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---
title: "Publications"
---
```{r, echo = FALSE}
knitr::include_graphics("images/bodega_banner.jpg")
```
<br>
### Articles in review or revision
**Bogan SN**, Strader ME, and Hofmann GE. [Parental stress alters the fitness effects and genetic correlation of offspring performance traits and their gene expression pathways](https://www.biorxiv.org/content/10.1101/2024.10.07.617098v2). *bioRxiv*. (in revision)
**Bogan SN**, Sasaki M, and Kelley JL. Improving evolutionary and genomic tests of selection on phenotypic plasticity and plasticity-first evolution. (in revision)
Tashi E\*, **Bogan SN**, Lugardo L, Webber J, Boston L, Grimwood J, Harkess A, and Kelley JL. A chromosome-scale genome of the elusive Hubbs' beaked whale reveals demography, inbreeding, and introgression in *Mesoplodon*. (in review)
<br>
### Peer reviewed articles
<div align="center">
**2026**
</div>
10\. Cai T^†^, **Bogan SN**, Tanner RL, Kelley JL, and Dowd WW. 2026. [Tissue-specific plasticity of DNA methylation across intertidal microhabitats in juvenile mussels (*Mytilus californianus*)](https://onlinelibrary.wiley.com/doi/10.1111/mec.70418). *Molecular Ecology* 35: e70418.
9\. Moosman OW\*, Kelley JL, **Bogan SN**. 2025. [Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes](https://www.nature.com/articles/s41437-025-00803-8). *Heredity* 135: 174-186.
<div align="center">
**2025**
</div>
8\. **Bogan SN**, Surendran N\*, Hotaling S, Desvignes T, Bista I, Lins LSF, Eilertsen MH, Le François NR, Algayer T, Hamilton SL, Frandsen PB, Hoffmann FG, and Kelley JL. 2025. [Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes](https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaf219/8251091). *Molecular Biology and Evolution*: msaf219.
<div align="center">
**2024**
</div>
7\. **Bogan SN**, Porat OI\*, Meneses M\*, and Hofmann GE. 2024. [Thermal Plasticity Has Greater Fitness Costs among Thermally Tolerant Genotypes of *Tigriopus californicus*](https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.14568). *Functional Ecology* 38: 1562–1577.
6\. **Bogan SN** and Yi SV. 2024. [Potential Role of DNA Methylation in Plastic Responses to the Environment across Cells, Organisms, and Populations](https://academic.oup.com/gbe/article/16/2/evae022/7602727). *Genome Biology and Evolution* 16: evae022.
<div align="center">
**2023**
</div>
5\. **Bogan SN**, Johns JW, Griffiths JS, Davenport DL, Schaal SM, Wuitchik SJS, Lotterhos KE, Lou RN, , McGirr JA, Downey-Wall AM, Rivera HE, Roberts SB, Puritz JB, and Silliman KE. 2023. [A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io](https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.14219). *Methods in Ecology and Evolution* 14: 2709–2716.
4\. **Bogan SN**, Strader ME, and Hofmann GE. 2023. [Associations between DNA Methylation and Gene Expression Depend on Chromatin Accessibility during Transgenerational Plasticity](https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-023-01645-8). *BMC Biology* 21: 149.
<div align="center">
**2020**
</div>
3\. **Bogan SN**, Johnson KM, and Hofmann GE. 2020. [Changes in Genome-wide Methylation and Gene Expression in Response to Future *p*CO2 Extremes in the Antarctic Pteropod *Limacina helicina antarctica*](https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2019.00788/full). *Frontiers in Marine Science* 6: 788.
<div align="center">
**2019**
</div>
2\. **Bogan SN** and Place SP. 2019. [Accelerated Evolution at Chaperone Promoters among Antarctic Notothenioid Fishes](https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-019-1524-y). *BMC Evolutionary Biology* 19: 205.
1\. **Bogan SN**, McMahon JB, Pechenik JA, and Pires A. 2019. [Legacy of Multiple Stressors: Ocean Acidification and Nutrition in Larvae and Juveniles of a Marine Gastropod](https://www.journals.uchicago.edu/doi/10.1086/702993). *Biological Bulletin* 236: 159–173.
\* = undergraduate mentee; \† = graduate student mentee