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2024 Contenders

  1. CEABiGR Yaamini, Sam et al
    Working Draft
    Paper Repo
    status

  2. CEABiGR lncRNA Zach, Yaamini et al
    Working Draft
    Paper Repo
    status

  3. Single cell RNA-seq - Mac
    Working Draft
    GitHub
    status

  4. Manila Clam Priming - Mac
    Working Draft
    GitHub
    status

  5. Diploid and triploid Pacific oysters display different DNA methylation patterns following desiccation stress - Matt
    Working Draft
    GitHub
    status

  6. 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
    status

  7. Thermal stress reduces photosynthate metabolism and disrupts carbon and nitrogen cycling in Montipora capitata coral larvae - Ariana
    Working draft
    Paper repo
    status

  8. 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
    status

  9. The impact of environmental stressors on the expression of byssal thread proteins - Matt
    Working Draft
    GitHub
    status

  10. Berdahl-sockeye-salmon manuscript - Matt
    Working Draft
    GitHub
    status

  11. Factors associated with Bitter Crab Syndrome in Southeast Alaskan Tanner crab - Aspen
    Working Draft
    GitHub
    status

  12. Geoduck OA and reproductive development - Shelly et al
    Working draft
    Paper repo
    status

  13. Geoduck OA transgenerational effects - Shelly et al
    Working draft
    Paper repo
    status

  14. Effects of OA on Manila and Littleneck clams - Larken et al Working draft
    Paper repo
    status

  15. Immune response of Pycnopodia helianthoides to Sea Star Wasting Disease - Grace C et al working draft
    paper repo
    status

  16. Size class/age class Pycnopodia helianthoides exposed to sea star wasting - Grace C et al working draft
    project repo
    status

  17. Geoduck Env Memory Genome Paper - Hollie and Shelly et al
    Working draft
    OSF GitHub
    status

  18. Mussel (Mytilus trossulus) heat stress response - Zach & Chris et al
    Working Draft
    Paper Repo
    status

  19. Tanner crab and Hematodinium gene expression - Aspen et al
    Working draft
    Paper repo
    status

  20. Pacific cod heat stress response - Kathleen
    Working Draft
    Project repo
    status

  21. E5 deep dive ncRNA gene expression - Kathleen , Zach, et al.
    Working Draft
    Project repo
    status

  22. Nature Opinion Chris
    Working Draft
    Google Drive Folder
    status

  23. Mussel Biomarkers Chris et al
    Working Draft
    Paper Repo
    status

  24. Yellow Island eDNA Chris et al
    Working Draft
    Paper Repo
    status

  25. Clam OA Differential Expression Megan
    Working Draft
    Repo
    status

  26. Ostrea lurida Sex-Determination Genes Megan
    Working Draft
    Repo placeholder
    status

  27. Botryllus schlosseri Nickel Genotoxciity Celeste
    Working Draft
    Repo placeholder
    status

  28. Anthopleura elegantissima Multiple Stressors Sarah
    Working Draft
    GitHub Project
    status

Pub-a-thon 2023

<iframe width="682" height="422" seamless frameborder="0" scrolling="no" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vQ3k1Br4DkiJyzH2nou51H-nORE9dVCgiwjD_nchL4CCsWcFBwSB-I562XG0ns2p32IROzNZ_PSFIqO/pubchart?oid=1185787774&format=interactive"></iframe>

  1. CEABiGR Yaamini, Sam et al
    Working Draft
    Paper Repo
    status

  2. Single cell RNA-seq - Mac
    Working Draft
    GitHub
    status

  3. Mussel (Mytilus trossulus) heat stress response - Zach & Chris et al
    Working Draft
    Paper Repo
    status

  4. Diploid and triploid Pacific oysters display different DNA methylation patterns following desiccation stress - Matt
    Working Draft
    GitHub
    status

  5. The impact of ploidy on the physiological and genetic response of Pacific oysters following multiple stress exposure - Matt
    Working Draft
    GitHub
    status

  6. Tanner crab and Hematodinium gene expression - Aspen et al
    Working draft
    Paper repo
    status

  7. Citrate Synthase Response and Multiple Stress in Pacific Oysters (C. gigas) - Olivia
    Working Draft
    Paper Repo
    status

  8. Coral nutritional exchange across ontogeny - Ariana et al
    Working draft
    Paper repo
    status

  9. Coral nutritional exchange in larvae under thermal stress - Ariana et al
    Working draft
    Paper repo
    status

  10. Coral phenotypes shaped by host and symbiont physiological plasticity across environments in Moorea French Polynesia - Ariana et al
    Working draft
    Paper repo
    status

  11. Comparative Transcriptome Analysis of Geoduck Clam (P. generosa) - Olivia
    Working Draft
    Paper Repo 1
    Paper Repo 2
    status

  12. The impact of environmental stressors on the expression of byssal thread proteins - Matt
    Working Draft
    GitHub
    status

  13. Berdahl-sockeye-salmon manuscript - Matt
    Working Draft
    GitHub
    status

  14. Factors associated with Bitter Crab Syndrome in Southeast Alaskan Tanner crab - Aspen
    Working Draft
    GitHub
    status

  15. Geoduck OA and reproductive development - Shelly et al
    Working draft
    Paper repo
    status

  16. Geoduck OA transgenerational effects - Shelly et al
    Working draft
    Paper repo
    status

  17. Temp and Salinity effects on Salmon with sea lice - Shelly et al
    Working draft
    Paper repo
    status

  18. Effects of OA on Manila and Littleneck clams - Larken et al Working draft
    Paper repo
    status

  19. Proteomic response of early juvenile Pacific Oysters to temperature - Grac et al
    Working Draft
    GitHub
    status
    Journal: PeerJ

  20. Geoduck Env Memory Genome Paper - Hollie and Shelly et al
    Working draft
    OSF GitHub
    status

Pub-a-thon 2021

Tier Red

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

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

  3. Geoduck OA transgenerational effects - Shelly et al
    Working draft
    Paper repo
    status
    Journal:

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

  5. Tanner crab and Hematodinium gene expression - Aspen et al
    Working draft
    Paper repo
    status
    Journal:

Tier Yellow

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

  2. Oly epigenetics by population - Laura, Katherine, Steven
    Working Draft
    GitHub
    status

  3. Oly pCO2 Carryover Gene Expression via QuantSeq - Laura
    Working Draft
    GitHub
    status

  4. Proteomic response of early juvenile Pacific Oysters to temperature - Grace
    Working Draft
    GitHub
    status

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

  6. Differential gonad methylation in female oysters - Yaamini
    Working Draft
    Github
    status

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

  8. Oly WGBS - Steven
    Working Draft
    GitHub
    status

  9. Differential gene expression in Hematodinium - Aspen
    Working Draft
    GitHub
    status

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

  11. Cvirg Methylation and Gene Expression Working Draft
    Github
    status

Tier Blue

  1. 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
    status
    Journal: Environmental Microbiome

  2. Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases - Shelly and Yaamini et al
    Working draft
    Paper repo
    status
    Journal: Molecular Ecology

  3. Latent effects of winter warming on Olympia oyster reproduction and larval viability - Laura
    https://doi.org/10.1016/j.jembe.2021.151604
    GitHub
    status
    Journal of Experimental Marine Biology and Ecology. doi:10.1016/j.jembe.2021.151604

  4. DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing - Jay
    https://doi.org/10.1093/g3journal/jkab148
    status
    GitHub
    Journal: G3

  5. OA impact on invertebrate reproduction - Laura and Yaamini
    Working Draft
    status

  6. 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
    Journal: Scientific Data
    Figshare

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

  6. Oly larvae food and temp - Laura
    draft
    status
    Journal: Aquaculture

  7. Oly epigenetics by population - Laura, Katherine, Steven
    Working Draft
    GitHub
    status

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

  9. Hatchery Microbiome - Emma
    Working Draft
    WSG Final Report
    Megan Files
    Megan Publications
    status

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

  11. 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

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

  4. Geoduck Outplant, pH/DNR
    Working Draft
    Repo
    status

  5. 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

  8. Virginica gonad methylation
    Working draft Repo
    status

  9. C.gigas methylation analysis
    Working draft
    Repo
    status

  10. 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

  2. Gigas DNR
    Working draft
    Repo
    status
    reviews
    Journal: Marine Ecological Progress Series

  3. Polydora risk to WA aquaculture
    Working Draft
    status

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

Pub-a-thon 2017

list of papers

  1. 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
  1. Shellfish Functional Genomics
    Repo-URL: https://github.com/sr320/fun-gen
    draft: on GoogleDocs
    status
    Journal: JSR
  1. 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
  1. Oyster Reproduction / Genetics and Epigenetics
    repo-URL:
    draft: googledoc
    status
    Submission - Book Chapter
  1. 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
  1. Juvenile Geoduck OA Exposure: Growth and Methylation (Hollie et al.)
    repo-URL: https://github.com/hputnam/project_juvenile_geoduck_OA
    draft: authorea
    status
  1. Geoduck Transcriptome
    repo-URL: https://osf.io/3xf6m/
    status
  1. Oly paper Megan (Megan)
    repo-URL: https://github.com/MeganHintz/Paper---Oly-fingerprinting
    draft: google-doc
    status - Paperpile
  1. Climate adaptability in Ostrea lurida (Laura)
    Repo-URL: https://github.com/laurahspencer/O.lurida_Temp-OA_Gonad
    draft: on GoogleDocs
    status
  1. C.gigas methylation analysis (Yaamini)
    repo-URL: https://github.com/RobertsLab/paper-gigas-metaanalysis
    draft: google-doc
    status
  1. Oyster Hatchery 2015 Proteomics
    repo-URL: https://github.com/RobertsLab/project-pacific.oyster-larvae
    draft: 2015 Google Doc
    status
  1. Geoduck OA Larval Proteomics Jose
    repo-URL:
    draft: GoogleDoc
    status
  1. Assessment of Toxicant Impact to Coho Salmon using a Novel Toxicogenetic Biomarker Assay
    Repo-URL:
    draft: on GoogleDocs
    status
  1. Oyster Hatchery 2016 Proteomics
    repo-URL: https://github.com/RobertsLab/project-pacific.oyster-larvae
    draft: 2016 Google Doc
    status
  1. Geoduck / Oyster DNR proteomics (Laura + Yaamini)
    repo-URL: https://github.com/RobertsLab/Paper-DNR-Proteomics
    draft: google-doc
    status - Paperpile
  1. Flounder Gene Expression
    Repo-URL:
    draft: on GoogleDocs
    status
  1. Oly Pop Gen (2bRAD - BS)
    repo-URL:
    draft:
    status
  1. 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
  1. What goes up must come down: Diel vertical migration in the deepwater sablefish (Anoplopoma fimbria) revealed by satellite popup tags
    status
    Journal: Fisheries Oceanography
  1. 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
  1. 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
  1. 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