WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing. - Carson Holt; Bojan Losic; Deepa Pai; Zhen Zhao; Quang Trinh; Sujata Syam; Niloofar Arshadi; Gun Ho Jang; Johar Ali; Tim Beck; John D. McPherson; Lakshmi B. Muthuswamy (Bioinform., 2014)

Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology. - Xintong Chen; Sander M. Houten; Kimaada Allette; Robert P. Sebra; Gustavo Stolovitzky; Bojan Losic (PSB, 2018)

STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts. - Nicholas K. Akers; Eric E. Schadt; Bojan Losic (Bioinform., 2018)