February 2025, Monthly Goals

monthly goals
Author

Kathleen Durkin

Published

February 5, 2025

February goals

  • Complete E5 tasks set at Jan. 31 2025 E5 Molecular meeting
    Mine include:

    • “There will be a suite of genes that a sRNA regulates that have similar function”
      Use functional annotation of the gene-miRNA interaction network to identify putative function of each miRNA based on function of associated genes. Kathleen Durkin

    • For predicted miRNA targets, compare functional composition of targets to functional composition of full reference.
      (Basically, I want to see whether miRNAs preferentially regulate any functional classes).

    • If an miRNA is formally described (e.g. mir-100), compare/contrast its described function with the putative function determined during (2)

    • “Some lncRNAs that act as sponges (bind) sRNA will impact gene expression sRNA regulate”
      Use miRanda to predict miRNA-lncRNA binding and evaluate correlated expression of putative binding pairs to generate miRNA-lncRNA interaction network.

    • “siRNA modulate DNA methylation through RNA-directed DNA methylation by binding to genomic region and recruiting protein machinery to direct methylation”
      Use miRanda/RNAhybrid to predict siRNA binding to the genome. Using simulated WGBS data, prep pipeline to test whether siRNA binding is significantly associated with methylation

    • siRNAs could also play a role in guiding DNA methylation to silence transposable elements
      Use miRanda/RNAhybrid to predict siRNA binding to TEs. Evaluate correlated expression of siRNAs and TEs (expecting a negative relationship).

  • Complete the following tasks for A.pulchra time series data (in preparation for EPIMAR talk in May):

    • evaluate patterns of binding and coexpression among miRNA, lncRNA, and genes

    • explore additional putative interactions (e.g. 3+)

    • annotate function through interacting genes

    • infer additional functional information through relationships with host and/or symbiont physiology data (e.g. WGCNA, edgeR)

    • start incorporating WGCNA data

  • Continue all January goals to maintain time management and logging habits:

    • Log activities daily in Lab Notebook

    • Log all data analysis work (e.g. running a WGCNA) in dedicated post in appropriate project page.

    • Spend maximum 50 hours/week working. Log daily hours in Lab Notebook.

Review January goals

  • Log activities daily in Lab Notebook.
    Last quarter I got overwhelmed with work and stopped posting my daily activities in my lab notebook. I want to reinstate that habit!

  • Log all data analysis work (e.g. running a WGCNA) in dedicated post in appropriate project page.
    Similar to the first goal, I’ve been relying on Github to log all the analysis work I’ve been doing. That work should also be detailed in my lab notebook.

  • Spend maximum 50 hours/week working. Log daily hours in Lab Notebook.
    Last quarter, with the intensive TA position, grant applications, committee prep, and transitioning to E5 expression work/leadership, I worked a lot, and I was really burned out by the end of the quarter. I want to hold myself accountable to a more manageable work schedule this quarter. This time logging will begin my first week back from SICB (Monday, Jan 13). I expect my time breakdown to be roughly:
    20hr/wk classes (SWED 101, FISH 513); 15hr/wk TAing (QSCI 381); 15hr/wk thesis work.