Advisor 1v1: April 8, 2026

1v1
Published

April 7, 2026

Agenda

  1. Update on written deliverables outlined in Alert letter
    1. Biomarker manuscript
    2. WDFW Mussel methylation manuscript
  2. DNA Methylation analysis progress
  3. Stretch Goal: PhD Proposal
  4. GPC Meeting
    1. Expectations & Alignments
    2. Status of deliverables in Alerts
    3. Moving Forward
    4. Decisions, Questions, Action Items

Item 1: Written Deliverables

1.1 Mussel Biomarker Manuscript (Deliverable 2 of 3 in Academic Alert)

Deadline: Per Alert letter, April 17th.

The current draft

The visualization folder

Next steps are listed in Section 4.

1.2 Mussel Methylation Manuscript (Deliverable 3 of 3 in Academic Alert)

Deadline: Per Alert letter, May 1st.

Status of manuscript: Nothing coherent currently. I’m reading and ‘brain dump’ style outlining, like this document.

Next Steps: Outlined below in Item 4, GPC meeting.

Item 2: DNA Methylation Analysis Progress

Analysis Status: Initial analysis up to methylation extraction, and generating coverage filtering, BedGraph, and QC files and reports up through the extraction.

  • All files/ outputs backed up to Gannet as of 04/06/2026.

Progress is outlined in the following daily posts:

Next steps are…

  • The analysis process as I understand it is outlined here

    • I am moving into step 5 once I understand my outputs.

Item 3: Stretch Goal - PhD Proposal for Bypass

PhD Proposal Status: Outlining and drafting in progress for Chapters 3 & 4.

Current process/ progress: Brainstorming manageable work for each chapter.

Chapter 3 - open source data to bring methylation and gene expression together to inform Chapter 4 and link Chapter 1 & 2 outcomes to expansion.

Chapter 4 - lab-based experiment to test potential methylation biomarkers of stress in mussels. based on the outline/ process outlined in these earlier posts.

Item 4: GPC, Advisor & Me

4.1 Expectations & Alignment

  • The expectation (as I understand it) is to align my work product output with my tenure in the program to demonstrate progress per policy 3.7.

    • As I understand it, progress in the policy is defined by 3 metrics with the caveat that individual plan adaptation is also acceptable as long as it is applied equitably.

      • Metric 1 - GPA at or above 3.0

      • Metric 2 - Annual meetings for regular progress review and feedback, evaluation and intervention are also included

      • Metric 3 - Milestone attainment per the department’s program requirements established in the enrollment year (2021).

  • I entered, and continue, in the program with the expectation that I will (1) put myself in a position to bypass into PhD, and (2) will be able and capable of completing a PhD.
    • With the understanding that timely manuscript production is a necessary component of the program, how are we defining progress and performance beyond manuscript production?
  • General Output Timeline to Date
    • 2021 - 22: Coursework
    • 2022 - 23: Yellow Island surveys and eDNA, Building and administering teaching/mentoring programs
    • 2023 - 24: WDFW Mussel Biomarkers, Yellow Island surveys and eDNA, administering teaching/ mentoring program, building and delivering interdisciplinary mentoring/ teaching program
    • 2024 - 25: WDFW Mussel Biomarkers, WDFW Mussel Methylation, Yellow Island surveys and eDNA, Kenya eDNA
    • 2025 - 2026: WDFW Mussel Biomarkers, WDFW Mussel Methylation, Yellow Island surveys and eDNA, developing PhD Proposal for bypass

      • October 2025 pivot per committee meeting (re: bypass) removed all eDNA and program building/ teaching/ mentoring to narrow scope and focus to demonstrate increasing mastery from MS to PhD. The pivot required:

        • A reading and lit review pivot from ecosystem- level integration into organismal impact, shift away from STEM pedagogy, interdisciplinary teaching of STEM- focused topics, and general invertebrate and coastal ecosystem research.

        • Splitting focus between the MS proposal, the biomarker manuscript, pushing the methylation analysis forward, redistributing/ delegating work to keep the Yellow and Kenya projects moving forward to meet the ‘parent organizations’ expectations for funding/ support provided.

4.2 Alert-defined Deliverables: Status

  • Academic Notification, November 4, 2025
    • No expectations met prior to the end of Fall 2025
  • Academic Alert, January 7, 2026

    • MS proposal submitted

    • Biomarker draft provided to Alison Gardell on January 23, 2026, and Steven on February 11, 2026 noting spatial analysis errors and needed results rewrite

    • Mussel Methylation manuscript draft - complete draft due April 17, 2026

  • Final Academic Alert, April 1, 2026

    • Biomarker manuscript due April 17, 2026

    • Mussel Methylation manuscript draft due on May 1, 2026

4.3 Moving Forward

  • Biomarker manuscript
    • Complete results updating to include corrected spatial analysis results
    • Write abstract
    • Put visualizations directly into manuscript and shift the others to the supplement folder
    • Complete edits/ revisions as received
  • Methylation manuscript
    • Analysis is approximately 40% complete - the remaining 60% can be completed by May 1st
    • Methods section and clearly outlined introduction and results sections can be completed by May 15th
    • Complete coherent draft, that includes completed methods, results, discussion/ conclusion and preliminary visualizations can be completed by June 1st
  • Explanation for extended window
    • I have 5 tide series of work on Yellow per the terms of funding provided by TNC
      • This is pure work, not teaching/ mentoring
      • Survey dates are as follows: April 18-22, May 14-21, May 28-June 5, June 11-20, with the potential 5th series June 25 - July 3
      • There’s power and WiFi on the island, so not off the grid, but primary focus shift
    • I also have a Student Assistantship through the end of Spring quarter.

4.4 Decisions, Questions, Action Items

  1. Biomarker manuscript delivered to committee by April 17th.
  2. Shift from weekly 1v1’s with Steven as check-ins to working sessions.
    1. Booked for 60 minutes from the week of April 12th - May 17th.
    2. May shift to 30 minutes depending on workflow.
  3. Pending committee approval, shifting the mussel methylation manuscript draft to June 10th delivery.
    1. High-level plan for delivery is above.
    2. Weekly and daily plan to be drafted and reviewed during first working session on April 15th.
  4. Continued progress, pending written product delivery by dates above, to include plan for bypass by August 15th.