From 703e00d34ccf551565fca657473d9e58064c4a10 Mon Sep 17 00:00:00 2001
From: Steven Roberts <sr320@uw.edu>
Date: Mon, 10 Jun 2024 12:19:53 -0700
Subject: [PATCH] added salmon sea lice paper

---
 docs/listings.json                            |   1 +
 docs/publications.html                        |  53 +-
 .../publications/articles/valenzuela2024.html | 692 ++++++++++++++++++
 docs/search.json                              |  30 +-
 docs/sitemap.xml                              |   6 +-
 publications/articles/valenzuela2024.qmd      |  28 +
 6 files changed, 786 insertions(+), 24 deletions(-)
 create mode 100644 docs/publications/articles/valenzuela2024.html
 create mode 100644 publications/articles/valenzuela2024.qmd

diff --git a/docs/listings.json b/docs/listings.json
index 60e81bf..3eb4bde 100644
--- a/docs/listings.json
+++ b/docs/listings.json
@@ -26,6 +26,7 @@
   {
     "listing": "/publications.html",
     "items": [
+      "/publications/articles/valenzuela2024.html",
       "/publications/articles/silliman-bogan2023.html",
       "/publications/articles/buckley2023.html",
       "/publications/articles/gallardo2023.html",
diff --git a/docs/publications.html b/docs/publications.html
index 47a6b60..1d93fa8 100644
--- a/docs/publications.html
+++ b/docs/publications.html
@@ -333,7 +333,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#recent-presentations" id="toc-recent-presentations" class="nav-link" data-scroll-target="#recent-presentations">Recent Presentations</a></li>
   </ul>
 </nav>
-    <h5 class="quarto-listing-category-title">Categories</h5><div class="quarto-listing-category category-default"><div class="category" data-category="">All <span class="quarto-category-count">(21)</span></div><div class="category" data-category="Caligus">Caligus <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Chionoecetes bairdi">Chionoecetes bairdi <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Crassostrea">Crassostrea <span class="quarto-category-count">(3)</span></div><div class="category" data-category="Hematodinium">Hematodinium <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Open Data Badge">Open Data Badge <span class="quarto-category-count">(2)</span></div><div class="category" data-category="Ostrea">Ostrea <span class="quarto-category-count">(3)</span></div><div class="category" data-category="Pacific oyster">Pacific oyster <span class="quarto-category-count">(2)</span></div><div class="category" data-category="Panopea">Panopea <span class="quarto-category-count">(3)</span></div><div class="category" data-category="RNA-sea">RNA-sea <span class="quarto-category-count">(1)</span></div><div class="category" data-category="RNA-seq">RNA-seq <span class="quarto-category-count">(3)</span></div><div class="category" data-category="SNP">SNP <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Tag-seq">Tag-seq <span class="quarto-category-count">(1)</span></div><div class="category" data-category="TagSeq">TagSeq <span class="quarto-category-count">(1)</span></div><div class="category" data-category="acidificaiton">acidificaiton <span class="quarto-category-count">(1)</span></div><div class="category" data-category="acidification">acidification <span class="quarto-category-count">(3)</span></div><div class="category" data-category="biodiversity">biodiversity <span class="quarto-category-count">(1)</span></div><div class="category" data-category="bitter crab disease">bitter crab disease <span class="quarto-category-count">(1)</span></div><div class="category" data-category="carryover">carryover <span class="quarto-category-count">(1)</span></div><div class="category" data-category="climate">climate <span class="quarto-category-count">(1)</span></div><div class="category" data-category="coral">coral <span class="quarto-category-count">(2)</span></div><div class="category" data-category="epigenetic">epigenetic <span class="quarto-category-count">(6)</span></div><div class="category" data-category="epigenetics">epigenetics <span class="quarto-category-count">(2)</span></div><div class="category" data-category="genome">genome <span class="quarto-category-count">(3)</span></div><div class="category" data-category="genomics">genomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="geoduck">geoduck <span class="quarto-category-count">(4)</span></div><div class="category" data-category="larvae">larvae <span class="quarto-category-count">(1)</span></div><div class="category" data-category="metagenomics">metagenomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="metaproteomics">metaproteomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="methods">methods <span class="quarto-category-count">(1)</span></div><div class="category" data-category="methylation">methylation <span class="quarto-category-count">(6)</span></div><div class="category" data-category="microbiome">microbiome <span class="quarto-category-count">(1)</span></div><div class="category" data-category="mussel">mussel <span class="quarto-category-count">(1)</span></div><div class="category" data-category="nanopore">nanopore <span class="quarto-category-count">(1)</span></div><div class="category" data-category="oyster">oyster <span class="quarto-category-count">(9)</span></div><div class="category" data-category="proteomics">proteomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="reproduction">reproduction <span class="quarto-category-count">(1)</span></div><div class="category" data-category="symbiosis">symbiosis <span class="quarto-category-count">(1)</span></div><div class="category" data-category="temperature">temperature <span class="quarto-category-count">(5)</span></div><div class="category" data-category="transcriptomic">transcriptomic <span class="quarto-category-count">(1)</span></div><div class="category" data-category="triploid">triploid <span class="quarto-category-count">(1)</span></div></div></div>
+    <h5 class="quarto-listing-category-title">Categories</h5><div class="quarto-listing-category category-default"><div class="category" data-category="">All <span class="quarto-category-count">(22)</span></div><div class="category" data-category="Caligus">Caligus <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Chionoecetes bairdi">Chionoecetes bairdi <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Crassostrea">Crassostrea <span class="quarto-category-count">(3)</span></div><div class="category" data-category="Hematodinium">Hematodinium <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Open Data Badge">Open Data Badge <span class="quarto-category-count">(2)</span></div><div class="category" data-category="Ostrea">Ostrea <span class="quarto-category-count">(3)</span></div><div class="category" data-category="Pacific oyster">Pacific oyster <span class="quarto-category-count">(2)</span></div><div class="category" data-category="Panopea">Panopea <span class="quarto-category-count">(3)</span></div><div class="category" data-category="RNA-sea">RNA-sea <span class="quarto-category-count">(1)</span></div><div class="category" data-category="RNA-seq">RNA-seq <span class="quarto-category-count">(4)</span></div><div class="category" data-category="SNP">SNP <span class="quarto-category-count">(1)</span></div><div class="category" data-category="Tag-seq">Tag-seq <span class="quarto-category-count">(1)</span></div><div class="category" data-category="TagSeq">TagSeq <span class="quarto-category-count">(1)</span></div><div class="category" data-category="acidificaiton">acidificaiton <span class="quarto-category-count">(1)</span></div><div class="category" data-category="acidification">acidification <span class="quarto-category-count">(3)</span></div><div class="category" data-category="biodiversity">biodiversity <span class="quarto-category-count">(1)</span></div><div class="category" data-category="bitter crab disease">bitter crab disease <span class="quarto-category-count">(1)</span></div><div class="category" data-category="carryover">carryover <span class="quarto-category-count">(1)</span></div><div class="category" data-category="climate">climate <span class="quarto-category-count">(1)</span></div><div class="category" data-category="coral">coral <span class="quarto-category-count">(2)</span></div><div class="category" data-category="epigenetic">epigenetic <span class="quarto-category-count">(6)</span></div><div class="category" data-category="epigenetics">epigenetics <span class="quarto-category-count">(2)</span></div><div class="category" data-category="genome">genome <span class="quarto-category-count">(3)</span></div><div class="category" data-category="genomics">genomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="geoduck">geoduck <span class="quarto-category-count">(4)</span></div><div class="category" data-category="larvae">larvae <span class="quarto-category-count">(1)</span></div><div class="category" data-category="metagenomics">metagenomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="metaproteomics">metaproteomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="methods">methods <span class="quarto-category-count">(1)</span></div><div class="category" data-category="methylation">methylation <span class="quarto-category-count">(7)</span></div><div class="category" data-category="microbiome">microbiome <span class="quarto-category-count">(1)</span></div><div class="category" data-category="mussel">mussel <span class="quarto-category-count">(1)</span></div><div class="category" data-category="nanopore">nanopore <span class="quarto-category-count">(1)</span></div><div class="category" data-category="oyster">oyster <span class="quarto-category-count">(9)</span></div><div class="category" data-category="proteomics">proteomics <span class="quarto-category-count">(1)</span></div><div class="category" data-category="reproduction">reproduction <span class="quarto-category-count">(1)</span></div><div class="category" data-category="salmon">salmon <span class="quarto-category-count">(1)</span></div><div class="category" data-category="sea lice">sea lice <span class="quarto-category-count">(1)</span></div><div class="category" data-category="symbiosis">symbiosis <span class="quarto-category-count">(1)</span></div><div class="category" data-category="temperature">temperature <span class="quarto-category-count">(6)</span></div><div class="category" data-category="transcriptomic">transcriptomic <span class="quarto-category-count">(1)</span></div><div class="category" data-category="triploid">triploid <span class="quarto-category-count">(1)</span></div></div></div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
@@ -375,7 +375,16 @@ <h1>Recent Papers</h1>
 </div>
 
 <ul class="pub-list list">
-  <li data-index="0" data-categories="methods,genomics" data-listing-file-modified-sort="1696855184433" data-listing-reading-time-sort="2">
+  <li data-index="0" data-categories="salmon,temperature,RNA-seq,methylation,sea lice" data-listing-file-modified-sort="1718047146618" data-listing-reading-time-sort="2">
+    <span class="listing-title lead">Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations</span><br>
+    <span class="listing-author">Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., &amp; Gallardo-Escarate, C</span><br>
+    <span class="listing-github fst-italic "></span>
+    <span class="listing-year">(2024)</span><br>
+    <a href="./publications/articles/valenzuela2024.html" class="btn btn-primary">
+      Details
+    </a>
+  </li>
+  <li data-index="1" data-categories="methods,genomics" data-listing-file-modified-sort="1696855184433" data-listing-reading-time-sort="2">
     <span class="listing-title lead">A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io</span><br>
     <span class="listing-author">Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., &amp; Silliman, K.</span><br>
     <span class="listing-github fst-italic "></span>
@@ -393,7 +402,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="1" data-categories="climate,biodiversity" data-listing-file-modified-sort="1694139711429" data-listing-reading-time-sort="2">
+  <li data-index="2" data-categories="climate,biodiversity" data-listing-file-modified-sort="1694139711429" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Characterizing biological responses to climate variability and extremes to improve biodiversity projections</span><br>
     <span class="listing-author">Lauren B Buckley, Emily Carrington, Michael E Dillon, Carlos García-Robledo, Steven B Roberts, Jill L Wegrzyn, Mark C Urban</span><br>
     <span class="listing-github fst-italic "></span>
@@ -408,7 +417,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-text"></i> eprint
     </a>
   </li>
-  <li data-index="2" data-categories="mussel,genome" data-listing-file-modified-sort="1694139842451" data-listing-reading-time-sort="2">
+  <li data-index="3" data-categories="mussel,genome" data-listing-file-modified-sort="1694139842451" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment</span><br>
     <span class="listing-author">Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, Fabian J Tapia, Marco Yévenes, Gonzalo Gajardo, Jorge E Toro, Pablo A Oyarzún, Gloria Arriagada, Beatriz Novoa, Antonio Figueras, Steven Roberts, Marco Gerdol</span><br>
     <span class="listing-github fst-italic "></span>
@@ -423,7 +432,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-text"></i> eprint
     </a>
   </li>
-  <li data-index="3" data-categories="oyster,methylation,SNP,epigenetic,Ostrea" data-listing-file-modified-sort="1694140050873" data-listing-reading-time-sort="2">
+  <li data-index="4" data-categories="oyster,methylation,SNP,epigenetic,Ostrea" data-listing-file-modified-sort="1694140050873" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Epigenetic and genetic population structure is coupled in a marine invertebrate</span><br>
     <span class="listing-author">Katherine Silliman, Laura H Spencer, Samuel J White, Steven B Roberts</span><br>
     <span class="listing-github fst-italic "></span>
@@ -444,7 +453,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="4" data-categories="oyster,Tag-seq,Ostrea" data-listing-file-modified-sort="1694629966924" data-listing-reading-time-sort="2">
+  <li data-index="5" data-categories="oyster,Tag-seq,Ostrea" data-listing-file-modified-sort="1694629966924" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Population-specific effects of ocean acidification in the Olympia oyster</span><br>
     <span class="listing-author">Laura H Spencer, Steven B Roberts, Katherine Silliman, </span><br>
     <span class="listing-github fst-italic "></span>
@@ -459,7 +468,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-text"></i> eprint
     </a>
   </li>
-  <li data-index="5" data-categories="oyster,RNA-seq,temperature" data-listing-file-modified-sort="1694135198520" data-listing-reading-time-sort="2">
+  <li data-index="6" data-categories="oyster,RNA-seq,temperature" data-listing-file-modified-sort="1694135198520" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge</span><br>
     <span class="listing-author">Roberto Arredondo-Espinoza, Ana M Ibarra, Steven B Roberts, Maria Teresa Sicard-González, Cristina Escobedo-Fregoso</span><br>
     <span class="listing-github fst-italic "></span>
@@ -471,7 +480,7 @@ <h1>Recent Papers</h1>
       DOI
     </a>
   </li>
-  <li data-index="6" data-categories="oyster,triploid,Pacific oyster,Crassostrea" data-listing-file-modified-sort="1694740432131" data-listing-reading-time-sort="2">
+  <li data-index="7" data-categories="oyster,triploid,Pacific oyster,Crassostrea" data-listing-file-modified-sort="1694740432131" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves</span><br>
     <span class="listing-author">Matthew N. George, Olivia Cattau, Mollie Middleton, Delaney Lawson, Brent Vadopalas, Mackenzie Gavery, Steven Roberts</span><br>
     <span class="listing-github fst-italic "></span>
@@ -489,7 +498,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-text"></i> eprint
     </a>
   </li>
-  <li data-index="7" data-categories="Open Data Badge,geoduck,Panopea,TagSeq,RNA-sea" data-listing-file-modified-sort="1696865030523" data-listing-reading-time-sort="2">
+  <li data-index="8" data-categories="Open Data Badge,geoduck,Panopea,TagSeq,RNA-sea" data-listing-file-modified-sort="1696865030523" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Acclimatory gene expression of primed clams enhances robustness to elevated pCO2</span><br>
     <span class="listing-author">Samuel J. Gurr, Shelly A. Wanamaker , Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam</span><br>
     <span class="listing-github fst-italic "></span>
@@ -504,7 +513,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="8" data-categories="Chionoecetes bairdi,Hematodinium,temperature,RNA-seq,bitter crab disease,transcriptomic" data-listing-file-modified-sort="1697467560505" data-listing-reading-time-sort="2">
+  <li data-index="9" data-categories="Chionoecetes bairdi,Hematodinium,temperature,RNA-seq,bitter crab disease,transcriptomic" data-listing-file-modified-sort="1697467560505" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)</span><br>
     <span class="listing-author">Grace Crandall, Pamela C. Jensen, Samuel J. White, Steven Roberts </span><br>
     <span class="listing-github fst-italic "></span>
@@ -522,7 +531,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="9" data-categories="oyster,methylation,epigenetic,acidification,Pacific oyster,Crassostrea" data-listing-file-modified-sort="1687560150682" data-listing-reading-time-sort="2">
+  <li data-index="10" data-categories="oyster,methylation,epigenetic,acidification,Pacific oyster,Crassostrea" data-listing-file-modified-sort="1687560150682" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification</span><br>
     <span class="listing-author">Yaamini Venkataraman, Samuel J White and Steven Roberts</span><br>
     <span class="listing-github fst-italic "></span>
@@ -543,7 +552,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="10" data-categories="geoduck,methylation,acidification,Panopea,genome,epigenetic" data-listing-file-modified-sort="1696865030525" data-listing-reading-time-sort="2">
+  <li data-index="11" data-categories="geoduck,methylation,acidification,Panopea,genome,epigenetic" data-listing-file-modified-sort="1696865030525" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams</span><br>
     <span class="listing-author">Hollie M. Putnam, Shelly A. Wanamaker , Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, Erich Jaeger, Jonathan Soohoo, Cristian Gallardo-Escárate, Frederick W. Goetz, Steven B. Roberts</span><br>
     <span class="listing-github fst-italic "></span>
@@ -558,7 +567,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="11" data-categories="oyster,methylation,acidification,epigenetic,Crassostrea" data-listing-file-modified-sort="1687557809601" data-listing-reading-time-sort="2">
+  <li data-index="12" data-categories="oyster,methylation,acidification,epigenetic,Crassostrea" data-listing-file-modified-sort="1687557809601" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment</span><br>
     <span class="listing-author">Dang, X., Lim, Y.-K., Li, Y., Roberts, S. B., Li, L., &amp; Thiyagarajan, V.</span><br>
     <span class="listing-github fst-italic "></span>
@@ -573,7 +582,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-text"></i> eprint
     </a>
   </li>
-  <li data-index="12" data-categories="oyster,proteomics,temperature" data-listing-file-modified-sort="1694137110851" data-listing-reading-time-sort="2">
+  <li data-index="13" data-categories="oyster,proteomics,temperature" data-listing-file-modified-sort="1694137110851" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature</span><br>
     <span class="listing-author">Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S.</span><br>
     <span class="listing-github fst-italic "></span>
@@ -588,7 +597,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="13" data-categories="geoduck,Panopea" data-listing-file-modified-sort="1696865030522" data-listing-reading-time-sort="2">
+  <li data-index="14" data-categories="geoduck,Panopea" data-listing-file-modified-sort="1696865030522" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam</span><br>
     <span class="listing-author">Samuel J. Gurr, Shelly A. Wanamaker , Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam</span><br>
     <span class="listing-github fst-italic "></span>
@@ -606,7 +615,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="14" data-categories="Caligus,genome" data-listing-file-modified-sort="1694137435051" data-listing-reading-time-sort="3">
+  <li data-index="15" data-categories="Caligus,genome" data-listing-file-modified-sort="1694137435051" data-listing-reading-time-sort="3">
     <span class="listing-title lead">Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis</span><br>
     <span class="listing-author">Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, Ana Teresa Gonçalves, Hugo Escobar-Sepulveda, Ivan Liachko, Bradley Nelson, Steven Roberts &amp; Wesley Warren</span><br>
     <span class="listing-github fst-italic "></span>
@@ -621,7 +630,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="15" data-categories="geoduck,microbiome,metagenomics,metaproteomics" data-listing-file-modified-sort="1694137969307" data-listing-reading-time-sort="2">
+  <li data-index="16" data-categories="geoduck,microbiome,metagenomics,metaproteomics" data-listing-file-modified-sort="1694137969307" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery</span><br>
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       <i class="bi bi-file-earmark-text"></i> eprint
     </a>
   </li>
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     <span class="listing-github fst-italic "></span>
@@ -654,7 +663,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="17" data-categories="oyster,epigenetics,temperature" data-listing-file-modified-sort="1694139085474" data-listing-reading-time-sort="2">
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     <span class="listing-title lead">Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas</span><br>
     <span class="listing-author">Arredondo-Espinoza Roberto, Ibarra Ana M., Roberts B. Steven, Sicard-Gonzalez Maria Teresa, Escobedo-Fregoso Cristina</span><br>
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@@ -666,7 +675,7 @@ <h1>Recent Papers</h1>
       DOI
     </a>
   </li>
-  <li data-index="18" data-categories="Open Data Badge,coral,methylation,epigenetic" data-listing-file-modified-sort="1696865030527" data-listing-reading-time-sort="2">
+  <li data-index="19" data-categories="Open Data Badge,coral,methylation,epigenetic" data-listing-file-modified-sort="1696865030527" data-listing-reading-time-sort="2">
     <span class="listing-title lead">Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases</span><br>
     <span class="listing-author">Shelly A. Wanamaker , Yaamini R. Venkataraman, Mackenzie R. Gavery, Steven B. Roberts, Debashish Bhattacharya, Alan Downey-Wall, Jose M. Eirin-Lopez, Kevin M. Johnson, Katie E. Lotterhos, Jonathan B. Puritz and Hollie M. Putnam</span><br>
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@@ -687,7 +696,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
-  <li data-index="19" data-categories="Ostrea,reproduction,larvae,temperature,carryover" data-listing-file-modified-sort="1694139398668" data-listing-reading-time-sort="3">
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     <span class="listing-title lead">Latent effects of winter warming on Olympia oyster reproduction and larval viability</span><br>
     <span class="listing-author">Laura H. Spencer, Erin Horkan, Ryan Crim, Steven B. Roberts</span><br>
     <span class="listing-github fst-italic "></span>
@@ -702,7 +711,7 @@ <h1>Recent Papers</h1>
       <i class="bi bi-file-earmark-zip"></i> Materials
     </a>
   </li>
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     <span class="listing-title lead">Oyster biomineralisation under ocean acidification: from genes to shell</span><br>
     <span class="listing-author">Chandra Rajan, K., Yuan, M., Yu, Z., Roberts, S.B. and Thiyagarajan, V. </span><br>
     <span class="listing-github fst-italic "></span>
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+<header id="title-block-header" class="quarto-title-block default">
+<div class="quarto-title">
+<h1 class="title">Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations</h1>
+  <div class="quarto-categories">
+    <div class="quarto-category">salmon</div>
+    <div class="quarto-category">temperature</div>
+    <div class="quarto-category">RNA-seq</div>
+    <div class="quarto-category">methylation</div>
+    <div class="quarto-category">sea lice</div>
+  </div>
+  </div>
+
+
+
+<div class="quarto-title-meta">
+
+    <div>
+    <div class="quarto-title-meta-heading">Author</div>
+    <div class="quarto-title-meta-contents">
+             <p>Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., &amp; Gallardo-Escarate, C </p>
+          </div>
+  </div>
+    
+  
+    
+  </div>
+  
+
+</header>
+
+<section id="citation" class="level2">
+<h2 class="anchored" data-anchor-id="citation">Citation</h2>
+<blockquote class="blockquote">
+<p>Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., &amp; Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2.</p>
+</blockquote>
+</section>
+<section id="abstract" class="level2">
+<h2 class="anchored" data-anchor-id="abstract">Abstract</h2>
+<p>The fish’s immune response is affected by different factors, including a wide range of environmental conditions that can also disrupt or promote changes in the host- pathogen interactions. How environmental conditions modulate the salmon genome during parasitism is poorly understood here. This study aimed to explore the environmental influence on the Salmo salar transcriptome and methylome infected with the sea louse Caligus rogercresseyi. Atlantic salmon were experimentally infected with lice at two temperatures (8 and 16oC) and salinity conditions (32 and 26PSU). Fish tissues were collected from the infected Atlantic salmon for reduced representation bisulfite sequencing (RRBS) and whole transcriptome sequencing (RNAseq) analysis. The parasitic load was highly divergent in the evaluated environmental conditions, where the lowest lice abundance was observed in fish infected at 8oC/26PSU. Notably, transcriptome profile differences were statistically associated with the number of alternative splicing events in fish exposed to low temperature/salinity conditions. Furthermore, the temperature significantly affected the methylation level, where high values of differential methylation regions were observed at 16oC. Also, the association between expression levels of spliced transcripts and their methylation levels was determined, revealing significant correlations with Ferroptosis and TLR KEEG pathways. This study supports the relevance of the environmental conditions during host-parasite interactions in marine ecosystems. The discovery of alternative splicing transcripts associated with DMRs is also discussed as a novel player in fish biology.</p>
+</section>
+<section id="data-availability" class="level2">
+<h2 class="anchored" data-anchor-id="data-availability">Data Availability</h2>
+
+
+</section>
+
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diff --git a/docs/search.json b/docs/search.json
index 69d8539..23fa1bc 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -11,7 +11,7 @@
     "href": "publications.html",
     "title": "Publications",
     "section": "",
-    "text": "Publications\nSee the table of contents at the right to jump to book chapters, preprints, theses, notebooks, and recent presentations. Search the entire website using the search icon in top right menu.\n\n\nRecent Papers\nRecent 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\nsee also: Google Scholar\n\n\n   \n     \n     \n       Order By\n       Default\n         \n          Title\n        \n         \n          Author\n        \n         \n          Publication\n        \n         \n          Year\n        \n     \n  \n    \n      \n      \n    \n\n\n\n  \n    A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io\n    Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K.\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Characterizing biological responses to climate variability and extremes to improve biodiversity projections\n    Lauren B Buckley, Emily Carrington, Michael E Dillon, Carlos García-Robledo, Steven B Roberts, Jill L Wegrzyn, Mark C Urban\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment\n    Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, Fabian J Tapia, Marco Yévenes, Gonzalo Gajardo, Jorge E Toro, Pablo A Oyarzún, Gloria Arriagada, Beatriz Novoa, Antonio Figueras, Steven Roberts, Marco Gerdol\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    Epigenetic and genetic population structure is coupled in a marine invertebrate\n    Katherine Silliman, Laura H Spencer, Samuel J White, Steven B Roberts\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Population-specific effects of ocean acidification in the Olympia oyster\n    Laura H Spencer, Steven B Roberts, Katherine Silliman, \n    \n    (2023)\n    \n      Details\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n  \n  \n    Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge\n    Roberto Arredondo-Espinoza, Ana M Ibarra, Steven B Roberts, Maria Teresa Sicard-González, Cristina Escobedo-Fregoso\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n  \n  \n    Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves\n    Matthew N. George, Olivia Cattau, Mollie Middleton, Delaney Lawson, Brent Vadopalas, Mackenzie Gavery, Steven Roberts\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n  \n  \n    Acclimatory gene expression of primed clams enhances robustness to elevated pCO2\n    Samuel J. Gurr, Shelly A. Wanamaker , Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)\n    Grace Crandall, Pamela C. Jensen, Samuel J. White, Steven Roberts \n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification\n    Yaamini Venkataraman, Samuel J White and Steven Roberts\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams\n    Hollie M. Putnam, Shelly A. Wanamaker , Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, Erich Jaeger, Jonathan Soohoo, Cristian Gallardo-Escárate, Frederick W. Goetz, Steven B. Roberts\n    \n    (2022)\n    \n      Details\n    \n    \n       Preprint\n    \n    \n       Materials\n    \n  \n  \n    Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment\n    Dang, X., Lim, Y.-K., Li, Y., Roberts, S. B., Li, L., & Thiyagarajan, V.\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature\n    Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S.\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam\n    Samuel J. Gurr, Shelly A. Wanamaker , Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis\n    Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, Ana Teresa Gonçalves, Hugo Escobar-Sepulveda, Ivan Liachko, Bradley Nelson, Steven Roberts & Wesley Warren\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery\n    Emma Timmins-Schiffman, Samuel J. White, Rhonda Elliott Thompson, Brent Vadopalas, Benoit Eudeline, Brook L. Nunn & Steven B. Roberts\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing\n    James L Dimond, Nhung Nguyen, Steven B Roberts\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas\n    Arredondo-Espinoza Roberto, Ibarra Ana M., Roberts B. Steven, Sicard-Gonzalez Maria Teresa, Escobedo-Fregoso Cristina\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n  \n  \n    Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases\n    Shelly A. Wanamaker , Yaamini R. Venkataraman, Mackenzie R. Gavery, Steven B. Roberts, Debashish Bhattacharya, Alan Downey-Wall, Jose M. Eirin-Lopez, Kevin M. Johnson, Katie E. Lotterhos, Jonathan B. Puritz and Hollie M. Putnam\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Latent effects of winter warming on Olympia oyster reproduction and larval viability\n    Laura H. Spencer, Erin Horkan, Ryan Crim, Steven B. Roberts\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Oyster biomineralisation under ocean acidification: from genes to shell\n    Chandra Rajan, K., Yuan, M., Yu, Z., Roberts, S.B. and Thiyagarajan, V. \n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n  \n\n\nNo matching items\n\n\n\n\nLess Recent Papers (2020 and older)\nShelly 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 BMC Genomics 21, 723 doi:10.1186/s12864-020-07127-3\n\nYong-Kian Lim, Khan Cheung, Xin Dang, Steven B. Roberts, Xiaotong Wang, Vengatesen Thiyagarajan (2020) DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis Marine Environmental Research, Volume 163 doi:10.1016/j.marenvres.2020.105214\nDowney-Wall Alan M., Cameron Louise P., Ford Brett M., McNally Elise M., Venkataraman Yaamini R., Roberts Steven B., Ries Justin B., Lotterhos Katie E (2020) Ocean Acidification Induces Subtle Shifts in Gene Expression and DNA Methylation in Mantle Tissue of the Eastern Oyster (Crassostrea virginica) Frontiers in Marine Science v7 p828 doi:10.3389/fmars.2020.566419\nCristian Gallardo-Escárate; Valentina Valenzuela-Muñoz; Gustavo Núñez-Acuña; Diego Valenzuela-Miranda; Bárbara P. Benaventel; Constanza Sáez-Vera; Homero Urrutia; Beatriz Novoa; Antonio Figueras; Steven Roberts; Paulina Assmann; Marta Bravo (2020) The wastewater microbiome: A novel insight for COVID-19 surveillance Science of The Total Environment Page: 142867 doi:10.1016/j.scitotenv.2020.142867\nBonnie J. Becker, Michael D. Behrens, Brian Allen, Megan Hintz, Hannah Parker, Michelle M. McCartha, and Sarah M. White (2020) Spatial and Temporal Distribution of the Early Life History Stages of the Native Olympia Oyster Ostrea lurida (Carpenter, 1864) in a Restoration Site in Northern Puget Sound, Wa Journal of Shellfish Research 39(1), 43-58. doi:/10.2983/035.039.0105\nEmma Timmins-Schiffman, José M. Guzmán, Rhonda Elliott Thompson, Brent Vadopalas, Benoit Eudeline and Steven B. Roberts (2020) Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates Scientific Reports 10, 6042. doi:10.1038/s41598-020-63218-x\nVenkataraman Yaamini R., Downey-Wall Alan M., Ries Justin, Westfield Isaac, White Samuel J., Roberts Steven B., Lotterhos Kathleen E (2020) General DNA Methylation Patterns and Environmentally-Induced Differential Methylation in the Eastern Oyster (Crassostrea virginica) Frontiers in Marine Science, Volume 7, Page 225. doi:10.3389/fmars.2020.00225\nGurr SJ, Vadopalas B, Roberts SB, Putnam HM (2020) Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck Panopea generosa following short-term exposure to acidified seawater Conservation Physiology, Volume 8, Issue 1, coaa024. doi:10.1093/conphys/coaa024\nSpencer, LH, Venkataraman, YR, Crim R, Ryan S, Horwith MJ, and Roberts SB (2020) Carryover effects of temperature and pCO2 across multiple Olympia oyster populations. Ecological Applications 00( 00):e02060. doi:10.1002/eap.2060\nDimond JL and Roberts SB. (2020) Convergence of DNA Methylation Profiles of the Reef Coral Porites astreoides in a Novel Environment Frontiers in Marine Science. vol 6. doi:10.3389/fmars.2019.00792\nVenkataraman YR, Spencer LH, Roberts SB. (2019) Larval Response to Parental Low pH Exposure in the Pacific Oyster Crassostrea gigas Journal of Shellfish Research, 38(3), 743-750. doi:10.2983/035.038.0325\nTimmins‐Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB. (2019) Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2. Ecol Evol.00: 1– 13. doi:10.1002/ece3.5885\n\nGallardo-Escárate C, Valenzuela-Muñoz V, Núñez-Acuña , Carrera C, Gonçalves AT, Valenzuela-Miranda D, Benavente BP, Roberts SB. (2019) Catching the complexity of salmon-louse interactions Fish & Shellfish Immunology. doi:10.1016/j.fsi.2019.04.065\nSpencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB. (2019) Pacific geoduck (Panopea generosa) resilience to natural pH variation Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. doi:10.1016/j.cbd.2019.01.010 bioRxiv\nVenkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB. (2019) Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences Mar Ecol Prog Ser 610:65-81. doi:10.3354/meps12858 bioRxiv\nJuárez, O., Lafarga-De la Cruz, F., Leyva-Valencia, I., López-Landavery, E., García-Esquivel, Z., Díaz, F., Re-Araujo, D., Vadopalas, B., and C. Galindo-Sánchez. (2018). Transcriptomic and metabolic response to chronic and acute thermal exposure of juvenile geoduck clams Panopea globosa. Marine Genomics. doi:10.1016/j.margen.2018.09.003\nJavier A. Rodriguez‐Casariego, Mark C. Ladd, Andrew A. Shantz, Christian Lopes, Manjinder S. Cheema, Bohyun Kim, Steven B. Roberts, James W. Fourqurean, Juan Ausio, Deron E. Burkepile, and Jose M. Eirin‐Lopez. (2018) Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis Ecol Evol. 2018;00:1–15. doi:10.1002/ece3.4678 pdf\nRoberts SB, Gavery MR. (2018) Opportunities in Functional Genomics: A Primer on Lab and Computational Aspects Journal of Shellfish Research 37(4):747-754. doi:10.2983/035.037.0406\nSilliman KE, Bowyer TK, Roberts SB. (2018) Consistent differences in fitness traits across multiple generations of Olympia oysters Scientific Reports volume 8, Article number:6080. doi:10.1038/s41598-018-24455-3\nHeare JE, White SJ, Vadopalas B, Roberts SB. (2018) Differential response to stress in Ostrea lurida as measured by gene expression PeerJ 6:e4261. doi: 10.7717/peerj.4261\nGoetz FW, Jasonowicz AJ, Roberts SB. (2017) What goes up must come down: Diel vertical migration in the deep-water sablefish (Anoplopoma fimbria) revealed by pop-up satellite archival tags Fish Oceanogr. 2017;00:1–16. doi: 10.1111/fog.12239\nGavery MR, Roberts SB. (2017) Epigenetic considerations in aquaculture PeerJ 5:e4147 doi: 10.7717/peerj.4147\n\n\n\n\n\nJake Emerson Heare, Brady Blake, Jonathan P Davis, Brent Vadopalas, Steven Roberts (2017) Evidence of Ostrea lurida Carpenter, 1864 population structure in Puget Sound, WA Marine Ecology 38:e12458 doi: 10.1111/maec.12458\nMegan Hintz, Katherine Gratz, Bonnie Becker, Brent Vadopalas, and Steven Roberts (2017) A Nonlethal Anesthesia Protocol for Accessing the Mantle Cavity of Olympia Oysters in the Laboratory or Field Journal of Shellfish Research 2017 36 (2), 353-357 doi: 10.2983/035.036.0207\nSamuel J. White, Brent Vadopalas, Katherine Silliman & Steven B. Roberts (2017) Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters, Ostrea lurida Scientific Data 4, Article number: 170130 doi: 10.1038/sdata.2017.130\nDimond JL, Gamblewood SK, Roberts SB. (2017) Genetic and epigenetic insight into morphospecies in a reef coral Molecular Ecology. 00:1–12. doi: 10.1111/mec.14252\nEmma B. Timmins-Schiffman, Grace A Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn and Steven Roberts (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 pdf\nC. Gallardo-Escárate V. Valenzuela-Muñoz S. Boltaña G. Nuñez-Acuña D. Valenzuela-Miranda A.T. Gonçalves C. Détrée E. Tarifeño-Saldivia R. Farlora S. Roberts H.M. Putnam (2017) The Caligus rogercresseyi miRNome: Discovery and transcriptome profiling during the sea lice ontogeny AgriGene doi: 10.1016/j.aggene.2017.03.002 eprint\nThe Aquaculture Genomics, Genetics and Breeding Workshop (2017) Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research BMC Genomics 18:191. doi: 10.1186/s12864-017-3557-1\nDetree C, Núñez-Acuña G, Roberts S, Gallardo-Escárate C (2016) Uncovering the Complex Transcriptome Response of Mytilus chilensis against Saxitoxin: Implications of Harmful Algal Blooms on Mussel Populations PLoS ONE 11(10): e0165231. doi:10.1371/journal.pone.0165231\n\nDimond JL and Roberts SB (2016), Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change Molecular Ecology doi:10.1111/mec.13414 preprint\nJasonowicz AJ, Goetz FW, Goetz GW, Nichols KM (2016) Love the one you’re with: Genomic evidence of panmixia in the sablefish (Anoplopoma fimbria) Canadian Journal of Fisheries and Aquatic Sciences doi: 10.1139/cjfas-2016-0012\nFroehlich HE, Roberts SB, Essington TE (2015) Evaluating hypoxia-inducible factor-1α mRNA expression in a pelagic fish, Pacific herring Clupea pallasii, as a biomarker for hypoxia exposure Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology doi:10.1016/j.cbpa.2015.07.016\nCook MA, Massee KC, Wade TH, Oden SM, Jensen C, Jasonowicz A, Immerman DA, Goetz FW (2015) Culture of sablefish (Anoplopoma fimbria) larvae in four experimental tank designs Aquacultural Engineering doi:10.1016/j.aquaeng.2015.09.003\n\nFuess LE, Eisenlord ME, Closek CJ, Tracy AM, Mauntz R, Gignoux-Wolfsohn S, Moritsch MM, Yoshioka R, Burge CA, Harvell CD, Friedman CS, Hewson I, Hershberger PK, Roberts SB (2015) Up in Arms: Immune and Nervous System Response To Sea Star Wasting Disease PLoS ONE doi:10.1371/journal.pone.0133053\nTimmins-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\nImmerman DA and Goetz FW (2014). The activation and cryopreservation of sablefish (Anoplopoma fimbria) sperm Aquaculture doi:10.1016/j.aquaculture.2014.04.010\nOlson CE and Roberts SB. (2014). Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes Frontiers in Physiology. 5:224. doi: 10.3389/fphys.2014.0022\nGavery MR and Roberts SB. (2014) A context specific role for DNA methylation in bivalves Briefings in Functional Genomics. doi:10.1093/bfgp/elt054 (pdf)\nGavery MR and Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc PeerJ 1:e215. doi:10.7717/peerj.215\n\n\n\nGarcia-Vedrenne AE, Groner M, Page-Karjian A, Siegmund G-F, Singhal S, Sziklay J and Roberts SB. (2013) Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression PLoS ONE 8(9): e74196. doi:10.1371/journal.pone.0074196\nStorer CS, Quinn TP and Roberts SB. (2013) Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon Biogerontology. doi:10.1007/s10522-013-9448-1 (pdf)\nBurge CA, Mouchka ME, Harvell CD and Roberts SB. (2013) Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing Frontiers in Physiology 4:180. doi:10.3389/fphys.2013.00180\nTimmins-Schiffman EB, Nunn BL, Goodlett DR and Roberts SB. (2013) Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster Conservation Physiology. doi:10.1093/conphys/cot009\nTimmins-Schiffman EB, Friedman CS, Metzger DC, White SJ and Roberts SB. (2013) Genomic resource development for shellfish of conservation concern Molecular Ecology Resources. doi:10.1111/1755-0998.12052\nTimmins-Schiffman EB and 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\n\n\nStorer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW and Seeb JE. (2012) Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism PLoS ONE 7(11): e49018. doi:10.1371/journal.pone.0049018\nTimmins-Schiffman EB, O’Donnell M, Friedman CS, and Roberts SB. (2012) Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas Marine Biology. doi:10.1007/s00227-012-2055-x pdf\nBurge CA, Douglas N, Conti-Jerpe I, Weil E, Roberts SB, Friedman CS and CD Harvell. (2012) Friend or foe: the association of Labyrinthulomycetes with the Caribbean sea fan, Gorgonia ventalina Diseases of Aquatic Organisms 101:1-12. doi:10.3354/dao02487\nMetzger DC, Pratt P and Roberts SB. (2012) Characterizing the effects of heavy metal and Vibrio exposure on hsp70 expression in Crassostrea gigas gill tissue Journal of Shellfish Research 31(3):627-630. doi:10.2983/035.031.0305 pdf\nRoberts SB, Hauser L, Seeb LW and Seeb JE (2012) Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing PLoS ONE 7(2): e30908. doi:10.1371/journal.pone.0030908\nRoberts SB and Gavery MR (2012) Is there a relationship between DNA methylation and phenotypic plasticity in invertebrates? Frontiers in Physiology 2:116. doi:10.3389/fphys.2011.00116\nGavery MR and Roberts SB (2012) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 7:2 94-99. doi:10.1016/j.cbd.2011.12.003\nMorera D, Roher N, Ribas L, Balasch JC, Doñate C, Callol A, Boltaña A, Roberts SB, Goetz G, Goetz FW and Mackenzie SA. (2011) RNA-Seq reveals an integrated immune response in nucleated erythrocytes PLoS ONE 6(10): e26998. doi:10.1371/journal.pone.0026998\nRoberts SB, Sunila I, and Wikfors G. (2011) Immune response and mechanical stress susceptibility in diseased oysters, Crassostrea virginica Journal of Comparative Physiology B 182:1 41-48. doi:10.1007/s00360-011-0605-z\nSeeb JE, Carvalho G, Hauser L, Naish K, Roberts SB and Seeb LW. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms Molecular Ecology Resources 11 1–8. doi:10.1111/j.1755-0998.2010.02979.x\nSeeb JE, Pascal CE, Graue ED, Seeb LW, Templin WD, Harkins T and Roberts SB. (2010) Transcriptome sequencing and high-resolution melt analysis advance single nucleotidepolymorphism discovery in duplicated salmonids Molecular Ecology Resources. doi: 10.1111/j.1755-0998.2010.02936.x\nGavery MR and Roberts SB. (2010) DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas) BMC Genomics 11:483. doi:10.1186/1471-2164-11-483\nMathger L, Roberts SB, and Hanlon R. (2010) Evidence for distributed light sensing in the skin of cuttlefish, Sepia officinalis Biology Letters. doi: 10.1098/rsbl.2010.0223\nGoetz FW, Rosauer D, Sitar S, Goetz G, Simchick C, Roberts SB, Johnson R, Murphy C, Bronte C, and Mackenzie S. (2010) A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush) Molecular Ecology 19 176–196.\nDefaveri J*, Smolowitz R, and Roberts S (2009) Development and validation of a real-time quantitative PCR assay for the detection and quantification of Perkinsus marinus in the Eastern oyster, Crassostrea virginica Journal of Shellfish Research Vol. 28 No. 3 459-464. eprint\nRoberts SB, Goetz G, White S, and Goetz F (2009) Analysis of genes isolated from plated hemocytes of the Pacific Oyster, Crassostrea gigas Marine Biotechnology 11:24-44. doi: 10.1007/s10126-008-9117-6\nRoberts SB, Gueguen Y, de Lorgeril J, and Goetz F. (2008) Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure Developmental and Comparative Immunology 32, 1099-1104. doi: 10.1016/j.dci.2008.02.006\n\n\nLyons MM*, Lau Y-T, Carden WE, Ward JE, Roberts SB, Smolowitz R, Vallino J, and Allam B. (2007) Characteristics of marine aggregates in shallow-water ecosystems: Implications for disease ecology EcoHealth 4, 406–420.\nWeiss E, Bennie M, Hodgins-Davis A, Roberts SB, and Gerlach G. (2007) Characterization of new SSR-EST markers in cod, Gadus morhua Molecular Ecology Notes 7: 866–867. doi: 10.1111/j.1471-8286.2007.01731.x\nHodgins-Davis A*, Roberts SB, Cowan D, Atema J, Avolio C, Defaveri J, and Gerlach G. (2007) Characterization of SSRs from the American lobster, Homarus americanus Molecular Ecology Notes 7:330-332.\nRodgers BD, Roalson EH, Weber GM, Roberts SB, Goetz FW. (2007) A Proposed Nomenclature Consensus for the Myostatin Gene Family AJP- Endocrinology and Metabolism 292(2):E371-2.\nLyons MM*, Smolowitz R, Dungan C, and Roberts SB. (2006) Development of a real-time quantitative PCR assay for the hard clam pathogen, Quahog Parasite Unknown (QPX) Diseases of Aquatic Organisms 72(1):45-52.\nBiga PR, Roberts SB, Iliev DB, McCauley LA, Moon JS, Collodi P, and Goetz FW. (2005) The isolation, characterization, and expression of a novel GDF11 gene and a second myostatin form in zebrafish, Danio rerio. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 141: 218-230.\nRoberts SB, Romano C, and Gerlach G. (2005) Characterization of EST derived SSRs from the bay scallop, Argopectens irradiansMolecular Ecology Notes 5: 567-568.\nJentoft S, Topp N, Seeliger M, Malison JA, Barry TP, Held JA, Roberts SB, and Goetz FW. (2005) Lack of growth enhancement by exogenous growth hormone treatment in yellow perch in four separate experiments Aquaculture 250:471-479.\nHollis DM, Goetz FW, Roberts SB, and Boyd SK. (2004) Acute neurosteroid modulation and subunit isolation of the GABAa receptor in the bullfrog, Rana catesbeiana Journal of Molecular Endocrinology 32(3):921-34.\nBiga PR, Cain KD, Hardy RW, Schelling GT, Overturf K, Roberts SB, Goetz FW, Ott TL. (2004) Growth hormone differentially regulates muscle myostatin1 and -2 and increases circulating cortisol in rainbow trout Oncorhynchus mykiss General and Comparative Endocrinology Vol 138(1):32-41.\nRoberts SB, McCauley LAR, Devlin RH, Goetz FW. (2004) Transgenic salmon over-expressing growth hormone exhibit decreased myostatin transcript and protein expression Journal of Experimental Biology 207(Pt 21):3741-8.\nKim H-W, Mykles DL, Goetz FW, Roberts SB. (2004) Characterization of an invertebrate myostatin homologue from the bay scallop, Argopecten irradians BBA – Gene Structure and Expression 1679(2):174-9.\nRoberts SB, Barry T, Malison J, Goetz FW. (2004) Production of a recombinantly-derived growth hormone antibody and the characterization of growth hormone levels in yellow perch Aquaculture Vol.232/1-4: 591-602.\nRoberts SB, Goetz FW. (2003) Expressed sequence tag analysis of genes expressed in the bay scallop, Argopecten irradians Biological Bulletin 205: 227-228.\nRoberts SB, Goetz FW. (2003) Myostatin protein and mRNA transcript levels in adult and developing brook trout Molecular and Cellular Endocrinology 210(1-2): 9-20.\nRoberts SB, Goetz FW. (2001) Differential skeletal muscle expression of myostatin across teleost species, and the isolation of multiple myostatin isoformsFEBS Letters Vol 49:3,212-216.\n\n\nRoberts SB, Langenau DM, Goetz FW. (2000) Cloning and characterization of prostaglandin endoperoxide synthase-1 and -2 from the brook trout ovary Molecular and Cellular Endocrinology 160(1-2):89-97.\n\n\nMoser ML, Roberts SB. (2000) Effects of nonindigenous ictalurids and recreational electrofishing on the ictalurid community of the Cape Fear River drainage, North Carolina in Catfish 2000: Proceedings of the International Ictalurid Symposium; ER Irwin, WA Hubert, CF Rabeni, HL Schramm, Jr., and T Coon, editors. Davenport, IA. June 23-25, 1998. pp 479-485.\nRoberts SB, Langenau DM, Goetz FW. (2000) Isolation through cloning of fish prostaglandin endoperoxide synthase (cyclooxygenase) in Proceedings of the 6th International Symposium on the Reproductive Physiology of Fish; B Norberg, OS Kjesbu, GL Taranger, E Andersson, and SO Stefansson, editors. Bergen, Norway. July 4-9, 1999. p 197.\nLangenau DM, Goetz FW, Roberts SB. (1999) The upregulation of messenger ribonucleic acids during 17a, 20b-dihydroxy-4-pregnen-3-one-induced ovulation in the perch ovary Journal of Molecular Endocrinology 23(2):137-52.\nRoberts SB, Jackson LF, King WK, Taylor RG, Grier HJ, Sullivan CV. (1999) Annual reproductive cycle of the common snook: Endocrine correlates of maturation Transactions of the American Fisheries Society 128:426-445.\n\n\n\nBook Chapters\nMoreira Sanmartín R, Roberts SB, Figueras A. (2016) Molluscs. pages 223-245, in Genomics in Aquaculture. Editors: Simon A. MacKenzie and Sissel Jentoft. ISBN: 978-0-12-801418-9\nGavery, M., & Roberts, S. (2018). Genetics & Epigenetics in Life History and Reproduction: Oysters. 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\n\n\n\nPreprints\nShelly 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 devleopmental processes and temperature-influenced physiological response differences in a bivalve mollusc. bioRxiv. https://doi.org/10.1101/2020.06.05.137059\nEmma 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 doi: https://doi.org/10.1101/094615\nHeare 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\nGavery 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\nHeare 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 http://dx.doi.org/10.7287/peerj.preprints.704v1\nClaire E. Olson, Steven B. Roberts. Indication of family-specific DNA methylation patterns in developing oysters bioRxiv doi: http://dx.doi.org/10.1101/012831\nRoberts et al. Sequence Data that never made it. https://www.authorea.com/users/3858/articles/3989/_show_article\nDavid 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 peer reviews: BMC, MB\nDavid 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 peer reviews: AB\nStorer C, Goetz F, Roberts S. (preprint) Transcriptional variation in lake trout (Salvelinus namaycush) ecotypes raised under constant environmental conditions. Status: Available for Comment\nSteven Roberts, Roxanna Smolowitz, Richard Karney, Mackenzie Gavery et al. (preprint) Disease tolerance in the eastern oyster. Status: Available for Comment\nRoberts et al. (preprint) Hard clam gene expression analysis. Status: Available for Comment\nArchived\nDimond 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\nMackenzie Gavery and Steven Roberts (preprint) A context specific role for DNA methylation in bivalves. Status: Archived download (Revised and later accepted at Briefings in Functional Genomics 10.1093/bfgp/elt054\nEmma Timmins-Schiffman, Carolyn Friedman, Steven Roberts, Sam White, Dave Metzger (preprint) Genomic resource development of shellfish of conservation concern. Status: on figshare (published - Molecular Ecology Resources)\nTimmins-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 (published - Marine Biology)\n\nLyons, Dungan, and Roberts – Thraustochytrid-like isolates from marine bivalve mollusks\n\nSmolowitz, Schaff, DeFaveri, Roberts - Renal Trematodiasis of Largemouth Bass and Development of PCR Methods\n\nWhite SJ and Roberts S. (preprint) Identification of myostatin interacting proteins using a yeast-two hybrid approach. Status: Available for Comment\n\nGavery MR, White SJ, Roberts S (preprint) Characterization of prostaglandin endoperoxide synthase from the Pacific oyster, Crassostrea gigas. Status: Available for Comment\n\nThompson R and Roberts SB (preprint) Influence of carbon dioxide-induced acidification and mechanical stress on gene expression and microbial community composition in oysters. Status: Available for Comment\n\n\n\n\nTheses\nDeveloping Tools and Resources for Maturation Control in Bivalvia. Olivia Cattau. 2023 http://hdl.handle.net/1773/50826\nPatterns, dynamics, and potential roles of DNA methylation in reef corals and their allies. James Dimond. 2019 http://hdl.handle.net/1773/44815\nResponse of Olympia oysters (Ostrea lurida) to changing environmental conditions. Jake Heare. 2015 http://hdl.handle.net/1773/35206\nGenomic signatures of natural selection and population structure in West Coast and Alaskan sablefish (Anoplopoma fimbria). Andrew Jasonowicz. 2014 http://hdl.handle.net/1773/33907\nDNA methylation variation in gametes and larvae of the Pacific oyster, Crassostrea gigas. Claire Ellis Olson. 2014 http://hdl.handle.net/1773/27478\nEpigenomic and transcriptomic regulation of environmental responses in the Pacific oyster, Crassostrea gigas. Mackenzie Gavery. 2014. http://hdl.handle.net/1773/25984\nThe 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\nSablefish (Anoplopoma fimbria) sperm: The physiology of activation and the development of a cryopreservation protocol. Doug Immerman. 2014. http://hdl.handle.net/1773/25414\nGenetic and phenotypic diversity in sockeye salmon, Oncorhynchus nerka. Caroline Storer. 2012. figshare.  http://dx.doi.org/10.6084/m9.figshare.661720\nCharacterizing the effects of ocean acidification in larval and juvenile Manila clam, Ruditapes philippinarum, using a transcriptomic approach. David Metzger. 2012  download\n\n\n\nNotebooks\n\n\n\nPerson\nNotebook\nCommitment\n\n\n\n\nSteven Roberts\nsr320.github.io\n\n\n\nSam White\nrobertslab.github.io\n\n\n\nMatt George\nmattgeorgephd.github.io\n\n\n\nAspen Coyle\naspencoyle.github.io\n\n\n\nAriana Huffmyer\nahuffmyer.github.io\n\n\n\nChris Mantegna\nchrismantegna.github.io/cmlabsite\n\n\n\nZach Bengtsson\nzbengt.github.io\n\n\n\nCeleste Valdivia\nvaleste.github.io\n\n\n\nLarken Root\nlarkenr.github.io\n\n\n\nGrace Crandall\ngrace-ac.github.io\n\n\n\nKathleen Durkin\nshedurkin.github.io\n\n\n\n\n\n\n\nRecent Presentations\n\n2024\n\nPycnopodia helianthoides immune response to Sea Star Wasting Disease. Grace Crandall. Society of Integrative and Comparative Biology. January 2024.\nThermal stress reduces photosynthate metabolism and disrupts nitrogen cycling in coral larvae. Ariana S. Huffmyer. Society of Integrative and Comparative Biology. January 2024.\nBiodiversity Survey Methods: Using eDNA Metabarcoding to Complement Existing Methods. Chris Mantegna. Society of Integrative and Comparative Biology. January 2024.\nComparative analyses of long non-coding RNA activity in three coral species. Zachary Bengtsson. Society of Integrative and Comparative Biology. January 2024.\n\n\n\n2023\n\nPycnopodia helianthoides immune response to Sea Star Wasting Disease. Grace Crandall. Western Society of Naturalists, Monterey, California. November 2023.\nGenomic Applications in Sustainable Aquaculture. Steven Roberts. 1er Congreso de Biología Experimental y Aplicada, CICESE, Ensenada, Mexico. October 2023\nDevelopment of an Alternative Sterility Method for Shellfish Aquaculture: Identification of Candidate Genes Involved in Germ Cell Specification Mackenzie Gavery (NOAA Fisheries - NW Fisheries Science Center), Lauren Saunders, Lauren Vandepas, Brent Vadopalas, Adam Luckenbach, Cole Trapnell, Steven Roberts. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023\nEnvironmental Priming for Ocean Acidification: Potential hatchery practices to build resilience for clam aquaculture in the Puget Sound Larken Root (Univeristy of Washington/NOAA), Mackenzie Gavery, Ryan Crim. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023\nTriploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves Matthew George (University of Washington), Olivia Cattau, Mollie A. Middleton, Delaney Lawson, Brent Vadopalas, Mackenzie Gavery, Steven Roberts. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023\nTriploid Pacific oysters experience enhanced mortality following marine heatwaves Presentation. National Shellfish Association Annual Meeting, Baltimore, MD, March 30, 2023.\nDNA Methylaiton in Bivalves Keynote at Epigenomics in Aquaculture - January 25 2023, University of Concepcion, Chile\nPloidy mediates the stress response of Pacific oysters following marine heatwave exposure Presentation. Plant and Animal Genome Conference, San Diego, CA, January 14, 2023.\nTriploid Pacific oysters exhibit stress response dysregulation and elevated mortality following marine heatwaves Presentation. NOAA Fisheries Northwest Fisheries Science Center Physiology Group Meeting, Seattle, WA, January 11, 2023.\n\n\n\n2022\n\nMechanisms of tilapia salinity tolerance at the limits of osmoregulation Presentation. NOAA physiology program monthly meeting, Virtual, March 3, 2022.\nYellow Island Intertidal Ecological Monitoring Presentation. NWStraits Commission meeting, Virtual, August 12, 2022.\nComparative Response of Littleneck and Manila Clams from the Puget Sound to Ocean Acidification Conditions: Year 1 Presentation. Pacific Coast Shellfish Growers Association (PCSGA) annual meeting, Wenatchee, September 20, 2022.\nUsing aquaculture to turn the tide on aquatic ecosystem collapse Presentation. University of Puget Sound Weekly Science Seminar, Thompson Hall, September 29, 2022.\nPhysiological and multi-omic signatures of shifts in symbiotic nutritional exchange in reef-building coral early life history Presentation. Benthic Ecology Meeting. Portsmouth, New Hampshire. March 2022.\nUnderstanding shifts in symbiotic and physiological state in reef- building corals across developmental and environmental gradients Virtual seminar. Old Dominion University. December 2022.\nMulti-omic approaches to understand reef coral development and symbiosis Virtual seminar. University of Washington eScience Institute Postdoctoral Seminar Series. November 2022.\nThe contribution of summer heatwaves to ‘triploid mortality’ events observed during commercial pacific oyster production in Washington State Presentation. The Society of Integrative and Comparative Biology, Virtual, January 4, 2022.\n\n\n\n2021\n\nDiversity in animal response to environmental change Presentation. Academic Data Science Alliance (ADSA) 2021 Data Science Coast to Coast Seminar Series, Virtual May 19, 2021 3pm.\nExploring the tolerance of Pacific geoduck to low pH through comparative physiology, genomics, and DNA methylation Presentation. The Society for Integrative and Comparative Biology (SICB) 2021 Annual Meeting, Virtual January - February 2021\nA perspective on DNA methylation in bivalves Presentation. The Society for Integrative and Comparative Biology (SICB) 2021 Annual Meeting, Virtual January - February 2021\nHow do dynamic conditions shape coral symbiosis and metabolism and drive energetic-epigenetic linkages? Presentation. 2021 Moorea Coral Reef Long Term Ecological Research All Invesitgator Meeting. November 2021.\n\n\n\n2020\n\nHarnessing the power of single-cell RNA sequencing to control reproductive development in bivalves 74th Annual Pacific Coast Shellfish Growers Association Conference, Virtual October 2020\nCarryover effects of winter warming in the Olympia oyster. Presentation. 74th Annual Pacific Coast Shellfish Growers Association Conference, Virtual October 2020\nOysters, Ocean Acidification, and -Omics Presentation, Friday Harbor Laboratories Summer Seminar Series, June 2020\nInfluence of ocean acidification on eastern (Crassostrea virginica) and Pacific oyster (Crassostrea gigas) DNA methylation Poster, Ocean Sciences Meeting 2020, San Diego, CA February 2020\nDNA methylation associations with growth rate in Olympia oyster populations presentation, Aquaculture America 2020, Honolulu, HI, February 2020\nInfluence of ocean acidification on DNA methylation patterns in geoduck Presentation, The Plant and Animal Genome XXVII Conference (PAG), San Diego, CA, January 2020"
+    "text": "Publications\nSee the table of contents at the right to jump to book chapters, preprints, theses, notebooks, and recent presentations. Search the entire website using the search icon in top right menu.\n\n\nRecent Papers\nRecent 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\nsee also: Google Scholar\n\n\n   \n     \n     \n       Order By\n       Default\n         \n          Title\n        \n         \n          Author\n        \n         \n          Publication\n        \n         \n          Year\n        \n     \n  \n    \n      \n      \n    \n\n\n\n  \n    Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations\n    Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C\n    \n    (2024)\n    \n      Details\n    \n  \n  \n    A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io\n    Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K.\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Characterizing biological responses to climate variability and extremes to improve biodiversity projections\n    Lauren B Buckley, Emily Carrington, Michael E Dillon, Carlos García-Robledo, Steven B Roberts, Jill L Wegrzyn, Mark C Urban\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment\n    Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, Fabian J Tapia, Marco Yévenes, Gonzalo Gajardo, Jorge E Toro, Pablo A Oyarzún, Gloria Arriagada, Beatriz Novoa, Antonio Figueras, Steven Roberts, Marco Gerdol\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    Epigenetic and genetic population structure is coupled in a marine invertebrate\n    Katherine Silliman, Laura H Spencer, Samuel J White, Steven B Roberts\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Population-specific effects of ocean acidification in the Olympia oyster\n    Laura H Spencer, Steven B Roberts, Katherine Silliman, \n    \n    (2023)\n    \n      Details\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n  \n  \n    Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge\n    Roberto Arredondo-Espinoza, Ana M Ibarra, Steven B Roberts, Maria Teresa Sicard-González, Cristina Escobedo-Fregoso\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n  \n  \n    Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves\n    Matthew N. George, Olivia Cattau, Mollie Middleton, Delaney Lawson, Brent Vadopalas, Mackenzie Gavery, Steven Roberts\n    \n    (2023)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n  \n  \n    Acclimatory gene expression of primed clams enhances robustness to elevated pCO2\n    Samuel J. Gurr, Shelly A. Wanamaker , Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)\n    Grace Crandall, Pamela C. Jensen, Samuel J. White, Steven Roberts \n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification\n    Yaamini Venkataraman, Samuel J White and Steven Roberts\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams\n    Hollie M. Putnam, Shelly A. Wanamaker , Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, Erich Jaeger, Jonathan Soohoo, Cristian Gallardo-Escárate, Frederick W. Goetz, Steven B. Roberts\n    \n    (2022)\n    \n      Details\n    \n    \n       Preprint\n    \n    \n       Materials\n    \n  \n  \n    Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment\n    Dang, X., Lim, Y.-K., Li, Y., Roberts, S. B., Li, L., & Thiyagarajan, V.\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature\n    Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S.\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam\n    Samuel J. Gurr, Shelly A. Wanamaker , Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam\n    \n    (2022)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis\n    Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Gustavo Nuñez-Acuña, Diego Valenzuela-Miranda, Ana Teresa Gonçalves, Hugo Escobar-Sepulveda, Ivan Liachko, Bradley Nelson, Steven Roberts & Wesley Warren\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery\n    Emma Timmins-Schiffman, Samuel J. White, Rhonda Elliott Thompson, Brent Vadopalas, Benoit Eudeline, Brook L. Nunn & Steven B. Roberts\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n  \n  \n    DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing\n    James L Dimond, Nhung Nguyen, Steven B Roberts\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas\n    Arredondo-Espinoza Roberto, Ibarra Ana M., Roberts B. Steven, Sicard-Gonzalez Maria Teresa, Escobedo-Fregoso Cristina\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n  \n  \n    Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases\n    Shelly A. Wanamaker , Yaamini R. Venkataraman, Mackenzie R. Gavery, Steven B. Roberts, Debashish Bhattacharya, Alan Downey-Wall, Jose M. Eirin-Lopez, Kevin M. Johnson, Katie E. Lotterhos, Jonathan B. Puritz and Hollie M. Putnam\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Preprint\n    \n    \n       eprint\n    \n    \n       Materials\n    \n  \n  \n    Latent effects of winter warming on Olympia oyster reproduction and larval viability\n    Laura H. Spencer, Erin Horkan, Ryan Crim, Steven B. Roberts\n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n    \n       Materials\n    \n  \n  \n    Oyster biomineralisation under ocean acidification: from genes to shell\n    Chandra Rajan, K., Yuan, M., Yu, Z., Roberts, S.B. and Thiyagarajan, V. \n    \n    (2021)\n    \n      Details\n    \n    \n      DOI\n    \n  \n\n\nNo matching items\n\n\n\n\nLess Recent Papers (2020 and older)\nShelly 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 BMC Genomics 21, 723 doi:10.1186/s12864-020-07127-3\n\nYong-Kian Lim, Khan Cheung, Xin Dang, Steven B. Roberts, Xiaotong Wang, Vengatesen Thiyagarajan (2020) DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis Marine Environmental Research, Volume 163 doi:10.1016/j.marenvres.2020.105214\nDowney-Wall Alan M., Cameron Louise P., Ford Brett M., McNally Elise M., Venkataraman Yaamini R., Roberts Steven B., Ries Justin B., Lotterhos Katie E (2020) Ocean Acidification Induces Subtle Shifts in Gene Expression and DNA Methylation in Mantle Tissue of the Eastern Oyster (Crassostrea virginica) Frontiers in Marine Science v7 p828 doi:10.3389/fmars.2020.566419\nCristian Gallardo-Escárate; Valentina Valenzuela-Muñoz; Gustavo Núñez-Acuña; Diego Valenzuela-Miranda; Bárbara P. Benaventel; Constanza Sáez-Vera; Homero Urrutia; Beatriz Novoa; Antonio Figueras; Steven Roberts; Paulina Assmann; Marta Bravo (2020) The wastewater microbiome: A novel insight for COVID-19 surveillance Science of The Total Environment Page: 142867 doi:10.1016/j.scitotenv.2020.142867\nBonnie J. Becker, Michael D. Behrens, Brian Allen, Megan Hintz, Hannah Parker, Michelle M. McCartha, and Sarah M. White (2020) Spatial and Temporal Distribution of the Early Life History Stages of the Native Olympia Oyster Ostrea lurida (Carpenter, 1864) in a Restoration Site in Northern Puget Sound, Wa Journal of Shellfish Research 39(1), 43-58. doi:/10.2983/035.039.0105\nEmma Timmins-Schiffman, José M. Guzmán, Rhonda Elliott Thompson, Brent Vadopalas, Benoit Eudeline and Steven B. Roberts (2020) Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates Scientific Reports 10, 6042. doi:10.1038/s41598-020-63218-x\nVenkataraman Yaamini R., Downey-Wall Alan M., Ries Justin, Westfield Isaac, White Samuel J., Roberts Steven B., Lotterhos Kathleen E (2020) General DNA Methylation Patterns and Environmentally-Induced Differential Methylation in the Eastern Oyster (Crassostrea virginica) Frontiers in Marine Science, Volume 7, Page 225. doi:10.3389/fmars.2020.00225\nGurr SJ, Vadopalas B, Roberts SB, Putnam HM (2020) Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck Panopea generosa following short-term exposure to acidified seawater Conservation Physiology, Volume 8, Issue 1, coaa024. doi:10.1093/conphys/coaa024\nSpencer, LH, Venkataraman, YR, Crim R, Ryan S, Horwith MJ, and Roberts SB (2020) Carryover effects of temperature and pCO2 across multiple Olympia oyster populations. Ecological Applications 00( 00):e02060. doi:10.1002/eap.2060\nDimond JL and Roberts SB. (2020) Convergence of DNA Methylation Profiles of the Reef Coral Porites astreoides in a Novel Environment Frontiers in Marine Science. vol 6. doi:10.3389/fmars.2019.00792\nVenkataraman YR, Spencer LH, Roberts SB. (2019) Larval Response to Parental Low pH Exposure in the Pacific Oyster Crassostrea gigas Journal of Shellfish Research, 38(3), 743-750. doi:10.2983/035.038.0325\nTimmins‐Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB. (2019) Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2. Ecol Evol.00: 1– 13. doi:10.1002/ece3.5885\n\nGallardo-Escárate C, Valenzuela-Muñoz V, Núñez-Acuña , Carrera C, Gonçalves AT, Valenzuela-Miranda D, Benavente BP, Roberts SB. (2019) Catching the complexity of salmon-louse interactions Fish & Shellfish Immunology. doi:10.1016/j.fsi.2019.04.065\nSpencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB. (2019) Pacific geoduck (Panopea generosa) resilience to natural pH variation Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. doi:10.1016/j.cbd.2019.01.010 bioRxiv\nVenkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB. (2019) Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences Mar Ecol Prog Ser 610:65-81. doi:10.3354/meps12858 bioRxiv\nJuárez, O., Lafarga-De la Cruz, F., Leyva-Valencia, I., López-Landavery, E., García-Esquivel, Z., Díaz, F., Re-Araujo, D., Vadopalas, B., and C. Galindo-Sánchez. (2018). Transcriptomic and metabolic response to chronic and acute thermal exposure of juvenile geoduck clams Panopea globosa. Marine Genomics. doi:10.1016/j.margen.2018.09.003\nJavier A. Rodriguez‐Casariego, Mark C. Ladd, Andrew A. Shantz, Christian Lopes, Manjinder S. Cheema, Bohyun Kim, Steven B. Roberts, James W. Fourqurean, Juan Ausio, Deron E. Burkepile, and Jose M. Eirin‐Lopez. (2018) Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis Ecol Evol. 2018;00:1–15. doi:10.1002/ece3.4678 pdf\nRoberts SB, Gavery MR. (2018) Opportunities in Functional Genomics: A Primer on Lab and Computational Aspects Journal of Shellfish Research 37(4):747-754. doi:10.2983/035.037.0406\nSilliman KE, Bowyer TK, Roberts SB. (2018) Consistent differences in fitness traits across multiple generations of Olympia oysters Scientific Reports volume 8, Article number:6080. doi:10.1038/s41598-018-24455-3\nHeare JE, White SJ, Vadopalas B, Roberts SB. (2018) Differential response to stress in Ostrea lurida as measured by gene expression PeerJ 6:e4261. doi: 10.7717/peerj.4261\nGoetz FW, Jasonowicz AJ, Roberts SB. (2017) What goes up must come down: Diel vertical migration in the deep-water sablefish (Anoplopoma fimbria) revealed by pop-up satellite archival tags Fish Oceanogr. 2017;00:1–16. doi: 10.1111/fog.12239\nGavery MR, Roberts SB. (2017) Epigenetic considerations in aquaculture PeerJ 5:e4147 doi: 10.7717/peerj.4147\n\n\n\n\n\nJake Emerson Heare, Brady Blake, Jonathan P Davis, Brent Vadopalas, Steven Roberts (2017) Evidence of Ostrea lurida Carpenter, 1864 population structure in Puget Sound, WA Marine Ecology 38:e12458 doi: 10.1111/maec.12458\nMegan Hintz, Katherine Gratz, Bonnie Becker, Brent Vadopalas, and Steven Roberts (2017) A Nonlethal Anesthesia Protocol for Accessing the Mantle Cavity of Olympia Oysters in the Laboratory or Field Journal of Shellfish Research 2017 36 (2), 353-357 doi: 10.2983/035.036.0207\nSamuel J. White, Brent Vadopalas, Katherine Silliman & Steven B. Roberts (2017) Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters, Ostrea lurida Scientific Data 4, Article number: 170130 doi: 10.1038/sdata.2017.130\nDimond JL, Gamblewood SK, Roberts SB. (2017) Genetic and epigenetic insight into morphospecies in a reef coral Molecular Ecology. 00:1–12. doi: 10.1111/mec.14252\nEmma B. Timmins-Schiffman, Grace A Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn and Steven Roberts (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 pdf\nC. Gallardo-Escárate V. Valenzuela-Muñoz S. Boltaña G. Nuñez-Acuña D. Valenzuela-Miranda A.T. Gonçalves C. Détrée E. Tarifeño-Saldivia R. Farlora S. Roberts H.M. Putnam (2017) The Caligus rogercresseyi miRNome: Discovery and transcriptome profiling during the sea lice ontogeny AgriGene doi: 10.1016/j.aggene.2017.03.002 eprint\nThe Aquaculture Genomics, Genetics and Breeding Workshop (2017) Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research BMC Genomics 18:191. doi: 10.1186/s12864-017-3557-1\nDetree C, Núñez-Acuña G, Roberts S, Gallardo-Escárate C (2016) Uncovering the Complex Transcriptome Response of Mytilus chilensis against Saxitoxin: Implications of Harmful Algal Blooms on Mussel Populations PLoS ONE 11(10): e0165231. doi:10.1371/journal.pone.0165231\n\nDimond JL and Roberts SB (2016), Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change Molecular Ecology doi:10.1111/mec.13414 preprint\nJasonowicz AJ, Goetz FW, Goetz GW, Nichols KM (2016) Love the one you’re with: Genomic evidence of panmixia in the sablefish (Anoplopoma fimbria) Canadian Journal of Fisheries and Aquatic Sciences doi: 10.1139/cjfas-2016-0012\nFroehlich HE, Roberts SB, Essington TE (2015) Evaluating hypoxia-inducible factor-1α mRNA expression in a pelagic fish, Pacific herring Clupea pallasii, as a biomarker for hypoxia exposure Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology doi:10.1016/j.cbpa.2015.07.016\nCook MA, Massee KC, Wade TH, Oden SM, Jensen C, Jasonowicz A, Immerman DA, Goetz FW (2015) Culture of sablefish (Anoplopoma fimbria) larvae in four experimental tank designs Aquacultural Engineering doi:10.1016/j.aquaeng.2015.09.003\n\nFuess LE, Eisenlord ME, Closek CJ, Tracy AM, Mauntz R, Gignoux-Wolfsohn S, Moritsch MM, Yoshioka R, Burge CA, Harvell CD, Friedman CS, Hewson I, Hershberger PK, Roberts SB (2015) Up in Arms: Immune and Nervous System Response To Sea Star Wasting Disease PLoS ONE doi:10.1371/journal.pone.0133053\nTimmins-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\nImmerman DA and Goetz FW (2014). The activation and cryopreservation of sablefish (Anoplopoma fimbria) sperm Aquaculture doi:10.1016/j.aquaculture.2014.04.010\nOlson CE and Roberts SB. (2014). Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes Frontiers in Physiology. 5:224. doi: 10.3389/fphys.2014.0022\nGavery MR and Roberts SB. (2014) A context specific role for DNA methylation in bivalves Briefings in Functional Genomics. doi:10.1093/bfgp/elt054 (pdf)\nGavery MR and Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc PeerJ 1:e215. doi:10.7717/peerj.215\n\n\n\nGarcia-Vedrenne AE, Groner M, Page-Karjian A, Siegmund G-F, Singhal S, Sziklay J and Roberts SB. (2013) Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression PLoS ONE 8(9): e74196. doi:10.1371/journal.pone.0074196\nStorer CS, Quinn TP and Roberts SB. (2013) Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon Biogerontology. doi:10.1007/s10522-013-9448-1 (pdf)\nBurge CA, Mouchka ME, Harvell CD and Roberts SB. (2013) Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing Frontiers in Physiology 4:180. doi:10.3389/fphys.2013.00180\nTimmins-Schiffman EB, Nunn BL, Goodlett DR and Roberts SB. (2013) Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster Conservation Physiology. doi:10.1093/conphys/cot009\nTimmins-Schiffman EB, Friedman CS, Metzger DC, White SJ and Roberts SB. (2013) Genomic resource development for shellfish of conservation concern Molecular Ecology Resources. doi:10.1111/1755-0998.12052\nTimmins-Schiffman EB and 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\n\n\nStorer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW and Seeb JE. (2012) Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism PLoS ONE 7(11): e49018. doi:10.1371/journal.pone.0049018\nTimmins-Schiffman EB, O’Donnell M, Friedman CS, and Roberts SB. (2012) Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas Marine Biology. doi:10.1007/s00227-012-2055-x pdf\nBurge CA, Douglas N, Conti-Jerpe I, Weil E, Roberts SB, Friedman CS and CD Harvell. (2012) Friend or foe: the association of Labyrinthulomycetes with the Caribbean sea fan, Gorgonia ventalina Diseases of Aquatic Organisms 101:1-12. doi:10.3354/dao02487\nMetzger DC, Pratt P and Roberts SB. (2012) Characterizing the effects of heavy metal and Vibrio exposure on hsp70 expression in Crassostrea gigas gill tissue Journal of Shellfish Research 31(3):627-630. doi:10.2983/035.031.0305 pdf\nRoberts SB, Hauser L, Seeb LW and Seeb JE (2012) Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing PLoS ONE 7(2): e30908. doi:10.1371/journal.pone.0030908\nRoberts SB and Gavery MR (2012) Is there a relationship between DNA methylation and phenotypic plasticity in invertebrates? Frontiers in Physiology 2:116. doi:10.3389/fphys.2011.00116\nGavery MR and Roberts SB (2012) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 7:2 94-99. doi:10.1016/j.cbd.2011.12.003\nMorera D, Roher N, Ribas L, Balasch JC, Doñate C, Callol A, Boltaña A, Roberts SB, Goetz G, Goetz FW and Mackenzie SA. (2011) RNA-Seq reveals an integrated immune response in nucleated erythrocytes PLoS ONE 6(10): e26998. doi:10.1371/journal.pone.0026998\nRoberts SB, Sunila I, and Wikfors G. (2011) Immune response and mechanical stress susceptibility in diseased oysters, Crassostrea virginica Journal of Comparative Physiology B 182:1 41-48. doi:10.1007/s00360-011-0605-z\nSeeb JE, Carvalho G, Hauser L, Naish K, Roberts SB and Seeb LW. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms Molecular Ecology Resources 11 1–8. doi:10.1111/j.1755-0998.2010.02979.x\nSeeb JE, Pascal CE, Graue ED, Seeb LW, Templin WD, Harkins T and Roberts SB. (2010) Transcriptome sequencing and high-resolution melt analysis advance single nucleotidepolymorphism discovery in duplicated salmonids Molecular Ecology Resources. doi: 10.1111/j.1755-0998.2010.02936.x\nGavery MR and Roberts SB. (2010) DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas) BMC Genomics 11:483. doi:10.1186/1471-2164-11-483\nMathger L, Roberts SB, and Hanlon R. (2010) Evidence for distributed light sensing in the skin of cuttlefish, Sepia officinalis Biology Letters. doi: 10.1098/rsbl.2010.0223\nGoetz FW, Rosauer D, Sitar S, Goetz G, Simchick C, Roberts SB, Johnson R, Murphy C, Bronte C, and Mackenzie S. (2010) A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush) Molecular Ecology 19 176–196.\nDefaveri J*, Smolowitz R, and Roberts S (2009) Development and validation of a real-time quantitative PCR assay for the detection and quantification of Perkinsus marinus in the Eastern oyster, Crassostrea virginica Journal of Shellfish Research Vol. 28 No. 3 459-464. eprint\nRoberts SB, Goetz G, White S, and Goetz F (2009) Analysis of genes isolated from plated hemocytes of the Pacific Oyster, Crassostrea gigas Marine Biotechnology 11:24-44. doi: 10.1007/s10126-008-9117-6\nRoberts SB, Gueguen Y, de Lorgeril J, and Goetz F. (2008) Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure Developmental and Comparative Immunology 32, 1099-1104. doi: 10.1016/j.dci.2008.02.006\n\n\nLyons MM*, Lau Y-T, Carden WE, Ward JE, Roberts SB, Smolowitz R, Vallino J, and Allam B. (2007) Characteristics of marine aggregates in shallow-water ecosystems: Implications for disease ecology EcoHealth 4, 406–420.\nWeiss E, Bennie M, Hodgins-Davis A, Roberts SB, and Gerlach G. (2007) Characterization of new SSR-EST markers in cod, Gadus morhua Molecular Ecology Notes 7: 866–867. doi: 10.1111/j.1471-8286.2007.01731.x\nHodgins-Davis A*, Roberts SB, Cowan D, Atema J, Avolio C, Defaveri J, and Gerlach G. (2007) Characterization of SSRs from the American lobster, Homarus americanus Molecular Ecology Notes 7:330-332.\nRodgers BD, Roalson EH, Weber GM, Roberts SB, Goetz FW. (2007) A Proposed Nomenclature Consensus for the Myostatin Gene Family AJP- Endocrinology and Metabolism 292(2):E371-2.\nLyons MM*, Smolowitz R, Dungan C, and Roberts SB. (2006) Development of a real-time quantitative PCR assay for the hard clam pathogen, Quahog Parasite Unknown (QPX) Diseases of Aquatic Organisms 72(1):45-52.\nBiga PR, Roberts SB, Iliev DB, McCauley LA, Moon JS, Collodi P, and Goetz FW. (2005) The isolation, characterization, and expression of a novel GDF11 gene and a second myostatin form in zebrafish, Danio rerio. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 141: 218-230.\nRoberts SB, Romano C, and Gerlach G. (2005) Characterization of EST derived SSRs from the bay scallop, Argopectens irradiansMolecular Ecology Notes 5: 567-568.\nJentoft S, Topp N, Seeliger M, Malison JA, Barry TP, Held JA, Roberts SB, and Goetz FW. (2005) Lack of growth enhancement by exogenous growth hormone treatment in yellow perch in four separate experiments Aquaculture 250:471-479.\nHollis DM, Goetz FW, Roberts SB, and Boyd SK. (2004) Acute neurosteroid modulation and subunit isolation of the GABAa receptor in the bullfrog, Rana catesbeiana Journal of Molecular Endocrinology 32(3):921-34.\nBiga PR, Cain KD, Hardy RW, Schelling GT, Overturf K, Roberts SB, Goetz FW, Ott TL. (2004) Growth hormone differentially regulates muscle myostatin1 and -2 and increases circulating cortisol in rainbow trout Oncorhynchus mykiss General and Comparative Endocrinology Vol 138(1):32-41.\nRoberts SB, McCauley LAR, Devlin RH, Goetz FW. (2004) Transgenic salmon over-expressing growth hormone exhibit decreased myostatin transcript and protein expression Journal of Experimental Biology 207(Pt 21):3741-8.\nKim H-W, Mykles DL, Goetz FW, Roberts SB. (2004) Characterization of an invertebrate myostatin homologue from the bay scallop, Argopecten irradians BBA – Gene Structure and Expression 1679(2):174-9.\nRoberts SB, Barry T, Malison J, Goetz FW. (2004) Production of a recombinantly-derived growth hormone antibody and the characterization of growth hormone levels in yellow perch Aquaculture Vol.232/1-4: 591-602.\nRoberts SB, Goetz FW. (2003) Expressed sequence tag analysis of genes expressed in the bay scallop, Argopecten irradians Biological Bulletin 205: 227-228.\nRoberts SB, Goetz FW. (2003) Myostatin protein and mRNA transcript levels in adult and developing brook trout Molecular and Cellular Endocrinology 210(1-2): 9-20.\nRoberts SB, Goetz FW. (2001) Differential skeletal muscle expression of myostatin across teleost species, and the isolation of multiple myostatin isoformsFEBS Letters Vol 49:3,212-216.\n\n\nRoberts SB, Langenau DM, Goetz FW. (2000) Cloning and characterization of prostaglandin endoperoxide synthase-1 and -2 from the brook trout ovary Molecular and Cellular Endocrinology 160(1-2):89-97.\n\n\nMoser ML, Roberts SB. (2000) Effects of nonindigenous ictalurids and recreational electrofishing on the ictalurid community of the Cape Fear River drainage, North Carolina in Catfish 2000: Proceedings of the International Ictalurid Symposium; ER Irwin, WA Hubert, CF Rabeni, HL Schramm, Jr., and T Coon, editors. Davenport, IA. June 23-25, 1998. pp 479-485.\nRoberts SB, Langenau DM, Goetz FW. (2000) Isolation through cloning of fish prostaglandin endoperoxide synthase (cyclooxygenase) in Proceedings of the 6th International Symposium on the Reproductive Physiology of Fish; B Norberg, OS Kjesbu, GL Taranger, E Andersson, and SO Stefansson, editors. Bergen, Norway. July 4-9, 1999. p 197.\nLangenau DM, Goetz FW, Roberts SB. (1999) The upregulation of messenger ribonucleic acids during 17a, 20b-dihydroxy-4-pregnen-3-one-induced ovulation in the perch ovary Journal of Molecular Endocrinology 23(2):137-52.\nRoberts SB, Jackson LF, King WK, Taylor RG, Grier HJ, Sullivan CV. (1999) Annual reproductive cycle of the common snook: Endocrine correlates of maturation Transactions of the American Fisheries Society 128:426-445.\n\n\n\nBook Chapters\nMoreira Sanmartín R, Roberts SB, Figueras A. (2016) Molluscs. pages 223-245, in Genomics in Aquaculture. Editors: Simon A. MacKenzie and Sissel Jentoft. ISBN: 978-0-12-801418-9\nGavery, M., & Roberts, S. (2018). Genetics & Epigenetics in Life History and Reproduction: Oysters. 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\n\n\n\nPreprints\nShelly 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 devleopmental processes and temperature-influenced physiological response differences in a bivalve mollusc. bioRxiv. https://doi.org/10.1101/2020.06.05.137059\nEmma 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 doi: https://doi.org/10.1101/094615\nHeare 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\nGavery 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\nHeare 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 http://dx.doi.org/10.7287/peerj.preprints.704v1\nClaire E. Olson, Steven B. Roberts. Indication of family-specific DNA methylation patterns in developing oysters bioRxiv doi: http://dx.doi.org/10.1101/012831\nRoberts et al. Sequence Data that never made it. https://www.authorea.com/users/3858/articles/3989/_show_article\nDavid 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 peer reviews: BMC, MB\nDavid 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 peer reviews: AB\nStorer C, Goetz F, Roberts S. (preprint) Transcriptional variation in lake trout (Salvelinus namaycush) ecotypes raised under constant environmental conditions. Status: Available for Comment\nSteven Roberts, Roxanna Smolowitz, Richard Karney, Mackenzie Gavery et al. (preprint) Disease tolerance in the eastern oyster. Status: Available for Comment\nRoberts et al. (preprint) Hard clam gene expression analysis. Status: Available for Comment\nArchived\nDimond 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\nMackenzie Gavery and Steven Roberts (preprint) A context specific role for DNA methylation in bivalves. Status: Archived download (Revised and later accepted at Briefings in Functional Genomics 10.1093/bfgp/elt054\nEmma Timmins-Schiffman, Carolyn Friedman, Steven Roberts, Sam White, Dave Metzger (preprint) Genomic resource development of shellfish of conservation concern. Status: on figshare (published - Molecular Ecology Resources)\nTimmins-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 (published - Marine Biology)\n\nLyons, Dungan, and Roberts – Thraustochytrid-like isolates from marine bivalve mollusks\n\nSmolowitz, Schaff, DeFaveri, Roberts - Renal Trematodiasis of Largemouth Bass and Development of PCR Methods\n\nWhite SJ and Roberts S. (preprint) Identification of myostatin interacting proteins using a yeast-two hybrid approach. Status: Available for Comment\n\nGavery MR, White SJ, Roberts S (preprint) Characterization of prostaglandin endoperoxide synthase from the Pacific oyster, Crassostrea gigas. Status: Available for Comment\n\nThompson R and Roberts SB (preprint) Influence of carbon dioxide-induced acidification and mechanical stress on gene expression and microbial community composition in oysters. Status: Available for Comment\n\n\n\n\nTheses\nDeveloping Tools and Resources for Maturation Control in Bivalvia. Olivia Cattau. 2023 http://hdl.handle.net/1773/50826\nPatterns, dynamics, and potential roles of DNA methylation in reef corals and their allies. James Dimond. 2019 http://hdl.handle.net/1773/44815\nResponse of Olympia oysters (Ostrea lurida) to changing environmental conditions. Jake Heare. 2015 http://hdl.handle.net/1773/35206\nGenomic signatures of natural selection and population structure in West Coast and Alaskan sablefish (Anoplopoma fimbria). Andrew Jasonowicz. 2014 http://hdl.handle.net/1773/33907\nDNA methylation variation in gametes and larvae of the Pacific oyster, Crassostrea gigas. Claire Ellis Olson. 2014 http://hdl.handle.net/1773/27478\nEpigenomic and transcriptomic regulation of environmental responses in the Pacific oyster, Crassostrea gigas. Mackenzie Gavery. 2014. http://hdl.handle.net/1773/25984\nThe 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\nSablefish (Anoplopoma fimbria) sperm: The physiology of activation and the development of a cryopreservation protocol. Doug Immerman. 2014. http://hdl.handle.net/1773/25414\nGenetic and phenotypic diversity in sockeye salmon, Oncorhynchus nerka. Caroline Storer. 2012. figshare.  http://dx.doi.org/10.6084/m9.figshare.661720\nCharacterizing the effects of ocean acidification in larval and juvenile Manila clam, Ruditapes philippinarum, using a transcriptomic approach. David Metzger. 2012  download\n\n\n\nNotebooks\n\n\n\nPerson\nNotebook\nCommitment\n\n\n\n\nSteven Roberts\nsr320.github.io\n\n\n\nSam White\nrobertslab.github.io\n\n\n\nMatt George\nmattgeorgephd.github.io\n\n\n\nAspen Coyle\naspencoyle.github.io\n\n\n\nAriana Huffmyer\nahuffmyer.github.io\n\n\n\nChris Mantegna\nchrismantegna.github.io/cmlabsite\n\n\n\nZach Bengtsson\nzbengt.github.io\n\n\n\nCeleste Valdivia\nvaleste.github.io\n\n\n\nLarken Root\nlarkenr.github.io\n\n\n\nGrace Crandall\ngrace-ac.github.io\n\n\n\nKathleen Durkin\nshedurkin.github.io\n\n\n\n\n\n\n\nRecent Presentations\n\n2024\n\nPycnopodia helianthoides immune response to Sea Star Wasting Disease. Grace Crandall. Society of Integrative and Comparative Biology. January 2024.\nThermal stress reduces photosynthate metabolism and disrupts nitrogen cycling in coral larvae. Ariana S. Huffmyer. Society of Integrative and Comparative Biology. January 2024.\nBiodiversity Survey Methods: Using eDNA Metabarcoding to Complement Existing Methods. Chris Mantegna. Society of Integrative and Comparative Biology. January 2024.\nComparative analyses of long non-coding RNA activity in three coral species. Zachary Bengtsson. Society of Integrative and Comparative Biology. January 2024.\n\n\n\n2023\n\nPycnopodia helianthoides immune response to Sea Star Wasting Disease. Grace Crandall. Western Society of Naturalists, Monterey, California. November 2023.\nGenomic Applications in Sustainable Aquaculture. Steven Roberts. 1er Congreso de Biología Experimental y Aplicada, CICESE, Ensenada, Mexico. October 2023\nDevelopment of an Alternative Sterility Method for Shellfish Aquaculture: Identification of Candidate Genes Involved in Germ Cell Specification Mackenzie Gavery (NOAA Fisheries - NW Fisheries Science Center), Lauren Saunders, Lauren Vandepas, Brent Vadopalas, Adam Luckenbach, Cole Trapnell, Steven Roberts. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023\nEnvironmental Priming for Ocean Acidification: Potential hatchery practices to build resilience for clam aquaculture in the Puget Sound Larken Root (Univeristy of Washington/NOAA), Mackenzie Gavery, Ryan Crim. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023\nTriploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves Matthew George (University of Washington), Olivia Cattau, Mollie A. Middleton, Delaney Lawson, Brent Vadopalas, Mackenzie Gavery, Steven Roberts. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023\nTriploid Pacific oysters experience enhanced mortality following marine heatwaves Presentation. National Shellfish Association Annual Meeting, Baltimore, MD, March 30, 2023.\nDNA Methylaiton in Bivalves Keynote at Epigenomics in Aquaculture - January 25 2023, University of Concepcion, Chile\nPloidy mediates the stress response of Pacific oysters following marine heatwave exposure Presentation. Plant and Animal Genome Conference, San Diego, CA, January 14, 2023.\nTriploid Pacific oysters exhibit stress response dysregulation and elevated mortality following marine heatwaves Presentation. NOAA Fisheries Northwest Fisheries Science Center Physiology Group Meeting, Seattle, WA, January 11, 2023.\n\n\n\n2022\n\nMechanisms of tilapia salinity tolerance at the limits of osmoregulation Presentation. NOAA physiology program monthly meeting, Virtual, March 3, 2022.\nYellow Island Intertidal Ecological Monitoring Presentation. NWStraits Commission meeting, Virtual, August 12, 2022.\nComparative Response of Littleneck and Manila Clams from the Puget Sound to Ocean Acidification Conditions: Year 1 Presentation. Pacific Coast Shellfish Growers Association (PCSGA) annual meeting, Wenatchee, September 20, 2022.\nUsing aquaculture to turn the tide on aquatic ecosystem collapse Presentation. University of Puget Sound Weekly Science Seminar, Thompson Hall, September 29, 2022.\nPhysiological and multi-omic signatures of shifts in symbiotic nutritional exchange in reef-building coral early life history Presentation. Benthic Ecology Meeting. Portsmouth, New Hampshire. March 2022.\nUnderstanding shifts in symbiotic and physiological state in reef- building corals across developmental and environmental gradients Virtual seminar. Old Dominion University. December 2022.\nMulti-omic approaches to understand reef coral development and symbiosis Virtual seminar. University of Washington eScience Institute Postdoctoral Seminar Series. November 2022.\nThe contribution of summer heatwaves to ‘triploid mortality’ events observed during commercial pacific oyster production in Washington State Presentation. The Society of Integrative and Comparative Biology, Virtual, January 4, 2022.\n\n\n\n2021\n\nDiversity in animal response to environmental change Presentation. Academic Data Science Alliance (ADSA) 2021 Data Science Coast to Coast Seminar Series, Virtual May 19, 2021 3pm.\nExploring the tolerance of Pacific geoduck to low pH through comparative physiology, genomics, and DNA methylation Presentation. The Society for Integrative and Comparative Biology (SICB) 2021 Annual Meeting, Virtual January - February 2021\nA perspective on DNA methylation in bivalves Presentation. The Society for Integrative and Comparative Biology (SICB) 2021 Annual Meeting, Virtual January - February 2021\nHow do dynamic conditions shape coral symbiosis and metabolism and drive energetic-epigenetic linkages? Presentation. 2021 Moorea Coral Reef Long Term Ecological Research All Invesitgator Meeting. November 2021.\n\n\n\n2020\n\nHarnessing the power of single-cell RNA sequencing to control reproductive development in bivalves 74th Annual Pacific Coast Shellfish Growers Association Conference, Virtual October 2020\nCarryover effects of winter warming in the Olympia oyster. Presentation. 74th Annual Pacific Coast Shellfish Growers Association Conference, Virtual October 2020\nOysters, Ocean Acidification, and -Omics Presentation, Friday Harbor Laboratories Summer Seminar Series, June 2020\nInfluence of ocean acidification on eastern (Crassostrea virginica) and Pacific oyster (Crassostrea gigas) DNA methylation Poster, Ocean Sciences Meeting 2020, San Diego, CA February 2020\nDNA methylation associations with growth rate in Olympia oyster populations presentation, Aquaculture America 2020, Honolulu, HI, February 2020\nInfluence of ocean acidification on DNA methylation patterns in geoduck Presentation, The Plant and Animal Genome XXVII Conference (PAG), San Diego, CA, January 2020"
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     "title": "Diversity, Equity, and Inclusion",
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     "text": "We assert that the diversity of our community, inclusive of various ethnicity, genders, sexual orientations, and social backgrounds, is key the impact of our research. We recognize that diverse perspectives lead to novel solutions and that inclusion cultivates an environment where members are valued, supported, and encouraged to succeed.\nSpecifically we strive to\n- Recognize our differences as strengths\n- Promote continuing education in diversity, equity, and inclusion.\n- Provide educational and emotional support for each other\n- Provide resources for personal and professional growth\nActionable Steps\nIn our effort to continue growing and learning we\n\nHave regular DEI lab discussions. Currently we are reading and discussing: Race After Technology: Abolitionist Tools for the New Jim Code. Other focuses have been reading articles, watching videos, and we have completed the following books: Invisible Women, The Disorded Cosmas, and Fresh Banana Leaves.\nIncorporate our values into projects. Examples include projects aimed at bringing marine sciences to a local high school and another one we partner with Sea Potential and Black in Marine Science to engage underrepresented students through an Art + Science collaborative education practice.\n\nSeveral current and former students are integrating these values in their core activities. For instance Chris Mantegna mentors students in pursuit of enhancing diversity within the marine sciences. and Ariana Huffmyer is partnering with Reva Atea, a local organization in Mo’orea, French Polynesia to develop an education programs.\nInvitation to Partnership\nWe invite those including current and prospective collaborators, and the wider scientific community, to join us in actively cultivating an environment where every individual is provided the opportunity to be successful.\n\n\n\n\n\n\n\n\n\nNo matching items"
+  },
+  {
+    "objectID": "publications/articles/valenzuela2024.html",
+    "href": "publications/articles/valenzuela2024.html",
+    "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations",
+    "section": "",
+    "text": "Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2."
+  },
+  {
+    "objectID": "publications/articles/valenzuela2024.html#citation",
+    "href": "publications/articles/valenzuela2024.html#citation",
+    "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations",
+    "section": "",
+    "text": "Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2."
+  },
+  {
+    "objectID": "publications/articles/valenzuela2024.html#abstract",
+    "href": "publications/articles/valenzuela2024.html#abstract",
+    "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations",
+    "section": "Abstract",
+    "text": "Abstract\nThe fish’s immune response is affected by different factors, including a wide range of environmental conditions that can also disrupt or promote changes in the host- pathogen interactions. How environmental conditions modulate the salmon genome during parasitism is poorly understood here. This study aimed to explore the environmental influence on the Salmo salar transcriptome and methylome infected with the sea louse Caligus rogercresseyi. Atlantic salmon were experimentally infected with lice at two temperatures (8 and 16oC) and salinity conditions (32 and 26PSU). Fish tissues were collected from the infected Atlantic salmon for reduced representation bisulfite sequencing (RRBS) and whole transcriptome sequencing (RNAseq) analysis. The parasitic load was highly divergent in the evaluated environmental conditions, where the lowest lice abundance was observed in fish infected at 8oC/26PSU. Notably, transcriptome profile differences were statistically associated with the number of alternative splicing events in fish exposed to low temperature/salinity conditions. Furthermore, the temperature significantly affected the methylation level, where high values of differential methylation regions were observed at 16oC. Also, the association between expression levels of spliced transcripts and their methylation levels was determined, revealing significant correlations with Ferroptosis and TLR KEEG pathways. This study supports the relevance of the environmental conditions during host-parasite interactions in marine ecosystems. The discovery of alternative splicing transcripts associated with DMRs is also discussed as a novel player in fish biology."
+  },
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+    "objectID": "publications/articles/valenzuela2024.html#data-availability",
+    "href": "publications/articles/valenzuela2024.html#data-availability",
+    "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations",
+    "section": "Data Availability",
+    "text": "Data Availability"
   }
 ]
\ No newline at end of file
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 3bd0542..d70e75e 100644
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@@ -10,7 +10,7 @@
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   <url>
     <loc>https://faculty.washington.edu/sr320/publications.html</loc>
-    <lastmod>2024-06-02T20:43:59.156Z</lastmod>
+    <lastmod>2024-06-10T19:19:14.435Z</lastmod>
   </url>
   <url>
     <loc>https://faculty.washington.edu/sr320/publications/notebooks/crandall2022.html</loc>
@@ -272,4 +272,8 @@
     <loc>https://faculty.washington.edu/sr320/dei.html</loc>
     <lastmod>2024-06-02T20:44:03.383Z</lastmod>
   </url>
+  <url>
+    <loc>https://faculty.washington.edu/sr320/publications/articles/valenzuela2024.html</loc>
+    <lastmod>2024-06-10T19:19:16.348Z</lastmod>
+  </url>
 </urlset>
diff --git a/publications/articles/valenzuela2024.qmd b/publications/articles/valenzuela2024.qmd
new file mode 100644
index 0000000..a53819e
--- /dev/null
+++ b/publications/articles/valenzuela2024.qmd
@@ -0,0 +1,28 @@
+---
+title: "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations"
+type: "article"
+author: "Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C"
+year: "2024"
+publication: "Fish and Shellfish Immunology"
+preprint: ""
+doi: ""
+materials: ""
+eprint: ""
+toc: FALSE
+categories:
+  - salmon
+  - temperature
+  - RNA-seq
+  - methylation
+  - sea lice
+---
+
+## Citation
+
+> Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2.
+
+## Abstract
+
+The fish's immune response is affected by different factors, including a wide range of environmental conditions that can also disrupt or promote changes in the host- pathogen interactions. How environmental conditions modulate the salmon genome during parasitism is poorly understood here. This study aimed to explore the environmental influence on the Salmo salar transcriptome and methylome infected with the sea louse Caligus rogercresseyi. Atlantic salmon were experimentally infected with lice at two temperatures (8 and 16oC) and salinity conditions (32 and 26PSU). Fish tissues were collected from the infected Atlantic salmon for reduced representation bisulfite sequencing (RRBS) and whole transcriptome sequencing (RNAseq) analysis. The parasitic load was highly divergent in the evaluated environmental conditions, where the lowest lice abundance was observed in fish infected at 8oC/26PSU. Notably, transcriptome profile differences were statistically associated with the number of alternative splicing events in fish exposed to low temperature/salinity conditions. Furthermore, the temperature significantly affected the methylation level, where high values of differential methylation regions were observed at 16oC. Also, the association between expression levels of spliced transcripts and their methylation levels was determined, revealing significant correlations with Ferroptosis and TLR KEEG pathways. This study supports the relevance of the environmental conditions during host-parasite interactions in marine ecosystems. The discovery of alternative splicing transcripts associated with DMRs is also discussed as a novel player in fish biology.
+
+## Data Availability