November 2022 Goals

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Fall is in full swing! I focused on analyses for different conference presentations this month.

October Goals Recap

Virginica Methylation and Expression:

Killifish Methylation and Expression:

  • Reviewed methylation landscape analysis
  • Didn’t test BAT_DMRcorrelating to match RRBS and RNA-Seq data because only one DMR was located in a gene, and that gene was not differentially expressed
  • I was missing information to conduct the pathway analysis, so I looked at HIF and AHR pathways instead
  • Tracked down SNPs information for populations, but couldn’t find pre-existing SNP information for Scorton Creek
  • Gave a talk at the APS Comparative Physiology Conference!

Green Crab Pilot Experiment:

  • Emailed Sara and Mikayla to determine which parts of the analyses they were interested in working on


November Goals

This month, I want to focus on postdoc projects so I can work towards getting a publication ready soon.

*Coral Transcriptomics:

  • Run a WGCNA
  • Dig into gene functions for assigned categories
  • Update methods and results

Killifish Methylation and Expression:

  • Continue BAT workflow with new genome
  • Conduct formal pathway analysis for RNA-Seq data
  • Review existing lab data
  • 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:

  • 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 respiration data analysis
  • Determine workflow for metabolomics sample processing


  • Review supplementary material for eelgrass transcriptomics paper
  • Distribute results of postdoctoral mentorship experiences survey
  • Launch the postdoctoral mentoring program

Deep Freeze

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

Hawaii Gigas Methylation:

I will revisit this paper in December.

  • Address Rajan’s edits
  • Return to methylKit for better interpretation
  • Extract SNPs with EpiDiverse and create a relatedness matrix
  • Look at methylation islands and non-methylated regions
  • Examine overlaps between DML and other epigenomic datasets from Sascha

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 November 1, 2022