Emma Timmins-Schiffman
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Publications

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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

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

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.
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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
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
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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

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

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

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

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
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