My research interests focus on the development of statistical methods and open-source bioinformatic tools to analyze data from a wide range of high-throughput genomic, transcriptomic, and proteomic technologies. I am particularly interested in developing methods and software for the Bioconductor Project. One of the key purposes of the methods I develop is to identify molecular features, such as genomic coordinates, genes/transcripts, or proteins that change in accessibility, expression, or abundance, respectively, between experimental conditions. At Pitt, I collaborate with research groups from the Department of Orthopedic Surgery to understand genomic and molecular mechanisms in spine-related diseases, other orthopedic issues, and patients with traumatic brain injury. These collaborations are the foundation from which my methodological and computational ideas originate.
2020 | University of North Carolina at Chapel Hill, NC | PhD in Biostatistics
2014 | University of Campinas, Brazil | MSc in Statistics
2012 | University of Campinas, Brazil | BSc in Statistics
Chen Y, Chen L, Lun AT, Baldoni PL, Smyth GK. edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets Nucleic Acids Res. 2025 Jan 27;53(2): gkaf018. doi: 10.1093/nar/gkaf018. PMID: 39844453; PMCID: PMC11754124.
Baldoni PL, Chen L, Li M, Chen Y, Smyth GK. Dividing out quantification uncertainty enables assessment of differential transcript usage with diffSplice. bioRxiv. 2025.04.07.647659.
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.
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.
Dong X, Du MRM, Gouil Q, Tian L, Jabbari JS, Bowden R, Baldoni PL, Chen Y, Smyth GK, Amarasinghe SL, Law CW, Ritchie ME. Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Nat Methods. 2023 Nov;20(11):1810-1821. doi: 10.1038/s41592-023-02026-3. Epub 2023 Oct 2. PMID: 37783886.
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, 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.
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.
