2025

May 8, 2025

  • Chris presented on APCs (antibody secreting cells) and the role of iBALTs persisting after flu infection. This is notable because B cell dysregulation is implicated in PAH. Potential link: epigenetic regulation via Kmt2a, which could drive pathological B-cell proliferation in PAH. ### May 7, 2025
  • N/A. ### May 6, 2025
  • Revised AIM-AHEAD proposal. Highlighted the need to frame drug prioritization via interpretability-focused AI models in cancer and cardiometabolic disease contexts. ### May 2, 2025
  • Outlined review structure for PAH-related hub genes. Key insight: co-expression networks may reveal under-characterized transcriptional regulators worth validating cross-cohort. ### May 1, 2025
  • Compared Stanford’s Data Ocean Certificate to UAB programs. Focus: integrating structured and unstructured EHR data for modeling risk in precision medicine. ### April 29, 2025
  • Discussed integrating DSRP systems thinking into PAH research. Idea: relationships among hub genes, phenotypic presentation, and variant burden as multiscale system layers. ### April 18, 2025
  • Drafted project goals: PAH hub gene meta-analysis, drug repositioning framework, and dbGaP exome processing. Emphasis on reproducibility and integrative workflows across variant and transcriptomic layers. ### April 12, 2025
  • Planned structure for qualifying exam slides. Strategy: trace hub gene discovery through WGCNA and link to functional prioritization in Aim 2. ### April 10, 2025
  • Outlined WGCNA and variant analysis milestones for Aim 1. Identified integration point with signatureSearch outputs for network-level drug prioritization. ### April 3, 2025
  • Evaluated PANDA network inference for PAH bulk expression data. Considered potential tissue-specific bias and TF-target validation needs. ### March 29, 2025
  • Discussed integrating public advocacy with scientific training. Parallel insight: reproducible genomic pipelines can serve as both scientific and community tools for equity. ### March 25, 2025
  • Outlined LLM-based chatbot workflow using PubTator for hypothesis generation. Highlight: cluster abstracts by topic, then summarize key gene-disease relationships. ### March 1, 2025
  • Identified limitations in TxGNN-style drug repurposing methods. Strategy: build interpretable, disease-aware graph framework tailored for PAH therapeutic prioritization. ### February 12, 2025
  • Refined scientific presentation style to prioritize clarity, brevity, and mechanistic logic. Focused on trimming transitions and emphasizing core arguments. ### February 11, 2025
  • Examined methods for communicating model assumptions and linking them to PAH-specific data features in oral exams and slide decks. ### January 13, 2025
  • Connected WGCNA hub genes with prioritized variants. Noted convergence between expression and genotype data in highlighting candidate modifiers. ### January 6, 2025
  • Clarified Aim 1 independence from Aim 2 in the proposal. Defined modular analysis structure: variants and WGCNA remain independent until network integration.