Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). - Gregory R. Grant; Michael H. Farkas; Angel D. Pizarro; Nicholas F. Lahens; Jonathan Schug; Brian P. Brunk; Christian J. Stoeckert Jr.; John B. Hogenesch; Eric A. Pierce (Bioinform., 2011)

CircaDB: a database of mammalian circadian gene expression profiles. - Angel D. Pizarro; Katharina Hayer; Nicholas F. Lahens; John B. Hogenesch (Nucleic Acids Res., 2013)

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. - Katharina E. Hayer; Angel D. Pizarro; Nicholas F. Lahens; John B. Hogenesch; Gregory R. Grant (Bioinform., 2015)

Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. - Scott S. Norton; Jorge Vaquero-Garcia; Nicholas F. Lahens; Gregory R. Grant; Yoseph Barash (Bioinform., 2018)

Comparative evaluation of full-length isoform quantification from RNA-Seq. - Dimitra Sarantopoulou; Thomas G. Brooks; Soumyashant Nayak; Antonijo Mrcela; Nicholas F. Lahens; Gregory R. Grant (BMC Bioinform., 2021)

BEERS2: RNA-Seq simulation through high fidelity in silico modeling. - Thomas G. Brooks; Nicholas F. Lahens; Antonijo Mrcela; Dimitra Sarantopoulou; Soumyashant Nayak; Amruta Naik; Shaon Sengupta; Peter S. Choi; Gregory R. Grant (Briefings Bioinform., 2024)