Identification of novel transcripts in annotated genomes using RNA-Seq. - Adam Roberts; Harold Pimentel; Cole Trapnell; Lior Pachter (Bioinform., 2011)

Near-optimal RNA-Seq quantification. - Nicolas Bray; Harold Pimentel; Páll Melsted; Lior Pachter (CoRR, 2015)

The Lair: a resource for exploratory analysis of published RNA-Seq data. - Harold Pimentel; Pascal Sturmfels; Nicolas Bray; Páll Melsted; Lior Pachter (BMC Bioinform., 2016)

Fast and accurate quantification and differential analysis of transcriptomes. - Harold Pimentel (2016)

Pseudoalignment for metagenomic read assignment. - Lorian Schaeffer; Harold Pimentel; Nicolas Bray; Páll Melsted; Lior Pachter (Bioinform., 2017)

Biclustering by sparse canonical correlation analysis. - Harold Pimentel; Zhiyue Hu; Haiyan Huang (Quant. Biol., 2018)

dotears: Scalable, consistent DAG estimation using observational and interventional data. - Albert Xue; Jingyou Rao; Sriram Sankararaman; Harold Pimentel (CoRR, 2023)

Accounting for isoform expression increases power to identify genetic regulation of gene expression. - Nathan LaPierre; Harold Pimentel (PLoS Comput. Biol., 2024)