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Pub-a-thon 2021

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1) Geoduck Env Memory Genome Paper - Hollie et al
Working draft
OSF GitHub status

2) Coupled Microbiome Analyses Highlights Relative Functional Roles of Bacteria in a Bivalve Hatchery - Emma et al
https://www.researchsquare.com/article/rs-90268/v1
status
Journal: Environmental Microbiome

3) Choice of DNA methylation analyses in invertebrates requires consideration of genome characteristics and the methylation landscape - Shelly and Yaamini et al
Working draft
Paper repo
status
Journal: BMC Genome Biology

4) Geoduck OA and reproductive development - Shelly et al
Working draft
Paper repo
status
Journal:

5) Geoduck OA transgenerational effects - Shelly et al
Working draft
Paper repo
status
Journal:

6) Temp and Salinity effects on Salmon with sea lice - Shelly et al
Working draft
Paper repo
status
Journal:

7) Oly larvae food and temp - Laura
Working Draft
GitHub (not cleaned up yet, though)
status
Journal: Ecological Applications

8) Oly epigenetics by population - Laura, Katherine, Steven
Working Draft
GitHub
status

9) Oly pCO2 Carryover Gene Expression via QuantSeq - Laura
Working Draft
GitHub
status

10) Single cell RNA-seq - Mac
Working Draft
GitHub
status

11) Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi) - Grace
Working Draft
GitHub
status

12) Proteomic response of early juvenile Pacific Oysters to temperature - Grace
Working Draft
GitHub
status

13) Differential methylation in response to OA with diploid and triploid oysters - Yaamini
Working Draft
Github
status

14) Differential gonad methylation in female oysters - Yaamini
Draft link coming soon!
Github
status

15) Harnessing the Power of Single-cell RNA Sequencing to Control Reproductive Development in Bivalves - Mac
Working Draft
GitHub
status

16) DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING - Jay
https://www.biorxiv.org/content/10.1101/2021.02.01.429278v1
status
GitHub
Journal: G3

17) Oly WGBS - Steven
Working Draft
GitHub
status

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
status
Figshare

20) Differential gene expression in Hematodinium - Aidan
Working Draft
GitHub
status

21) OA impact on invertebrate reproduction - Laura and Yaamini Workding Draft status

22) Epigenetic response of diploidy and triploid Pacific Oysters to desiccation stress - Matt
Working Draft
GitHub status

Pub-a-thon 2020

1) Oyster larval proteomics - 2015 - Grace
Working draft
Rhonda's repo
Paper repo (clean repo)
status

2) Crab project - 2020 - Grace
First transcriptome working draft
New transcriptome working draft
Crab project repo
status

3) Virginica gonad methylation - Yaamini
Working draft Repo
status
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
status
Journal: Aquaculture

6) Oly epigenetics by population - Laura, Katherine, Steven
Working Draft
GitHub
status

7) Geoduck Env Memory Genome Paper - Hollie et al
Working draft
OSF
GitHub
status
Journal:

8) Hatchery Microbiome - Emma
Working Draft
WSG Final Report
Megan Files
Megan Publications
status

9) Polydora risk to WA aquaculture - Laura
Submitted Draft (pre-reviewer edits)
status

10) Oly pCO2 Carryover Gene Expression via QuantSeq - Laura
DRAFT LINK COMING SOON
status

Pub-a-thon 2019

WSG Bracket

a) Hatchery Microbiome - Emma
Working Draft
status

b) Geoduck pH proteomic - Emma
Working Draft
status

c) Oyster larval proteomics - 2015 - Grace
Working draft
Rhonda's repo
Paper repo (clean repo)
status

d) 2016 Temperature treated C.gigas larvae - Shelly
status
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
status

d) Oly larvae food and temp - Laura
draft
status

Pub-a-thon 2018

list of papers

1) Geoduck epigenetics and genome sequencing
1-Authorea
2-Draft - Genome Sequencing (G Docs)
Repo (URL needed)
status

2) Olympia Oyster WGBS
Draft

14) Oly DNA methylation and population structure.
Sam
Early Draft (Overleaf)
Repo URL Needed
status

2) Geoduck Outplant, pH/DNR
Working Draft
Repo
status

4) 2018 Oly experiment
Working Draft
Repo

6) Oil Exposure and DNA methylation in oysters
repo-URL: https://github.com/sr320/paper-Cvirg-oil
status

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
status

10) Virginica gonad methylation
Working draft Repo
status

11) C.gigas methylation analysis
Working draft
Repo
status

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
status
reviews
Journal: JSR

7) Gigas DNR
Working draft
Repo
status
reviews
Journal: Marine Ecological Progress Series

3) Polydora risk to WA aquaculture
Working Draft
status

10) Geoduck Transcriptome
repo-URL: https://osf.io/3xf6m/
status

Pub-a-thon 2017

list of papers

17) Aquaculture and Epigenetics
Repo-URL:
draft: on GoogleDocs
status
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
status
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/
status
Review Response: GoogleDocs

21) Oyster Reproduction / Genetics and Epigenetics
repo-URL:
draft: googledoc
status
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
status - 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
status

10) Geoduck Transcriptome
repo-URL: https://osf.io/3xf6m/
status

13) Oly paper Megan (Megan)
repo-URL: https://github.com/MeganHintz/Paper---Oly-fingerprinting
draft: google-doc
status - Paperpile

15) Climate adaptability in Ostrea lurida (Laura)
Repo-URL: https://github.com/laurahspencer/O.lurida_Temp-OA_Gonad
draft: on GoogleDocs
status

14) C.gigas methylation analysis (Yaamini)
repo-URL: https://github.com/RobertsLab/paper-gigas-metaanalysis
draft: google-doc
status

11) Oyster Hatchery 2015 Proteomics
repo-URL: https://github.com/RobertsLab/project-pacific.oyster-larvae
draft: 2015 Google Doc
status

23) Geoduck OA Larval Proteomics Jose
repo-URL:
draft: GoogleDoc
status

20) Assessment of Toxicant Impact to Coho Salmon using a Novel Toxicogenetic Biomarker Assay
Repo-URL:
draft: on GoogleDocs
status

22) Oyster Hatchery 2016 Proteomics
repo-URL: https://github.com/RobertsLab/project-pacific.oyster-larvae
draft: 2016 Google Doc
status

12) Geoduck / Oyster DNR proteomics (Laura + Yaamini)
repo-URL: https://github.com/RobertsLab/Paper-DNR-Proteomics
draft: google-doc
status - Paperpile

18) Flounder Gene Expression
Repo-URL:
draft: on GoogleDocs
status

8) Oly Pop Gen (2bRAD - BS)
repo-URL:
draft:
status

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
status
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
status
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
status
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
status
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/
status
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
Status Details
Review Response: on GoogleDocs
Journal: Scientific Data