Pub-a-thon 2021
Not able to make the call? You can register your goals here. (and see what folks register here)
1) Geoduck Env Memory Genome Paper - Hollie et al
Working draft
OSF
GitHub
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
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
Journal: BMC Genome Biology
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:
6) Temp and Salinity effects on Salmon with sea lice - Shelly et al
Working draft
Paper repo
Journal:
7) Oly larvae food and temp - Laura
Working Draft
GitHub (not cleaned up yet, though)
Journal: Ecological Applications
8) Oly epigenetics by population - Laura, Katherine, Steven
Working Draft
GitHub
9) Oly pCO2 Carryover Gene Expression via QuantSeq - Laura
Working Draft
GitHub
10) Single cell RNA-seq - Mac
Working Draft
GitHub
11) Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi) - Grace
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
Draft link coming soon!
Github
15) Harnessing the Power of Single-cell RNA Sequencing to Control Reproductive Development in Bivalves - Mac
Working Draft
GitHub
16) DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING - Jay
https://www.biorxiv.org/content/10.1101/2021.02.01.429278v1
GitHub
Journal: G3
17) Oly WGBS - Steven
Working Draft
GitHub
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
Figshare
20) Differential gene expression in Hematodinium - Aidan
Working Draft
GitHub
21) OA impact on invertebrate reproduction - Laura and Yaamini
Workding Draft
22) Epigenetic response of diploidy and triploid Pacific Oysters to desiccation stress - Matt
Working Draft
GitHub
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