publications.qmd

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title: "Publications"
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# Papers

Papers can be searched by sorting and/or using filter function. Filter function works on author and title. Recent papers can also be identified by categories

*see also*: [Google Scholar](https://scholar.google.com/citations?hl=en&user=aAoYWVUAAAAJ&view_op=list_works&sortby=pubdate)

::: {#articles}
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# Podcast

<iframe allow="autoplay *; encrypted-media *; fullscreen *; clipboard-write" frameborder="0" height="450" style="width:100%;max-width:660px;overflow:hidden;border-radius:10px;" sandbox="allow-forms allow-popups allow-same-origin allow-scripts allow-storage-access-by-user-activation allow-top-navigation-by-user-activation" src="https://embed.podcasts.apple.com/us/podcast/gene-pooling/id1802677296">

</iframe>

# Book Chapters

Moreira Sanmartín R, Roberts SB, Figueras A. (2016) [Molluscs. pages 223-245, in Genomics in Aquaculture](http://www.sciencedirect.com/science/book/9780128014189). Editors: Simon A. MacKenzie and Sissel Jentoft. ISBN: 978-0-12-801418-9

Gavery, M., & Roberts, S. (2018). [Genetics & Epigenetics in Life History and Reproduction: Oysters](http://dx.doi.org/10.1016/B978-0-12-809633-8.20621-3). In M. K. Skinner (Ed.), Encyclopedia of Reproduction. vol. 6, pp. 736--742. Academic Press: Elsevier. doi: 10.1016/B978-0-12-809633-8.20621-3 [pdf](http://eagle.fish.washington.edu/whale/pub/C20621.pdf)

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# Preprints

Huffmyer AS, Strand EL, Hackerott S, Wong KH, Becker DM, Conetta D, Terpis KX, Pfab F, Wong JM, Dellaert Z, Oliaro FJ, Cunning R, Eirin-Lopez JM, Roberts SB, Nisbet RM, Putnam HM. Seasonal plasticity of symbiotic strategies clarifies coral holobiont resistance and resilience. **bioRxiv**. https://doi.org/10.1101/2025.11.20.689604

Huffmyer AS, N Ozguner, M Baird, C Elvrum, C Kounellas, D Dicksion, SJ White, L Plough, MR Gavery, N Krebs, W Walton, J Small, M Pitsenbarger, H Ealy-Whitfield, S Roberts. From blue to pink: Resazurin as a high-throughput proxy for metabolic rate in oysters. **bioRxiv**. http://doi.org/10.1101/2025.11.06.686367.

Ashey J, JA Rodriquez-Casariego, KM Durkin, Z Bengtsson, AS Huffmyer, SJ White, DM Becker, JM Eirin-Lopez, HM Putnam, S Roberts. Non-coding RNA repertoire in reef-building corals. bioRxiv. https://doi.org/10.1101/2025.03.15.643469.

Shelly A Wanamaker , Kaitlyn R Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B Timmins-Schiffman, Steven B Roberts (2020). Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc. **bioRxiv**. https://doi.org/10.1101/2020.06.05.137059

Emma B. Timmins-Schiffman, Grace A. Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn, Steven B. Roberts (2016) Integrating proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation. **bioRxiv** https://doi.org/10.1101/094615

Heare JE, White SJ, Roberts SB. (2015) Differential response to stress in *Ostrea lurida* (Carpenter 1864) as measured by gene expression. PeerJ PrePrints 3:e1595v1 <https://doi.org/10.7287/peerj.preprints.1595v1>

Gavery MR, Delrow J, Basom R, Roberts SB. (2015) Influence of 17α-ethinylestradiol on DNA Methylation in Oysters. **GitHub / Zenodo** <https://github.com/sr320/paper-Oyster-EE2>

Heare JE, Blake B, Davis JP, Vadopalas B, Roberts SB. (2014) Evidence of Ostrea lurida (Carpenter 1894) population structure in Puget Sound, WA. **PeerJ PrePrints** 2:e704v1 https://doi.org/10.7287/peerj.preprints.704v1

Claire E. Olson, Steven B. Roberts. Indication of family-specific DNA methylation patterns in developing oysters **bioRxiv** https://doi.org/10.1101/012831

Roberts *et al.* Sequence Data that never made it. <https://www.authorea.com/users/3858/articles/3989/_show_article>

David C. Metzger, Paul McElhany, Shallin Busch, Carolyn S. Friedman, Steven B. Roberts (**preprint**) Underlying impact of ocean acidification on Manila clam (*Ruditapes philippinarum*) larvae revealed through RNA-Seq analysis. Status: [Available for Comment](https://docs.google.com/document/d/1Ii1lODz2oThiyxZtHBblUEdzyhIVq92n8jkEjhkuuts/edit) peer reviews: BMC, MB

David C. Metzger, Carolyn S. Friedman, Emma B. Timmins-Schiffman and Steven B. Roberts (**preprint**) Thermal tolerance and gene expression characterization in Manila clams (*Ruditapes philippinarum*) exposed to elevated carbon dioxide. Status: [Available for Comment](https://docs.google.com/document/d/1xbVdGEOeRfJH36aT9vyf4gZh3Fk4jLPCB-wYjD7QQWI/edit) peer reviews: AB

Storer C, Goetz F, Roberts S. (**preprint**) Transcriptional variation in lake trout (*Salvelinus namaycush*) ecotypes raised under constant environmental conditions. Status: [Available for Comment](https://docs.google.com/document/d/11l7PpHWa_Xt1IiiRJvFrwKmnW_YFMfpXgLR3du_QZr8/edit)

Steven Roberts, Roxanna Smolowitz, Richard Karney, Mackenzie Gavery et al. (**preprint**) Disease tolerance in the eastern oyster. Status: [Available for Comment](https://docs.google.com/document/d/16DFIFQw_QhOh1TX979r9T6VV1CJ34HtWdpoUNzaTnhc/edit?usp=sharing)

Roberts et al. (**preprint**) Hard clam gene expression analysis. Status: [Available for Comment](https://docs.google.com/document/d/1Z0F3482O4itEumL2zNuroRrnQAs4cMhxUJ9cjZKzu8A/edit)

*Archived*

Dimond JL and Roberts SB (2015) Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change UW ResearchWorks Archive uri:<http://hdl.handle.net/1773/34298>

Mackenzie Gavery and Steven Roberts (**preprint**) A context specific role for DNA methylation in bivalves. Status: *Archived* [download](https://dl.dropboxusercontent.com/u/115356/Gavery_Roberts_context2013.pdf) (*Revised and later accepted at* [Briefings in Functional Genomics](https://10.1093/bfgp/elt054) 10.1093/bfgp/elt054

Emma Timmins-Schiffman, Carolyn Friedman, Steven Roberts, Sam White, Dave Metzger (**preprint**) Genomic resource development of shellfish of conservation concern. Status: [*on figshare*](http://dx.doi.org/10.6084/m9.figshare.97205) (*published* - Molecular Ecology Resources)

Timmins-Schiffman E, O'Donnell M, Friedman C, and Roberts S. (**preprint**) Elevated pCO2 causes developmental delay in early larval Pacific oysters, *Crassostrea gigas* Status: [*on figshare*](http://dx.doi.org/10.6084/m9.figshare.95828) (*published* - Marine Biology)

</p>

Lyons, Dungan, and Roberts -- <a href="http://faculty.washington.edu/sr320/wordpress/wp-content/uploads/2012/07/Thraustochtrid_Lyons.pdf">Thraustochytrid-like isolates from marine bivalve mollusks</a>

</p>

Smolowitz, Schaff, DeFaveri, Roberts - <a href="https://www.evernote.com/shard/s10/sh/fbad2028-32a9-4ed0-86e5-95c391748984/77f2df51a2d62815631c0850ab3a8467">Renal Trematodiasis of Largemouth Bass and Development of PCR Methods</a>

</p>

White SJ and Roberts S. (**preprint**) Identification of myostatin interacting proteins using a yeast-two hybrid approach. Status: <a href="https://docs.google.com/document/d/1HpDSM2ELJX3cxLsAy7vmmBuN1MnJVBYhcNIHfu52tZ0/edit">Available for Comment</a>

</p>

Gavery MR, White SJ, Roberts S (**preprint**) Characterization of prostaglandin endoperoxide synthase from the Pacific oyster, <em>Crassostrea gigas</em>. Status: <a href="https://docs.google.com/document/d/188LU32GF04gZIcLYce8tVsIJIcEW3em7HG0PvaOjBcs/edit" target="_blank">Available for Comment</a>

</p>

Thompson R and Roberts SB (**preprint**) Influence of carbon dioxide-induced acidification and mechanical stress on gene expression and microbial community composition in oysters. Status: <a href="https://docs.google.com/document/d/1jYvaWR4RsSonl95ElqNX29epsO69LE4af5Rgd4xC8EI/edit">Available for Comment</a>

</p>

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# Theses

Causes of Infection and Disease Progression of *Hematodinium sp*. in the Tanner crab, *Chionoecetes bairdi.* Aspen Coyle 2024. <https://hdl.handle.net/1773/52794>

Developing Tools and Resources for Maturation Control in Bivalvia. Olivia Cattau. 2023 <http://hdl.handle.net/1773/50826>

Patterns, dynamics, and potential roles of DNA methylation in reef corals and their allies. James Dimond. 2019 <http://hdl.handle.net/1773/44815>

Response of Olympia oysters (*Ostrea lurida*) to changing environmental conditions. Jake Heare. 2015 <http://hdl.handle.net/1773/35206>

Genomic signatures of natural selection and population structure in West Coast and Alaskan sablefish (*Anoplopoma fimbria*). Andrew Jasonowicz. 2014 <http://hdl.handle.net/1773/33907>

DNA methylation variation in gametes and larvae of the Pacific oyster, *Crassostrea gigas*. Claire Ellis Olson. 2014 <http://hdl.handle.net/1773/27478>

Epigenomic and transcriptomic regulation of environmental responses in the Pacific oyster, *Crassostrea gigas*. Mackenzie Gavery. 2014. <http://hdl.handle.net/1773/25984>

The Effects of Ocean Acidification on Multiple Life History Stages of the Pacific Oyster, *Crassostrea gigas*: Implications for Physiological Trade-offs. Emma Timmins-Schiffman. 2014. <http://hdl.handle.net/1773/25413>

Sablefish (*Anoplopoma fimbria*) sperm: The physiology of activation and the development of a cryopreservation protocol. Doug Immerman. 2014. <http://hdl.handle.net/1773/25414>

Genetic and phenotypic diversity in sockeye salmon, <em>Oncorhynchus nerka</em>. Caroline Storer. 2012. figshare. <a href="http://dx.doi.org/10.6084/m9.figshare.661720"> http://dx.doi.org/10.6084/m9.figshare.661720</a>

Characterizing the effects of ocean acidification in larval and juvenile Manila clam, <em>Ruditapes philippinarum</em>, using a transcriptomic approach. David Metzger. 2012 <a href="http://fish.washington.edu/research/publications/ms_phd/Metzger_D_MS_Sp12.pdf"> download</a>

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# Notebooks

| Person | Notebook | Commitment |
|------------------|-----------------------|--------------------------------|
| Steven Roberts | [sr320.github.io](https://sr320.github.io/tumbling-oysters/) | ![GitHub last commit](https://img.shields.io/github/last-commit/sr320/tumbling-oysters) |
| Sam White | [robertslab.github.io](https://robertslab.github.io/sams-notebook/) | ![GitHub last commit](https://img.shields.io/github/last-commit/RobertsLab/sams-notebook) |
| Matt George | [mattgeorgephd.github.io](https://mattgeorgephd.github.io/notebook/) | ![GitHub last commit](https://img.shields.io/github/last-commit/mattgeorgephd/mattgeorgephd.github.io) |
| Aspen Coyle | [aspencoyle.github.io](https://aspencoyle.github.io) | ![GitHub last commit](https://img.shields.io/github/last-commit/aspencoyle/aspencoyle.github.io) |
| Ariana Huffmyer | [ahuffmyer.github.io](https://ahuffmyer.github.io/ASH_Putnam_Lab_Notebook/) | ![GitHub last commit](https://img.shields.io/github/last-commit/AHuffmyer/ASH_Putnam_Lab_Notebook) |
| Chris Mantegna | [chrismantegna.github.io](https://chrismantegna.github.io/cmlabsite/) | ![GitHub last commit](https://img.shields.io/github/last-commit/ChrisMantegna/cmlabsite) |
| Zach Bengtsson | [zbengt.github.io](https://zbengt.github.io/notebook/) | ![GitHub last commit](https://img.shields.io/github/last-commit/zbengt/zbengt.github.io) |
| Celeste Valdivia | [valeste.github.io](https://valeste.github.io/tough-tunicates/) | ![GitHub last commit](https://img.shields.io/github/last-commit/valeste/tough-tunicates) |
| Grace Crandall | [grace-ac.github.io](https://grace-ac.github.io/) | ![GitHub last commit](https://img.shields.io/github/last-commit/grace-ac/grace-ac.github.io) |
| Kathleen Durkin | [shedurkin.github.io](https://shedurkin.github.io/Roberts-LabNotebook/) | ![GitHub last commit](https://img.shields.io/github/last-commit/shedurkin/Roberts-LabNotebook) |
| Megan Ewing | [mewing-notebook](https://meganewing.github.io/mewing-notebook/) | ![GitHub last commit](https://img.shields.io/github/last-commit/meganewing/mewing-notebook) |

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# Recent Presentations

#### 2026

-   [Sparse Tensor Decomposition and Elastic Net Regression for Multi-Species Gene Expression Analysis](https://github.com/sr320/talk-escience-2026) University of Washington eScience Institute Seminar Series. Seattle, WA. March 2026. Steven Roberts & Kathleen Durkin.

-   [Environmental Memory: The Missing State Variable in Marine Biology](https://github.com/sr320/talk-UNCW-2026) UNCW Biology Seminar Series. Wilmington, NC. March 2026. Steven Roberts.

-   [Shellfish Environmental Memory — Beyond Epigenetics](https://github.com/sr320/talk-EpiAqua-2026) EpiAqua 2026 - January 2026, University of Concepcion, Chile. Steven Roberts.



#### 2025

-   [Diverse nutritional strategies mediate early life thermal responses in reef-building corals in Moorea](https://github.com/AHuffmyer/presentations/blob/master/2025/Huffmyer_MCR_AIM_2025.pdf). Ariana S. Huffmyer. Moorea Coral Reef Long Term Ecological Research All-Investigators Meeting. Virtual. December 12, 2025.

-   [Stress hardening and metabolic screening: Tools to assess oyster performance and resilience](https://github.com/AHuffmyer/presentations/blob/master/2025/Huffmyer_PCSGA_2025.pdf). Ariana S. Huffmyer. Pacific Coast Shellfish Growers Association Conference 2025. Vancouver, WA. September 10, 2025.

-   [Developing an integrated approach for multiomic epigenetic analyses](https://github.com/shedurkin/Roberts-LabNotebook/blob/master/presentations/Durkin_Session5_EPIMAR_2025.pptx). Kathleen Durkin. Epigenetics in Marine and Aquatic Research 2025. Barcelona, Spain. May, 2025.

-   [STRUCTURAL GENOMIC VARIATION IN TRIPLOID PACIFIC OYSTERS: Insight into differential physiology?](https://github.com/sr320/talk-AA-2025) Aquaculture 2025. New Orleans, LA. March 10, 2025.

-   [Shellfish environmental memory: Implications and opportunities](https://github.com/sr320/talk-WSG-2025). Washington SeaGrant Shellfish Growers Meeting.

-   [IMPROVING OYSTER AQUACULTURE WITH RESILIENCE BIOMARKERS FROM OMICS META-ANALYSIS](https://github.com/Resilience-Biomarkers-for-Aquaculture/Resilience-Biomarkers-for-Aquaculture.github.io/blob/master/docs/AQ_2025/20250310_AQ25_SAW.pptx). Shelly Wanamaker. Aquaculture 2025. New Orleans, LA. March 10, 2025.

-   [Parental Priming for Ocean Acidification Resilience in Manila Clams: Mechanistic Insights Gained Through Egg Transcriptome Analysis](https://meganewing.github.io/mewing-notebook/posts/2025-03/Aquaculture25_presentation.html). Megan Ewing. Aquaculture 2025. New Orleans, LA. March 10, 2025.

-   [Molecular mechanisms of heatwave mortality in Pacific cod early life stages](https://github.com/RobertsLab/project-cod-temperature/blob/main/reports/Spencer%2CLH_Poster-AMSS-2025-final.pdf). Laura Spencer. Alaska Marine Science Symposium. Anchorage, AK. January 2025.

-   [Exploring functional roles of non-coding RNA in stony corals](https://github.com/shedurkin/Roberts-LabNotebook/blob/master/presentations/Durkin_SICB_2025.pptx). Kathleen Durkin. Society of Integrative and Comparative Biology. Atlanta, GA. January, 2025

#### 2024

-   [Molecular indicators of performance in Pacific cod exposed to climate stressors](https://github.com/RobertsLab/project-cod-temperature/blob/main/reports/Groundfish%20Seminar%2C%202024.pdf). Laura Spencer. NOAA AFSC Groundfish Seminar. Seattle, WA. December 2024.

-   [Molecular indicators of performance in a marine fish exposed to temperature stress](https://github.com/RobertsLab/project-cod-temperature/blob/main/reports/Manchester-Presentation-Dec2024.pdf). Laura Spencer. NOAA NWFSC Manchester Research Station. Manchester, WA. December 2024.

-   [Comparing sea star species with varying susceptibility to sea star wasting disease](https://github.com/grace-ac/presentations/blob/main/2024/Crandall_WSN_2024.pptx). Grace Crandall. Western Society of Naturalists. Portland, OR. November 2024.

-   [Marine invertebrate environmental memory: Implications, mechanisms, and opportunities.](https://github.com/sr320/talk-SZAN-2024) Steven Roberts. Stazione Zoologica Anton Dohrn, Naples, Italy. October 2024.

-   [Olympia Oyster (*Ostrea lurida*) Restoration in the United States A Physiology and Genomic Perspective](https://github.com/sr320/talk-ostras-2024). Steven Roberts. Concepcion, Chile. July 2024.

-   [Marine invertebrate environmental memory: Implications, mechanisms, and opportunities](https://github.com/sr320/talk-duke-2024). Steven Roberts. Duke Marine Laboratory, Beaufort, NC. February 2024.

-   [*Pycnopodia helianthoides* immune response to Sea Star Wasting Disease](https://github.com/grace-ac/presentations/blob/main/2024/Crandall_SICB_2024.pdf). Grace Crandall. Society of Integrative and Comparative Biology. January 2024.

-   [Thermal stress reduces photosynthate metabolism and disrupts nitrogen cycling in coral larvae](https://github.com/AHuffmyer/presentations/blob/master/2024/Huffmyer_SICB_2024.pdf). Ariana S. Huffmyer. Society of Integrative and Comparative Biology. January 2024.

-   [Biodiversity Survey Methods: Using eDNA Metabarcoding to Complement Existing Methods](https://github.com/ChrisMantegna/YellowIsland2023/blob/main/Mantegna_eDNA_presentation.pdf). Chris Mantegna. Society of Integrative and Comparative Biology. January 2024.

-   [Comparative analyses of long non-coding RNA activity in three coral species](https://github.com/zbengt/zbengt.github.io/blob/master/assets/SICB_Comparative%20analyses%20of%20%20long%20non-coding%20RNA%20activity%20in%20%20coral%20species.pdf). Zachary Bengtsson. Society of Integrative and Comparative Biology. January 2024.