Project References

This file collects foundational and frequently cited literature relevant to this project. It is grouped thematically and intended as a living resource. Use this file when drafting papers, proposals, or onboarding collaborators.

Variant Interpretation and Modifier Models

• Lek et al. (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285–291.

Rare Disease and PAH Mechanisms

• Austin et al. (2012). BMPR2 expression is reduced in endothelial cells exposed to serum from patients with heritable PAH. Circulation Research, 111(5), 561–574.

Computational Tools and Pipelines

• Love et al. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550.

Systems Modeling and Network Biology

• Barabási et al. (2011). Network medicine: a network-based approach to human disease. Nature Reviews Genetics, 12(1), 56–68.
• Greene et al. (2015). Understanding multicellular function and disease with human tissue-specific networks. Nature Genetics, 47(6), 569–576.

General Guidance for Computational Biology Projects

• Noble, W. S. (2022). Ten simple rules for defining a computational biology project. PLOS Computational Biology, 18(12), e1010742.

Ethics, Equity, and Reproducibility

• Sandve et al. (2013). Ten simple rules for reproducible computational research. PLOS Computational Biology, 9(10), e1003285.

Formatting Suggestions

• Prefer short citation blocks: Author, Year, Title, Journal
• Group by theme, not file
• Update when citing in major reports or methods