MAVID multiple alignment server. - Nicolas Bray; Lior Pachter (Nucleic Acids Res., 2003)

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)

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