2025 Contenders
Geoduck Env Memory Genome Paper - Hollie and Shelly et al
Working draft
OSF
GitHub
Geoduck OA and reproductive development - Shelly et al
Working draft
Paper repo
Geoduck OA transgenerational effects - Shelly et al
Working draft
Paper repo
CEABiGR lncRNA Zach, Yaamini et al
Working Draft
Paper Repo
Coral 3 species lncRNA Zach et al
Working Draft
Paper Repo
2024 Contenders
1) CEABiGR Yaamini, Sam et al
Working Draft
Paper Repo
10) Single cell RNA-seq - Mac
Working Draft
GitHub
41) Manila Clam Priming - Mac
Working Draft
GitHub
10) Diploid and triploid Pacific oysters display different DNA methylation patterns following desiccation stress - Matt
Working Draft
GitHub
3) Ontogenetic shifts in metabolism and symbiotic nutritional exchange across a developmental time series in a vertically-transmitting species of reef-building coral - Ariana et al
Working draft
Paper repo
4) Thermal stress reduces photosynthate metabolism and disrupts carbon and nitrogen cycling in Montipora capitata coral larvae - Ariana
Working draft
Paper repo
5) Seasonal environmental variation drives host and symbiont physiological state of three important reef-building coral species in Moorea, French Polynesia - Ariana
Working draft
Paper repo
12) The impact of environmental stressors on the expression of byssal thread proteins - Matt
Working Draft
GitHub
13) Berdahl-sockeye-salmon manuscript - Matt
Working Draft
GitHub
13) Factors associated with Bitter Crab Syndrome in Southeast Alaskan Tanner crab - Aspen
Working Draft
GitHub
14) Geoduck OA and reproductive development - Shelly et al
Working draft
Paper repo
14) Geoduck OA transgenerational effects - Shelly et al
Working draft
Paper repo
17) Effects of OA on Manila and Littleneck clams - Larken et al
Working draft
Paper repo
18) Immune response of Pycnopodia helianthoides to Sea Star Wasting Disease - Grace C et al
working draft
paper repo
19) Size class/age class Pycnopodia helianthoides exposed to sea star wasting - Grace C et al
working draft
project repo
2) Geoduck Env Memory Genome Paper - Hollie and Shelly et al
Working draft
OSF
GitHub
9) Mussel (Mytilus trossulus) heat stress response - Zach & Chris et al
Working Draft
Paper Repo
6) Tanner crab and Hematodinium gene expression - Aspen et al
Working draft
Paper repo
20) Pacific cod heat stress response - Kathleen
Working Draft
Project repo
21) E5 deep dive ncRNA gene expression - Kathleen , Zach, et al.
Working Draft
Project repo
22) Nature Opinion Chris
Working Draft
Google Drive Folder
23) Mussel Biomarkers Chris et al
Working Draft
Paper Repo
24) Yellow Island eDNA Chris et al
Working Draft
Paper Repo
25) Clam OA Differential Expression Megan
Working Draft
Repo
26) Ostrea lurida Sex-Determination Genes Megan
Working Draft
Repo placeholder
27) Botryllus schlosseri Nickel Genotoxciity Celeste
Working Draft
Repo placeholder
28) Anthopleura elegantissima Multiple Stressors Sarah
Working Draft
GitHub Project
Pub-a-thon 2023
15) CEABiGR Yaamini, Sam et al
Working Draft
Paper Repo
10) Single cell RNA-seq - Mac
Working Draft
GitHub
9) Mussel (Mytilus trossulus) heat stress response - Zach & Chris et al
Working Draft
Paper Repo
10) Diploid and triploid Pacific oysters display different DNA methylation patterns following desiccation stress - Matt
Working Draft
GitHub
11) The impact of ploidy on the physiological and genetic response of Pacific oysters following multiple stress exposure - Matt
Working Draft
GitHub
6) Tanner crab and Hematodinium gene expression - Aspen et al
Working draft
Paper repo
7) Citrate Synthase Response and Multiple Stress in Pacific Oysters (C. gigas) - Olivia
Working Draft
Paper Repo
3) Coral nutritional exchange across ontogeny - Ariana et al
Working draft
Paper repo
4) Coral nutritional exchange in larvae under thermal stress - Ariana et al
Working draft
Paper repo
5) Coral phenotypes shaped by host and symbiont physiological plasticity across environments in Moorea French Polynesia - Ariana et al
Working draft
Paper repo
8) Comparative Transcriptome Analysis of Geoduck Clam (P. generosa) - Olivia
Working Draft
Paper Repo 1
Paper Repo 2
12) The impact of environmental stressors on the expression of byssal thread proteins - Matt
Working Draft
GitHub
13) Berdahl-sockeye-salmon manuscript - Matt
Working Draft
GitHub
13) Factors associated with Bitter Crab Syndrome in Southeast Alaskan Tanner crab - Aspen
Working Draft
GitHub
14) Geoduck OA and reproductive development - Shelly et al
Working draft
Paper repo
14) Geoduck OA transgenerational effects - Shelly et al
Working draft
Paper repo
15) Temp and Salinity effects on Salmon with sea lice - Shelly et al
Working draft
Paper repo
17) Effects of OA on Manila and Littleneck clams - Larken et al
Working draft
Paper repo
1) Proteomic response of early juvenile Pacific Oysters to temperature - Grac et al
Working Draft
GitHub
Journal: PeerJ
2) Geoduck Env Memory Genome Paper - Hollie and Shelly et al
Working draft
OSF
GitHub
Pub-a-thon 2021
Tier Red
1) Geoduck Env Memory Genome Paper - Hollie et al
Working draft
OSF
GitHub
4) Geoduck OA and reproductive development - Shelly et al
Working draft
Paper repo
Journal:
5) Geoduck OA transgenerational effects - Shelly et al
Working draft
Paper repo
Journal:
11) Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi) - Grace
Working Draft
GitHub
Reviews
24) Tanner crab and Hematodinium gene expression - Aspen et al
Working draft
Paper repo
Journal:
Tier Yellow
6) Temp and Salinity effects on Salmon with sea lice - Shelly et al
Working draft
Paper repo
Journal:
8) Oly epigenetics by population - Laura, Katherine, Steven
Working Draft
GitHub
9) Oly pCO2 Carryover Gene Expression via QuantSeq - Laura
Working Draft
GitHub
12) Proteomic response of early juvenile Pacific Oysters to temperature - Grace
Working Draft
GitHub
13) Differential methylation in response to OA with diploid and triploid oysters - Yaamini
Working Draft
Github
14) Differential gonad methylation in female oysters - Yaamini
Working Draft
Github
15) Harnessing the Power of Single-cell RNA Sequencing to Control Reproductive Development in Bivalves - Mac
Working Draft
GitHub
17) Oly WGBS - Steven
Working Draft
GitHub
20) Differential gene expression in Hematodinium - Aspen
Working Draft
GitHub
22) Epigenetic response of diploidy and triploid Pacific Oysters to desiccation stress - Matt
Working Draft
GitHub
23) Cvirg Methylation and Gene Expression
Working Draft
Github
Tier Blue
2) Coupled Microbiome Analyses Highlights Relative Functional Roles of Bacteria in a Bivalve Hatchery - Emma et al
https://doi.org/10.1186/s40793-021-00376-z
Journal: Environmental Microbiome
3) Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases - Shelly and Yaamini et al
Working draft
Paper repo
Journal: Molecular Ecology
7) Latent effects of winter warming on Olympia oyster reproduction and larval viability - Laura
https://doi.org/10.1016/j.jembe.2021.151604
GitHub
Journal of Experimental Marine Biology and Ecology. doi:10.1016/j.jembe.2021.151604
16) DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing - Jay
https://doi.org/10.1093/g3journal/jkab148
GitHub
Journal: G3
21) OA impact on invertebrate reproduction - Laura and Yaamini
Working Draft
19) Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
https://doi.org/10.1038/s41597-021-00842-w
Journal: Scientific Data
Figshare
Pub-a-thon 2020
1) Oyster larval proteomics - 2015 - Grace
Working draft
Rhonda's repo
Paper repo (clean repo)
2) Crab project - 2020 - Grace
First transcriptome working draft
New transcriptome working draft
Crab project repo
3) Virginica gonad methylation - Yaamini
Working draft
Repo
Journal: Frontiers
4) Gigas/Virginica gonad/offspring methylation - Yaamini Associated repo and draft coming soon
5) Gigas/Virginica multiple tissue/method - Yaamini Associated repo and draft coming soon
5) Oly larvae food and temp - Laura
draft
Journal: Aquaculture
6) Oly epigenetics by population - Laura, Katherine, Steven
Working Draft
GitHub
7) Geoduck Env Memory Genome Paper - Hollie et al
Working draft
OSF
GitHub
Journal:
8) Hatchery Microbiome - Emma
Working Draft
WSG Final Report
Megan Files
Megan Publications
9) Polydora risk to WA aquaculture - Laura
Submitted Draft (pre-reviewer edits)
10) Oly pCO2 Carryover Gene Expression via QuantSeq - Laura
DRAFT LINK COMING SOON
Pub-a-thon 2019
WSG Bracket
a) Hatchery Microbiome - Emma
Working Draft
b) Geoduck pH proteomic - Emma
Working Draft
c) Oyster larval proteomics - 2015 - Grace
Working draft
Rhonda's repo
Paper repo (clean repo)
d) 2016 Temperature treated C.gigas larvae - Shelly
BioRxiv
Clean Manuscript Repo
Working Draft
Shelly's Repo (ASCA on NSAF values, proportions test and fold change analysis on total num spectra, network analysis)
Kaitlyn's Repo (with clustering analysis)
Rhonda's Repo (with original survival and development data, and initial analyses)
Rhonda's initial draft paper and Rhonda's other draft
e) Winter temp/pH affect Oly reproduction & larval viability (2017 exp.) - Laura
Working Draft
Repo
d) Oly larvae food and temp - Laura
draft
Pub-a-thon 2018
list of papers
1) Geoduck epigenetics and genome sequencing
1-Authorea
2-Draft - Genome Sequencing (G Docs)
Repo (URL needed)
2) Olympia Oyster WGBS
Draft
14) Oly DNA methylation and population structure.
Sam
Early Draft (Overleaf)
Repo URL Needed
2) Geoduck Outplant, pH/DNR
Working Draft
Repo
4) 2018 Oly experiment
Working Draft
Repo
6) Oil Exposure and DNA methylation in oysters
repo-URL: https://github.com/sr320/paper-Cvirg-oil
7) Effects of temperature change and Hematodinium sp. infection (Bitter Crab Disease) on Tanner crab
(Chionoecetes bairdi) (Grace)
Working draft
repo-URL: https://github.com/grace-ac/paper-bitter-crab
10) Virginica gonad methylation
Working draft
Repo
11) C.gigas methylation analysis
Working draft
Repo
5) Response of DNA methylation to experimental transplantation in Porites astreoides Repo coming soon
1) Adult low pH exposure influences larval abundance in Pacific oysters (Crassostrea gigas) - Yaamini
Working draft
Repo
reviews
Journal: JSR
7) Gigas DNR
Working draft
Repo
reviews
Journal: Marine Ecological Progress Series
3) Polydora risk to WA aquaculture
Working Draft
10) Geoduck Transcriptome
repo-URL: https://osf.io/3xf6m/
Pub-a-thon 2017
list of papers
17) Aquaculture and Epigenetics
Repo-URL:
draft: on GoogleDocs
Journal 1: NOAA Technical Note
Journal 2: PeerJ
Response to Reviews: on GoogleDocs
PeerJ Revisions: on Google Docs
19) Shellfish Functional Genomics
Repo-URL: https://github.com/sr320/fun-gen
draft: on GoogleDocs
Journal: JSR
6) Differential response to stress in Ostrea lurida (Carpenter 1864) as indicated by GENE EXPRESSION
repo-URL: https://github.com/RobertsLab/paper-Olurida-gene
draft: (see repo)
preprint: https://peerj.com/preprints/1595/
Review Response: GoogleDocs
21) Oyster Reproduction / Genetics and Epigenetics
repo-URL:
draft: googledoc
Submission - Book Chapter
4) Puget Sound Oly Larval Performance
repo-URL: https://github.com/ksil91/PS-Oly-Larvae-Growth
draft: google-doc, Scientific Report version google-doc
- Paperpile
Journal: Scientific Reports
5) Juvenile Geoduck OA Exposure: Growth and Methylation (Hollie et al.)
repo-URL: https://github.com/hputnam/project_juvenile_geoduck_OA
draft: authorea
10) Geoduck Transcriptome
repo-URL: https://osf.io/3xf6m/
13) Oly paper Megan (Megan)
repo-URL: https://github.com/MeganHintz/Paper---Oly-fingerprinting
draft: google-doc
- Paperpile
15) Climate adaptability in Ostrea lurida (Laura)
Repo-URL: https://github.com/laurahspencer/O.lurida_Temp-OA_Gonad
draft: on GoogleDocs
14) C.gigas methylation analysis (Yaamini)
repo-URL: https://github.com/RobertsLab/paper-gigas-metaanalysis
draft: google-doc
11) Oyster Hatchery 2015 Proteomics
repo-URL: https://github.com/RobertsLab/project-pacific.oyster-larvae
draft: 2015 Google Doc
23) Geoduck OA Larval Proteomics Jose
repo-URL:
draft: GoogleDoc
20) Assessment of Toxicant Impact to Coho Salmon using a Novel Toxicogenetic Biomarker Assay
Repo-URL:
draft: on GoogleDocs
22) Oyster Hatchery 2016 Proteomics
repo-URL: https://github.com/RobertsLab/project-pacific.oyster-larvae
draft: 2016 Google Doc
12) Geoduck / Oyster DNR proteomics (Laura + Yaamini)
repo-URL: https://github.com/RobertsLab/Paper-DNR-Proteomics
draft: google-doc
- Paperpile
18) Flounder Gene Expression
Repo-URL:
draft: on GoogleDocs
8) Oly Pop Gen (2bRAD - BS)
repo-URL:
draft:
2) A non-lethal, field-based anesthesia protocol for sampling the mantle cavity of Olympia oysters (Megan)
repo-URL:
draft:google doc
preprint: https://www.dropbox.com/s/dfwtw8e2s2ix6zf/AnesthesiaPaper_v87.docx?dl=0
Journal: Journal of Shellfish Research
16) What goes up must come down: Diel vertical migration in the deepwater sablefish (Anoplopoma fimbria) revealed by satellite popup tags
Journal: Fisheries Oceanography
9) Coral Epi RAD (Jay)
repo-URL: https://github.com/jldimond/Branching-Porites
preprint: http://biorxiv.org/content/early/2017/03/22/119156
Journal: Molecular Ecology
1) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation (Emma)
repo-URL:https://github.com/sr320/supp-geoduck-proteomics
draft:
preprint: https://doi.org/10.1101/094615
Journal: Journal of Proteome Research
3) Evidence of Ostrea lurida (Carpenter 1864) population structure in Puget Sound, WA
repo-URL: https://github.com/RobertsLab/OluridaSurvey2014
draft:
preprint: https://peerj.com/preprints/704/
Journal: Marine Ecology
7) Oly GBS (Sam)
data records repo-URL: https://osf.io/j8rc2/
draft repo-URL: https://github.com/kubu4/paper_oly_gbs
draft: https://www.authorea.com/users/4974/articles/149442
preprint (Overleaf): https://www.overleaf.com/read/mqbbvmwxhncg
preprint (PDF): https://osf.io/cdj7m/
Status Details
Review Response: on GoogleDocs
Journal: Scientific Data