2022
Timmins-Schiffman E, Maas A, Khanna R, Blanco-Bercial L, Huang E, Nunn B. Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod. preprint available
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. doi: 10.7717/peerj.14158
Maas A, Timmins-Schiffman E, Tarrant A, Nunn B, Park J, Blanco-Bercial L. submitted to Molecular Ecology. Diel metabolic tuning revealed by in situ transcriptome and proteome in a vertically migrating copepod. preprint available
Axworthy JB, Timmins-Schiffman E, Brown T, Rodrigues LJ, Nunn BL, Padilla-Gamino JL (2022). Shotgun proteomics identifies active metabolic pathways in bleached coral tissue and intraskeletal compartments. Frontiers in Marine Science DOI:10.3389/fmars.2022.797517
Boyd PB, Doney SC, Eggins S, Ellwood MJ, Fourquez M, Nunn BL, Strzepek R, Timmins-Schiffman E (2022) Transitioning global change experiments on Southern Ocean phytoplankton from lab to field settings: Insights and challenges. Limnology & Oceanography doi.org/10.1002/lno.12175
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. doi: 10.7717/peerj.14158
Maas A, Timmins-Schiffman E, Tarrant A, Nunn B, Park J, Blanco-Bercial L. submitted to Molecular Ecology. Diel metabolic tuning revealed by in situ transcriptome and proteome in a vertically migrating copepod. preprint available
Axworthy JB, Timmins-Schiffman E, Brown T, Rodrigues LJ, Nunn BL, Padilla-Gamino JL (2022). Shotgun proteomics identifies active metabolic pathways in bleached coral tissue and intraskeletal compartments. Frontiers in Marine Science DOI:10.3389/fmars.2022.797517
Boyd PB, Doney SC, Eggins S, Ellwood MJ, Fourquez M, Nunn BL, Strzepek R, Timmins-Schiffman E (2022) Transitioning global change experiments on Southern Ocean phytoplankton from lab to field settings: Insights and challenges. Limnology & Oceanography doi.org/10.1002/lno.12175
2021
Tisthammer KH, Timmins-Schiffman E, Seneca FO, Nunn BL, Richmond RH (2021). Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors. Scientific Reports 11: 3423.
Timmins-Schiffman E, White SJ, Elliott Thompson R, Vadopalas B, Eudeline B, Nunn BL, Roberts SB (2021) Coupled Microbiome Analyses Highlights Relative Functional Roles of Bacteria in a Bivalve Hatchery. Environmental Microbiome 16: 7
Timmins-Schiffman E, White SJ, Elliott Thompson R, Vadopalas B, Eudeline B, Nunn BL, Roberts SB (2021) Coupled Microbiome Analyses Highlights Relative Functional Roles of Bacteria in a Bivalve Hatchery. Environmental Microbiome 16: 7
2020
Trigg SA, Mitchell KR, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman EB, Roberts SR (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, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB (2020) Larval geoduck (Panopea generosa) proteomic response to ciliates. Scientific Reports 10:6042
Timmins-Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB (2020) Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2. Ecology and Evolution 10 (1): 185-197.
Timmins-Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB (2020) Larval geoduck (Panopea generosa) proteomic response to ciliates. Scientific Reports 10:6042
Timmins-Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB (2020) Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2. Ecology and Evolution 10 (1): 185-197.
2019
Krayushkina D, Timmins-Schiffman E, Faux J, May DH, Riffle M, Harvey R, Nunn BL (2019) Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi. Scientific Data 6: 303.
Mikan MP, Harvey HR, Timmins-Schiffman E, Riffle M, May DH, Salter I, Noble WS, Nunn BL (2019) Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. The ISME Journal doi: 10.1038/s41396-019-0503-z
Mikan MP, Harvey HR, Timmins-Schiffman E, Riffle M, May DH, Salter I, Noble WS, Nunn BL (2019) Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. The ISME Journal doi: 10.1038/s41396-019-0503-z
2018
Venkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB (2018) Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differences. Marine Ecology Progress Series 610 doi: 10.3354/meps12858
Spencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB (2018) Pacific geoduck (Panopea generosa) resilience to natural pH variation. Comparative Biochemistry and Physiology - Part D
Maas AE, Blanco-Bercial L, Lo A, Tarrant AM, Timmins-Schiffman E (2018) Variations in copepod proteome and respiration rate in association with diel vertical migration and circadian cycle. Biological Bulletin 235
Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL (2018) MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides. Scientific Reports doi:10.1038/s41598-018-27650-4
Smith M-C, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S (2018) Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome. Journal of Proteomics doi: doi.org/10.1016/j.jprot.2017.11.025
Spencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB (2018) Pacific geoduck (Panopea generosa) resilience to natural pH variation. Comparative Biochemistry and Physiology - Part D
Maas AE, Blanco-Bercial L, Lo A, Tarrant AM, Timmins-Schiffman E (2018) Variations in copepod proteome and respiration rate in association with diel vertical migration and circadian cycle. Biological Bulletin 235
Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL (2018) MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides. Scientific Reports doi:10.1038/s41598-018-27650-4
Smith M-C, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S (2018) Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome. Journal of Proteomics doi: doi.org/10.1016/j.jprot.2017.11.025
2017
Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jachob D, Noble WS, Nunn Bl (2017) MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. Proteomes. doi: 10.3390/proteomes6010002
Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation. Journal of Proteome Research. doi: 10.1021/acs.jproteome.7b00288
Waples RS, Elz A, Arnsberg BD, Faulkner JR, Hard JR, Timmins-Schiffman E, Park LK (2017) Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon. Evolutionary Applications. doi: 10.1111/eva.12468
Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation. Journal of Proteome Research. doi: 10.1021/acs.jproteome.7b00288
Waples RS, Elz A, Arnsberg BD, Faulkner JR, Hard JR, Timmins-Schiffman E, Park LK (2017) Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon. Evolutionary Applications. doi: 10.1111/eva.12468
2016
Timmins-Schiffman E, May DH, Mikan M, Riffle M, Frazar C, Harvey HR, Noble WS, Nunn BL (2016) Critical decision in metaproteomics: Achieving high confidence protein annotations in a sea of unknowns. ISME Journal. doi: 10.1038/ismej.2016.132
May DH, Timmins-Schiffman E, Mikan MP, Harvey HR, Borenstein E, Nunn BL, Noble WS (2016) An alignment-free “metapeptide” strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research, DOI: 10.1021/acs.jproteome.6b00239
Boyd PW, Armstrong E, Cornwall C, Dillingham P, Ringold-Gault M, Feng Y-Y, Hurd CL, McGraw C, Roleda MY, Nunn BL, Timmins-Schiffman E (2016) Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Nature Climate Change. doi:10.1038/nclimate2811
May DH, Timmins-Schiffman E, Mikan MP, Harvey HR, Borenstein E, Nunn BL, Noble WS (2016) An alignment-free “metapeptide” strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research, DOI: 10.1021/acs.jproteome.6b00239
Boyd PW, Armstrong E, Cornwall C, Dillingham P, Ringold-Gault M, Feng Y-Y, Hurd CL, McGraw C, Roleda MY, Nunn BL, Timmins-Schiffman E (2016) Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Nature Climate Change. doi:10.1038/nclimate2811
2015
Nunn BL, Slattery KV, Cameron KA, 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. DOI: 10.1111/1462-2920.12691
2014
Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH, Roberts SR (2014) Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. BMC Genomics, 15: 951, DOI: 10.1186/1471-2164-15-951
Winans G, Gayeski N, Timmins-Schiffman E (2014) All dam-affected trout populations are not alike: fine scale geographic variability in resident rainbow trout in Icicle Creek, WA, USA. Conservation Genetics. DOI: 10.1007/s10592-014-0659-z
Winans G, Gayeski N, Timmins-Schiffman E (2014) All dam-affected trout populations are not alike: fine scale geographic variability in resident rainbow trout in Icicle Creek, WA, USA. Conservation Genetics. DOI: 10.1007/s10592-014-0659-z
2013
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): DOI 10.1093/conphys/cot009
Timmins-Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB (2013) Genomic resource development for shellfish of conservation concern. Molecular Ecology Resources, 13(2): 295-305. DOI: 10.1111/1755-0998.12052
Timmins-Schiffman E, O’Donnell MJ, Friedman CS, Roberts SB. (2013) Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas. Marine Biology, 160: 1973-1982. DOI 10.1007/s00227-012-2055-x
Timmins-Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB (2013) Genomic resource development for shellfish of conservation concern. Molecular Ecology Resources, 13(2): 295-305. DOI: 10.1111/1755-0998.12052
Timmins-Schiffman E, O’Donnell MJ, Friedman CS, Roberts SB. (2013) Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas. Marine Biology, 160: 1973-1982. DOI 10.1007/s00227-012-2055-x
2012
Timmins-Schiffman E, Roberts SB. (2012) Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas). BMC Research Notes, 5:502. DOI 10.1186/1756-0500-5-502
