September 2022 Goals


I had really lofty goals for August without realizing that I was going to be visiting family for a good chunk of the month (aka decreased productivity). I made some headway on things, but most of these goals will rollover to make a very packed September.

August Goals Recap

Coral Transcriptomics:

  • Completed initial TagSeq mapping but not differential expression analysis
  • Haven’t written methods or results

Killifish Methylation and Expression:

  • I revisited the RNA-Seq results but did not get a chance to do anything else

Virginica Methylation and Expression:

  • Lots of great discussions but no actual work was done

Green Crab Pilot Experiment:


  • Started addressing reviewer comments on ocean acidification and reproduction review
  • Checked in about eelgrass transcriptomics paper and confirmed I don’t have any work to do with that paper
  • Evaluated projects in deep freeze…they’re oging to stay there a bit longer
  • Found relevant faculty positions I will apply to this cycle

September Goals

Coral Transcriptomics:

  • Finalize differential expression analysis
  • Complete gene enrichment analysis
  • Update methods and results
  • Outline discussion

Killifish Methylation and Expression:

  • Test BAT_DMRcorrelating to match RRBS and RNA-Seq data
  • Conduct pathway analysis for RNA-Seq data
  • Investigate SNP associations with RRBS data
  • Look into mQTL analysis
  • Start RRBS mapping with new genome
  • Update methods and results
  • Put together draft EPIMAR talk

Virginica Methylation and Expression:

  • Examine connections between transcript counts and methylation
  • Determine which hypothesis-driven analyses from the workshop should be incorporated into the paper or redone based on gene expression results
  • Finish transcriptional noise analysis
  • Return to SPLS

Green Crab Pilot Experiment:

  • Figure out which parts of the analysis Sara and Mikayla can work on
  • 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

Faculty Applications

  • Sign up for academic jobs workshop
  • Revise research statement
  • Revise teaching statement
  • Revise DEI statement
  • Revise cover letter
  • Update CV
  • Submit applications due in September and early October


  • Finish addressing reviewer comments on ocean acidification and reproduction review
  • 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 after EPIMAR.

  • 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 September 1, 2022