Pedro Baldoni

Contributions to Public Health

• I develop statistical methods to improve transcript-level differential expression analyses of RNA-seq data. My work addresses quantification uncertainty due to read-to-transcript ambiguity, enabling powerful and efficient analyses of gene expression data with broad applications in biomedical research.
  • Baldoni PL, Chen Y, Hediyeh-Zadeh S, Liao Y, Dong X, Ritchie ME, Shi W, Smyth GK. Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR. Nucleic Acids Res. 2024 Feb 9;52(3):e13. doi: 10.1093/nar/gkad1167. PMID: 38059347; PMCID: PMC10853777.
  • Baldoni PL, Chen L, Smyth GK. Faster and more accurate assessment of differential transcript expression with Gibbs sampling and edgeR v4. NAR Genom Bioinform. 2024 Nov 4;6(4):lqae151. doi: 10.1093/nargab/lqae151. PMID: 39498433; PMCID: PMC11532793.
• I design statistical models for analyzing epigenomic sequencing data. My methods improve the detection of consensus and differential protein-DNA binding sites across conditions, such as tumor vs. healthy tissues or genetically modified vs. wildtype organisms, for example. 
  Baldoni PL, Rashid NU, Ibrahim JG. Efficient detection and classification of epigenomic changes under multiple conditions.
  • Biometrics. 2022 Sep;78(3):1141-1154. doi: 10.1111/biom.13477. Epub 2021 May 3. PMID: 33860525.
  • Baldoni PL, Rashid NU, Ibrahim JG. Improved detection of epigenomic marks with mixed-effects hidden Markov models. Biometrics. 2019 Dec;75(4):1401-1413. doi: 10.1111/biom.13083. Epub 2019 Oct 17. PMID: 31081192; PMCID: PMC6851437.
• I develop statistical methods to correct for measurement error in epidemiologic studies using complex survey designs. My work improves the validity of associations between health outcomes and dietary exposures, for example, and have been applied to multicenter studies such as the HCHS/SOL.
  • Baldoni PL, Sotres-Alvarez D, Lumley T, Shaw PA. On the Use of Regression Calibration in a Complex Sampling Design With Application to the Hispanic Community Health Study/Study of Latinos. Am J Epidemiol. 2021 Jul 1;190(7):1366-1376. doi: 10.1093/aje/kwab008. PMID: 33506244; PMCID: PMC8245895.
• I developed and teach a core graduate-level course on Data Visualization for Health Data Science. The course equips students with tools to explore, interpret, and communicate health data effectively. It emphasizes accessibility and inclusivity, while highlighting how well-designed visualizations can advance public health.