
Amy Maas, Emma Timmins-Schiffman, Ann Tarrant, et al. Diel metabolic tuning revealed by in situ transcriptome and proteome in a vertically migratory copepod. Authorea. August 09, 2022.
Axworthy JB, Timmins-Schiffman E, Brown T, Rodrigues LJ, Nunn BL and Padilla-Gamiño JL (2022) Shotgun Proteomics Identifies Active Metabolic Pathways in Bleached Coral Tissue and Intraskeletal Compartments. Front. Mar. Sci. 9:797517.
Boyd, P.W., Doney, S.C., Eggins, S., Ellwood, M.J., Fourquez, M., Nunn, B.L., Strzepek, R. and Timmins-Schiffman, E. (2022), Transitioning global change experiments on Southern Ocean phytoplankton from lab to field settings: Insights and challenges. Limnol Oceanogr, 67: 1911-1930.
Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158
Robert F Strzepek, Brook L Nunn, Lennart T Bach, John A Berges, Erica B Young, Philip W Boyd, The ongoing need for rates: can physiology and omics come together to co-design the measurements needed to understand complex ocean biogeochemistry?, Journal of Plankton Research, Volume 44, Issue 4, July/August 2022, Pages 485–495.
Timmins-Schiffman, Emma and Maas, Amy and Khanna, Rayhan and Blanco-Bercial, Leo and Huang, Eric and Nunn, Brook, Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod.
2021
Glass, J.B., Ranjan, P., Kretz, C.B., Nunn, B.L., Johnson, A.M., Xu, M., McManus, J. and Stewart, F.J., (2021). Microbial metabolism and adaptations in Atribacteria‐dominated methane hydrate sediments. Environmental Microbiology.
Mehta, S., Kumar, P., Crane, M., Johnson, J. E., Sajulga, R., Nguyen, D. D. A., ... & Jagtap, P. D. (2021). Updates on metaQuantome Software for Quantitative Metaproteomics. Journal of Proteome Research, 20(4), 2130-2137.
Mudge, M. C., Nunn, B. L., Firth, E., Ewert, M., Hales, K., Fondrie, W. E., ... & Junge, K. A. (2021). Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. Environmental Microbiology.
Petrou, K., Nunn, B.L., Padula, M.P. et al. Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora. Sci Rep 11, 19061 (2021).
Pollara, S.B., Becker, J.W., Nunn, B.L., Boiteau, R., Repeta, D., Mudge, M.C., Downing, G., Chase, D., Harvey, E.L. and Whalen, K.E., (2021). Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality. Msphere, 6(3), pp.e00009-21.
Sajulga, R., Easterly, C., Riffle, M., Mesuere, B., Muth, T., Mehta, S., Kumar, P., Johnson, J., Gruening, B.A., Schiebenhoefer, H. and Kolmeder, C.A., 2020. Survey of metaproteomics software tools for functional microbiome analysis. PloS one, 15(11), p.e0241503.
Timmins-Schiffman, E., White, S. J., Thompson, R. E., Vadopalas, B., Eudeline, B., Nunn, B. L., & Roberts, S. B. (2021). Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Environmental Microbiome, 16(1), 1-12.
Tisthammer, K. H., Timmins-Schiffman, E., Seneca, F. O., Nunn, B. L., & Richmond, R. H. (2021). Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors. Scientific reports, 11(1), 1-11.
2020
Johnson, R.S., Searle, B.C., Nunn, B.L., Gilmore, J.M., Phillips, M., Amemiya, C.T., Heck, M., and MacCoss, M.J. (2020). Assessing Protein Sequence Database Suitability Using De Novo Sequencing. Mol Cell Proteomics 19, 198-208.
Szeinbaum, N., Nunn, B.L., Cavazos, A.R., Crowe, S.A., Stewart, F.J., DiChristina, T.J., Reinhard, C.T., and Glass, J.B. (2020). Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction. Environmental microbiology reports.
Kumar, P., Johnson, J.E., Easterly, C., Mehta, S., Sajulga, R., Nunn, B., Jagtap, P.D., and Griffin, T.J. (2020). A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases. J Proteome Res 19, 2772-2785.pubs.acs.org/doi/10.1021/acs.jproteome.0c00260
Trigg, S.A., Mitchell, K.R., Thompson, R.E., Eudeline, B., Vadopalas, B., Timmins-Schiffman, E.B., and Roberts, S.B. (2020). Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc. BMC Genomics 21, 723.
Timmins-Schiffman, E., Guzman, J.M., Elliott Thompson, R., Vadopalas, B., Eudeline, B., and Roberts, S.B. (2020). Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2. Ecol Evol 10, 185-197.
Timmins-Schiffman, E., Guzman, J.M., Elliott Thompson, R., Vadopalas, B., Eudeline, B., and Roberts, S.B. (2020). Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates. Sci Rep 10, 6042.
2019
Mikan, M. P., Harvey, H. R., Timmins-Schiffman, E., Riffle, M., May, D. H., Salter, I., ... & Nunn, B. L. (2019). Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. The ISME journal, 1-14.
Glass, J., Blanchard, J., Ranjan, P., Kretz, C.B., Nunn, B.L., Johnson, A.M., McManus, J., and Stewart., F.J. (2019). Adaptations of Atribacteria to life in methane hydrates: hot traits for cold life. bioRxiv.
Junge, K., Cameron, K., and Nunn, B.L. (2019). Diversity of Psychrophilic Bacteria in Sea and Glacier Ice Environments—Insights Through Genomics, Metagenomics, and Proteomics Approaches. . In Microbial Diversity in the Genomic Era S. Das, and H.R. Dash, eds. (Academic Press), pp. 197-216.
Saito, M.A., Bertrand, E.M., Duffy, M.E., Gaylord, D.A., Held, N.A., Hervey, W.J., Hettich, R.L., Jagtap, P.D., Janech, M.G., Kinkade, D.B., et al. (2019). Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. Journal of Proteome Research 18, 1461-1476.
Spencer, L.H., Horwith, M., Lowe, A.T., Venkataraman, Y.R., Timmins-Schiffman, E., Nunn, B.L., and Roberts, S.B. (2019). Pacific geoduck (Panopea generosa) resilience to natural pH variation. Comp Biochem Physiol Part D Genomics Proteomics 30, 91-101.
Szeinbaum, N., Nunn, B.L., Cavazos, A.R., Crowe, S.A., Stewart, F.J., DiChristina, T.J., Reinhard, C.T., and Glass, J.B. (2019). Expression of extracellular multiheme cytochromes discovered in a betaproteobacterium during Mn (III) reduction. bioRxiv.
Tisthammer, K.H., Nunn, B.L., F.O., S., Timmins-Schiffman, E., and Richmond, R.H. (2019). Physiological and Molecular Responses Suggest Local Adaptation of the Lobe Coral Porites lobata to the Nearshore Environment. biorRxiv.
Venkataraman, Y.R., Timmins-Schiffman, E., Horwith, M.J., Lowe, A.T., Nunn, B., Vadopalas, B., Spencer, L.H., and Roberts, S.B. (2019). Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences. Mar Ecol Prog Ser 610, 65-81.
2018
Junge, K.; Cameron, K.; Nunn, B.L. (2018) Diversity of Psychrophilic Bacteria in Sea and Glacier Ice Environments—Insights Through Genomics, Metagenomics, and Proteomics Approaches. Microbial Diversity in the Genomic Era. Ch.12; pp. 197-216
Riffle, M.; May, D.H.; Timmins-Schiffman, E.; Mikan, M.P.; Jaschob, D.; Noble, W.S.; Nunn, B.L. (2018) MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. Proteomes, 6, 2.
Blank, C., Easterly, C., Gruening, B., Johnson, J., Kolmeder, C.A., Kumar, P., May, D., Mehta, S., Mesuere, B., Brown, Z. and Elias, J.E., Hervey, J.E., McGowan, T, Muth, T., Nunn, B.L., Rudney, J., Tanca, A., Griffin T.J. and Jagtap, P.D. 2018. Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Proteomes, 6(1), p.7.
Marie-Caroline Smith, Emma Timmins-Schiffman, Monika Coton, Emmanuel Coton, Nolwenn Hymery, Brook L. Nunn, Stéphanie Madec. (2018) Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome, Journal of Proteomics, 173, pp 89-98.
Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL (2018) MS analysis of a dilution series of bacteria:phytoplankton to develop assays to detect bacteria in unfractionated POM. Scientific Reports, 8(1), 9276.
2017
Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation. Journal of Proteome Research, 16(9), pp 3298-3309.
Pino LK, Searle BC, Bollinger JG, Nunn BL, MacLean B, MacCoss MJ. (2017) The Skyline Ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrometry Reviews, epub before print.
Nunn, S., Chappell, P.D., Bonderenko, A., Jenkins, B., Nunn, B.L., (2017). Phytoplankton plastid proteomics: Cracking open diatoms to understand plastid biochemistry under iron limitation. Journal of Emerging Investigators 2, pp 1-8.
2016
Timmins-Schiffman, E., May, D.H., Mikan, M., Riffle, M., Frazar, C., Harvey, H.R., Noble, W.S., Nunn, B.L. (2016) Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. The ISME Journal doi: 10.1038/ismej.2016.132
May, D.H., Timmins-Schiffman, E., Mikan, M.P., Harvey, H.R., Borenstein, E., Nunn, B.L., Noble, W.S. (2016) An alignment-free "metapeptide" strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research 15, 2697-2705.
Boyd, P.W., Dillingham, P.W., McGraw, C.M., Armstrong, E.A., Cornwall, C.E., Feng, Y.y., Hurd, C.L., Gault-Ringold, M., Roleda, M.Y., Timmins-Schiffman, E., Nunn, B.L. (2016). Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Nature Climate Change 6, 207-213.
2015
Nunn, B.L., Slattery, K.; Cameron, K.A.; Timmins-Schiffman, E.; Junge, K. (2015) Proteomics of Colwellia psychrerythraea at subzero temperatures - a life with limited movement, flexible membranes and vital DNA repair. Environmental Microbiology. 111, 9009-9014.
Bridoux, M.C., Neibauer, J., Ingalls, A., Nunn, B.L., Keil, R.G., (2015). Suspended marine particulate proteins in coastal and oligotrophic waters. Journal of Marine Systems 143, 39-48.
2014
Poulson-Ellestad, K.L., Jones, C.M., Roy, J., Viant, M.R., Fernandez, F.M., Kubanek, J., and Nunn, B.L. 2014. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. Proc Natl Acad Sci U S A 111, 9009-9014.
Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH and Roberts SB. 2014. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. BMC Genomics 2014, 15:951 doi:10.1186/1471-2164-15-951
Moore EK, Harvey HR, Faux JF, Goodlett DR, Nunn BL. 2014. Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments. Chromatography. 1(4):176-193.
Moore, E.K., Faux, J., Goodlett, D.R., Harvey, H.R., and Nunn, B.L. 2014. Protein recycling in Bering Sea algal incubations. Marine Ecology Progress Series. 515:45-59.
2013
Nunn BL, Faux JF, Hippman AA, Maldonado MT, Harvey HR, Goodlett DR, Boyd PW, Strzepek RF. 2013. Diatom proteomics reveals unique acclimation strategies to mitigate Fe limitation. PloS ONE.
Mattes TE, Nunn BL, Marshall KT, Proskurowski G, Kelley DS, Kawka OE, Goodlett DR, Hansell DA, Morris RM. 2013. Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean. ISME Journal.
Morris RM, Nunn BL. 2013. Sample preparation and processing for planktonic microbial community proteomics. Methods in Enzymology 531:271-287.
Timmins-Schiffman E, Nunn BL, Goodlett DR, Roberts SB. 2013. Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. Conservation Physiology 1:1-9.
2012
Moore EK, Nunn BL, Goodlett DR, Harvey HR. 2012. Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments. Geochimica et Cosmochimica Acta 83:324-359.
Moore EK, Nunn BL, Goodlett DR, Harvey HR. 2012. Tracking proteins from the water column to the sediment in the Bering Sea using proteomics. Geochemica et Cosmochimica Acta 83:324-359.
Moore EK, Nunn BL, Faux JF, Goodlett DR, Harvey HR. 2012. Evaluation of electrophoretic protein extraction and database-driven protein identification from marine sediments. Limnology and Oceanography Methods 10:353-366.
2011
Velasquez I, Nunn BL, Ibisanmi E, Goodlett D, Hunter K, Sander S. 2011. Detection of hydroxamate siderophores in Neritic and Sub-Antarctic waters off the South Eastern Coast of New Zealand. Marine Chemistry 126:97-107.
2010
Nunn BL, Ting YS, Malmstroem L, Tsai YS, Squier A, Goodlett DR, Harvey HR. 2010. The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation. Limnology and Oceanography 55:1790-1804.
Morris RM, Nunn BL, Frazar C, Goodlett DR, Ting YS, Rocap G. 2010. Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME Journal 4:673-685.
McMillan DG, Velasquez I, Nunn BL, Goodlett DR, Hunter KA, Lamont I, Sander SG, Cook GM. 2010. Acquisition of Iron by Alkaliphilic Bacillus species Growing at Extreme pH. Applied and Environmental Microbiology 76:6955-6961.
2009
Nunn BL, Aker JR, Shaffer SA, Tsai YH, Strzepek RF, Boyd PW, Freeman TL, Brittnacher M, Malmstrom L, Goodlett DR. 2009. Deciphering diatom biochemical pathways via whole-cell proteomics. Aquatic Microbial Ecology 55:241-253.
Hengel SM, Shaffer SA, Nunn BL, Goodlett DR. 2009. Tandem mass spectrometry investigation of ADP-ribosylated kemptide. J Am Soc Mass Spectrom 20:477-483.
2007
Nunn BL, Timperman AT. 2007. Marine Proteomics. Marine Ecology Progress Series 332:281-289.
2006
Nunn BL, Shaffer SA, Scherl A, Gallis B, Wu M, Miller SI, Goodlett DR. 2006. Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO. Briefings in Functional Genomics and Proteomics 5:154-168.
Nunn BL, Keil RG. 2006. A comparison of non-hydrolytic methods for extracting amino acids and proteins from coastal marine sediments. Marine Chemistry 98:31-42.
2005
Nunn BL, Keil RG. 2005. Size distribution and chemistry of proteins in Washington coast sediments. Biogeochemistry 75:177-200.
2001
Holcombe B, Keil RG, Devol A. 2001. Determination of Pore water dissolved organic carbon fluxes from Mexican margin sediments. Limnology and Oceanography 46:298-308.
Ni, Z., Arevalo Jr, R., Bardyn, A., Willhite, L., Ray, S., Southard, A., ... & Nunn, B. L. (2023). Detection of Short Peptides as Putative Biosignatures of Psychrophiles via Laser Desorption Mass Spectrometry. Astrobiology, 23(6), 657-669.
Gomes, K. M., Nunn, B. L., Chappell, P. D., & Jenkins, B. D. (2023). Subcellular proteomics for determining iron‐limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta). Journal of Phycology, 59(5), 1085-1099.
Jaffe, M. D., Padilla-Gamino, J. L., Nunn, B. L., & Rodrigues, L. J. Coral trophic pathways impact the allocation of carbon and nitrogen for egg development after bleaching. Frontiers in Ecology and Evolution, 11, 1251220.
2022
Amy Maas, Emma Timmins-Schiffman, Ann Tarrant, et al. Diel metabolic tuning revealed by in situ transcriptome and proteome in a vertically migratory copepod. Authorea. August 09, 2022.
Axworthy JB, Timmins-Schiffman E, Brown T, Rodrigues LJ, Nunn BL and Padilla-Gamiño JL (2022) Shotgun Proteomics Identifies Active Metabolic Pathways in Bleached Coral Tissue and Intraskeletal Compartments. Front. Mar. Sci. 9:797517.
Boyd, P.W., Doney, S.C., Eggins, S., Ellwood, M.J., Fourquez, M., Nunn, B.L., Strzepek, R. and Timmins-Schiffman, E. (2022), Transitioning global change experiments on Southern Ocean phytoplankton from lab to field settings: Insights and challenges. Limnol Oceanogr, 67: 1911-1930.
Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158
Robert F Strzepek, Brook L Nunn, Lennart T Bach, John A Berges, Erica B Young, Philip W Boyd, The ongoing need for rates: can physiology and omics come together to co-design the measurements needed to understand complex ocean biogeochemistry?, Journal of Plankton Research, Volume 44, Issue 4, July/August 2022, Pages 485–495.
Timmins-Schiffman, Emma and Maas, Amy and Khanna, Rayhan and Blanco-Bercial, Leo and Huang, Eric and Nunn, Brook, Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod.
2021
Glass, J.B., Ranjan, P., Kretz, C.B., Nunn, B.L., Johnson, A.M., Xu, M., McManus, J. and Stewart, F.J., (2021). Microbial metabolism and adaptations in Atribacteria‐dominated methane hydrate sediments. Environmental Microbiology.
Mehta, S., Kumar, P., Crane, M., Johnson, J. E., Sajulga, R., Nguyen, D. D. A., ... & Jagtap, P. D. (2021). Updates on metaQuantome Software for Quantitative Metaproteomics. Journal of Proteome Research, 20(4), 2130-2137.
Mudge, M. C., Nunn, B. L., Firth, E., Ewert, M., Hales, K., Fondrie, W. E., ... & Junge, K. A. (2021). Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. Environmental Microbiology.
Petrou, K., Nunn, B.L., Padula, M.P. et al. Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora. Sci Rep 11, 19061 (2021).
Pollara, S.B., Becker, J.W., Nunn, B.L., Boiteau, R., Repeta, D., Mudge, M.C., Downing, G., Chase, D., Harvey, E.L. and Whalen, K.E., (2021). Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality. Msphere, 6(3), pp.e00009-21.
Sajulga, R., Easterly, C., Riffle, M., Mesuere, B., Muth, T., Mehta, S., Kumar, P., Johnson, J., Gruening, B.A., Schiebenhoefer, H. and Kolmeder, C.A., 2020. Survey of metaproteomics software tools for functional microbiome analysis. PloS one, 15(11), p.e0241503.
Timmins-Schiffman, E., White, S. J., Thompson, R. E., Vadopalas, B., Eudeline, B., Nunn, B. L., & Roberts, S. B. (2021). Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Environmental Microbiome, 16(1), 1-12.
Tisthammer, K. H., Timmins-Schiffman, E., Seneca, F. O., Nunn, B. L., & Richmond, R. H. (2021). Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors. Scientific reports, 11(1), 1-11.
2020
Johnson, R.S., Searle, B.C., Nunn, B.L., Gilmore, J.M., Phillips, M., Amemiya, C.T., Heck, M., and MacCoss, M.J. (2020). Assessing Protein Sequence Database Suitability Using De Novo Sequencing. Mol Cell Proteomics 19, 198-208.
Szeinbaum, N., Nunn, B.L., Cavazos, A.R., Crowe, S.A., Stewart, F.J., DiChristina, T.J., Reinhard, C.T., and Glass, J.B. (2020). Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction. Environmental microbiology reports.
Kumar, P., Johnson, J.E., Easterly, C., Mehta, S., Sajulga, R., Nunn, B., Jagtap, P.D., and Griffin, T.J. (2020). A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases. J Proteome Res 19, 2772-2785.pubs.acs.org/doi/10.1021/acs.jproteome.0c00260
Trigg, S.A., Mitchell, K.R., Thompson, R.E., Eudeline, B., Vadopalas, B., Timmins-Schiffman, E.B., and Roberts, S.B. (2020). Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc. BMC Genomics 21, 723.
Timmins-Schiffman, E., Guzman, J.M., Elliott Thompson, R., Vadopalas, B., Eudeline, B., and Roberts, S.B. (2020). Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2. Ecol Evol 10, 185-197.
Timmins-Schiffman, E., Guzman, J.M., Elliott Thompson, R., Vadopalas, B., Eudeline, B., and Roberts, S.B. (2020). Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates. Sci Rep 10, 6042.
2019
Mikan, M. P., Harvey, H. R., Timmins-Schiffman, E., Riffle, M., May, D. H., Salter, I., ... & Nunn, B. L. (2019). Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. The ISME journal, 1-14.
Glass, J., Blanchard, J., Ranjan, P., Kretz, C.B., Nunn, B.L., Johnson, A.M., McManus, J., and Stewart., F.J. (2019). Adaptations of Atribacteria to life in methane hydrates: hot traits for cold life. bioRxiv.
Junge, K., Cameron, K., and Nunn, B.L. (2019). Diversity of Psychrophilic Bacteria in Sea and Glacier Ice Environments—Insights Through Genomics, Metagenomics, and Proteomics Approaches. . In Microbial Diversity in the Genomic Era S. Das, and H.R. Dash, eds. (Academic Press), pp. 197-216.
Saito, M.A., Bertrand, E.M., Duffy, M.E., Gaylord, D.A., Held, N.A., Hervey, W.J., Hettich, R.L., Jagtap, P.D., Janech, M.G., Kinkade, D.B., et al. (2019). Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. Journal of Proteome Research 18, 1461-1476.
Spencer, L.H., Horwith, M., Lowe, A.T., Venkataraman, Y.R., Timmins-Schiffman, E., Nunn, B.L., and Roberts, S.B. (2019). Pacific geoduck (Panopea generosa) resilience to natural pH variation. Comp Biochem Physiol Part D Genomics Proteomics 30, 91-101.
Szeinbaum, N., Nunn, B.L., Cavazos, A.R., Crowe, S.A., Stewart, F.J., DiChristina, T.J., Reinhard, C.T., and Glass, J.B. (2019). Expression of extracellular multiheme cytochromes discovered in a betaproteobacterium during Mn (III) reduction. bioRxiv.
Tisthammer, K.H., Nunn, B.L., F.O., S., Timmins-Schiffman, E., and Richmond, R.H. (2019). Physiological and Molecular Responses Suggest Local Adaptation of the Lobe Coral Porites lobata to the Nearshore Environment. biorRxiv.
Venkataraman, Y.R., Timmins-Schiffman, E., Horwith, M.J., Lowe, A.T., Nunn, B., Vadopalas, B., Spencer, L.H., and Roberts, S.B. (2019). Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences. Mar Ecol Prog Ser 610, 65-81.
2018
Junge, K.; Cameron, K.; Nunn, B.L. (2018) Diversity of Psychrophilic Bacteria in Sea and Glacier Ice Environments—Insights Through Genomics, Metagenomics, and Proteomics Approaches. Microbial Diversity in the Genomic Era. Ch.12; pp. 197-216
Riffle, M.; May, D.H.; Timmins-Schiffman, E.; Mikan, M.P.; Jaschob, D.; Noble, W.S.; Nunn, B.L. (2018) MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. Proteomes, 6, 2.
Blank, C., Easterly, C., Gruening, B., Johnson, J., Kolmeder, C.A., Kumar, P., May, D., Mehta, S., Mesuere, B., Brown, Z. and Elias, J.E., Hervey, J.E., McGowan, T, Muth, T., Nunn, B.L., Rudney, J., Tanca, A., Griffin T.J. and Jagtap, P.D. 2018. Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Proteomes, 6(1), p.7.
Marie-Caroline Smith, Emma Timmins-Schiffman, Monika Coton, Emmanuel Coton, Nolwenn Hymery, Brook L. Nunn, Stéphanie Madec. (2018) Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome, Journal of Proteomics, 173, pp 89-98.
Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL (2018) MS analysis of a dilution series of bacteria:phytoplankton to develop assays to detect bacteria in unfractionated POM. Scientific Reports, 8(1), 9276.
2017
Timmins-Schiffman E, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SR (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation. Journal of Proteome Research, 16(9), pp 3298-3309.
Pino LK, Searle BC, Bollinger JG, Nunn BL, MacLean B, MacCoss MJ. (2017) The Skyline Ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrometry Reviews, epub before print.
Nunn, S., Chappell, P.D., Bonderenko, A., Jenkins, B., Nunn, B.L., (2017). Phytoplankton plastid proteomics: Cracking open diatoms to understand plastid biochemistry under iron limitation. Journal of Emerging Investigators 2, pp 1-8.
2016
Timmins-Schiffman, E., May, D.H., Mikan, M., Riffle, M., Frazar, C., Harvey, H.R., Noble, W.S., Nunn, B.L. (2016) Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. The ISME Journal doi: 10.1038/ismej.2016.132
May, D.H., Timmins-Schiffman, E., Mikan, M.P., Harvey, H.R., Borenstein, E., Nunn, B.L., Noble, W.S. (2016) An alignment-free "metapeptide" strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research 15, 2697-2705.
Boyd, P.W., Dillingham, P.W., McGraw, C.M., Armstrong, E.A., Cornwall, C.E., Feng, Y.y., Hurd, C.L., Gault-Ringold, M., Roleda, M.Y., Timmins-Schiffman, E., Nunn, B.L. (2016). Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Nature Climate Change 6, 207-213.
2015
Nunn, B.L., Slattery, K.; Cameron, K.A.; Timmins-Schiffman, E.; Junge, K. (2015) Proteomics of Colwellia psychrerythraea at subzero temperatures - a life with limited movement, flexible membranes and vital DNA repair. Environmental Microbiology. 111, 9009-9014.
Bridoux, M.C., Neibauer, J., Ingalls, A., Nunn, B.L., Keil, R.G., (2015). Suspended marine particulate proteins in coastal and oligotrophic waters. Journal of Marine Systems 143, 39-48.
2014
Poulson-Ellestad, K.L., Jones, C.M., Roy, J., Viant, M.R., Fernandez, F.M., Kubanek, J., and Nunn, B.L. 2014. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. Proc Natl Acad Sci U S A 111, 9009-9014.
Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH and Roberts SB. 2014. Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. BMC Genomics 2014, 15:951 doi:10.1186/1471-2164-15-951
Moore EK, Harvey HR, Faux JF, Goodlett DR, Nunn BL. 2014. Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments. Chromatography. 1(4):176-193.
Moore, E.K., Faux, J., Goodlett, D.R., Harvey, H.R., and Nunn, B.L. 2014. Protein recycling in Bering Sea algal incubations. Marine Ecology Progress Series. 515:45-59.
2013
Nunn BL, Faux JF, Hippman AA, Maldonado MT, Harvey HR, Goodlett DR, Boyd PW, Strzepek RF. 2013. Diatom proteomics reveals unique acclimation strategies to mitigate Fe limitation. PloS ONE.
Mattes TE, Nunn BL, Marshall KT, Proskurowski G, Kelley DS, Kawka OE, Goodlett DR, Hansell DA, Morris RM. 2013. Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean. ISME Journal.
Morris RM, Nunn BL. 2013. Sample preparation and processing for planktonic microbial community proteomics. Methods in Enzymology 531:271-287.
Timmins-Schiffman E, Nunn BL, Goodlett DR, Roberts SB. 2013. Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. Conservation Physiology 1:1-9.
2012
Moore EK, Nunn BL, Goodlett DR, Harvey HR. 2012. Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments. Geochimica et Cosmochimica Acta 83:324-359.
Moore EK, Nunn BL, Goodlett DR, Harvey HR. 2012. Tracking proteins from the water column to the sediment in the Bering Sea using proteomics. Geochemica et Cosmochimica Acta 83:324-359.
Moore EK, Nunn BL, Faux JF, Goodlett DR, Harvey HR. 2012. Evaluation of electrophoretic protein extraction and database-driven protein identification from marine sediments. Limnology and Oceanography Methods 10:353-366.
2011
Velasquez I, Nunn BL, Ibisanmi E, Goodlett D, Hunter K, Sander S. 2011. Detection of hydroxamate siderophores in Neritic and Sub-Antarctic waters off the South Eastern Coast of New Zealand. Marine Chemistry 126:97-107.
2010
Nunn BL, Ting YS, Malmstroem L, Tsai YS, Squier A, Goodlett DR, Harvey HR. 2010. The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation. Limnology and Oceanography 55:1790-1804.
Morris RM, Nunn BL, Frazar C, Goodlett DR, Ting YS, Rocap G. 2010. Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME Journal 4:673-685.
McMillan DG, Velasquez I, Nunn BL, Goodlett DR, Hunter KA, Lamont I, Sander SG, Cook GM. 2010. Acquisition of Iron by Alkaliphilic Bacillus species Growing at Extreme pH. Applied and Environmental Microbiology 76:6955-6961.
2009
Nunn BL, Aker JR, Shaffer SA, Tsai YH, Strzepek RF, Boyd PW, Freeman TL, Brittnacher M, Malmstrom L, Goodlett DR. 2009. Deciphering diatom biochemical pathways via whole-cell proteomics. Aquatic Microbial Ecology 55:241-253.
Hengel SM, Shaffer SA, Nunn BL, Goodlett DR. 2009. Tandem mass spectrometry investigation of ADP-ribosylated kemptide. J Am Soc Mass Spectrom 20:477-483.
2007
Nunn BL, Timperman AT. 2007. Marine Proteomics. Marine Ecology Progress Series 332:281-289.
2006
Nunn BL, Shaffer SA, Scherl A, Gallis B, Wu M, Miller SI, Goodlett DR. 2006. Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO. Briefings in Functional Genomics and Proteomics 5:154-168.
Nunn BL, Keil RG. 2006. A comparison of non-hydrolytic methods for extracting amino acids and proteins from coastal marine sediments. Marine Chemistry 98:31-42.
2005
Nunn BL, Keil RG. 2005. Size distribution and chemistry of proteins in Washington coast sediments. Biogeochemistry 75:177-200.
2001
Holcombe B, Keil RG, Devol A. 2001. Determination of Pore water dissolved organic carbon fluxes from Mexican margin sediments. Limnology and Oceanography 46:298-308.