December 2022 Goals


Final push for the year! I made some good progress on postdoc and side projects last month, and want to continue working on postdoc projects in particular so I can have a manuscript submitted in a month or so. I (once again) have lofty goals for this month because I have too many things that feel high priority right now! Perhaps next year (yikes) I can reassess.

November Goals Recap

Coral Transcriptomics:

  • Ran WGCNA and GO-MWU analyses!
  • Updated methods and results
  • Determined next steps for project

Killifish Methylation and Expression:

Green Crab Pilot Experiment:

  • Met with Chris to learn about respiration data analysis
  • Worked with Sara to analyze baseline demographic data by treatment and time!


  • Reviewed supplementary material for eelgrass transcriptomics paper
  • Finished applying for faculty positions

December Goals

Coral Transcriptomics:

  • Test OrthoFinder methods
  • Obtain lists of orthologous DEG from other studies
  • Update methods and results

Killifish Methylation and Expression:

  • Determine protocol for SNP identification
  • Conduct in silico RRBS digestion
  • Characterize DEG that overlap between populations
  • Quantify gene expression variability
  • Visualize DEG data

Green Crab Pilot Experiment:

  • Continue working with Sara on demographic data analysis
  • Analyze survivorship data by treatment and sex
  • Analyze time-to-right data by treatment, sex, weight, and integument color
  • Update methods and results
  • Determine workflow for metabolomics sample processing
  • Order materials for metabolomics samples

Hawaii Gigas Methylation:

  • Address Rajan’s edits
  • Return to methylKit for better interpretation
  • Conduct a randomization test for DML identification
  • Extract SNPs with EpiDiverse and create a relatedness matrix
  • Examine overlaps between DML and other epigenomic datasets from Sascha
  • Determine a method for assessing methylation variation by copy number
  • Update methods and results
  • Update discussion
  • Get paper ready for submission!


  • Launch postdoc mentoring program
  • Distribute postdoc mentoring survey results

Deep Freeze

Things that are not immediate enough to be on the backburner, so they’re stuck in the deep freeze.

Virginica Methylation and Expression:

I will revisit this paper after I finish the Hawaii paper.

  • Revisit transcriptional noise analysis
  • Try and recreate model from Aranda paper

Zebrafish DNMT:

I’ll think about this once I have a robust killifish paper draft.

  • Identify a stress condition to use for the zebrafish based on disease factors or conditions that are known to induce changes in methylation
  • Determine physiological endpoints to assess for embryos
  • Construct a project timeline
Written on December 1, 2022