BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. - Ken Chen 001; John W. Wallis; Cyriac Kandoth; Joelle M. Kalicki-Veizer; Karen L. Mungall; Andrew J. Mungall; Steven J. M. Jones; Marco A. Marra; Timothy J. Ley; Elaine R. Mardis; Richard K. Wilson; John N. Weinstein; et al. (Bioinform., 2012)

SomaticSniper: identification of somatic point mutations in whole genome sequencing data. - David E. Larson; Christopher C. Harris; Ken Chen 001; Daniel C. Koboldt; Travis E. Abbott; David J. Dooling; Timothy J. Ley; Elaine R. Mardis; Richard K. Wilson; Li Ding (Bioinform., 2012)

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. - Christopher A. Miller 002; Brian S. White; Nathan D. Dees; Malachi Griffith; John S. Welch; Obi L. Griffith; Ravi Vij; Michael H. Tomasson; Timothy A. Graubert; Matthew J. Walter; Matthew J. Ellis; William S. Schierding; et al. (PLoS Comput. Biol., 2014)

Bam-readcount - rapid generation of basepair-resolution sequence metrics. - Ajay Khanna; David E. Larson; Srivatsan Sridhar; Matthew Mosior; Travis E. Abbott; Susanna Kiwala; Timothy J. Ley; Eric J. Duncavage; Matthew J. Walter; Jason R. Walker; Obi L. Griffith; Malachi Griffith; et al. (J. Open Source Softw., 2022)