Frazee AC, Jaffe AE, Langmead B, Leek JT (2015). "Polyester: simulating RNA-seq datasets with differential transcript expression." Bioinformatics, doi:10.1093/bioinformatics/btv272. {software} {code} {open access preprint}

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT (2015). "Ballgown bridges the gap between transcriptome assembly and expression analysis." Nature Biotechnology 33:243-246. {software} {code} {open access preprint}

Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, and Leek JT (2014). "Differential expression analysis of RNA-seq data at single-base resolution." Biostatistics 15(3): 413-426. {open access} {software/code}

Frazee AC, Langmead B, and Leek JT (2011). "ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets." BMC Bioinformatics 12:449. {corresponding website} {open access}

Frazee AC, Collado Torres L, Jaffe AE, Langmead B, Leek JT (2014). “Measurement, Summary, and Methodological Variation in RNA-sequencing” in S. Datta and D. Nettleton (Eds.), Statistical Analysis of Next Generation Sequencing Data (pp. 115-128): Springer.