CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. - Yen-Yi Lin; Phuong Dao; Faraz Hach; Marzieh Bakhshi; Fan Mo; Anna Lapuk; Colin C. Collins; Süleyman Cenk Sahinalp (WABI, 2012)

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. - Phuong Dao; Ibrahim Numanagic; Yen-Yi Lin; Faraz Hach; Emre Karakoç; Nilgun Donmez; Colin C. Collins; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2014)

Discovery and genotyping of novel sequence insertions in many sequenced individuals. - Pinar Kavak; Yen-Yi Lin; Ibrahim Numanagic; Hossein Asghari; Tunga Güngör; Can Alkan; Faraz Hach (Bioinform., 2017)

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. - Alexander Gawronski; Michael Uhl; Yajia Zhang; Yen-Yi Lin; Yashar S. Niknafs; Varune R. Ramnarine; Rohit Malik; Felix Feng; Arul M. Chinnaiyan; Colin C. Collins; Süleyman Cenk Sahinalp; Rolf Backofen (Bioinform., 2018)

Computational identification of micro-structural variations and their proteogenomic consequences in cancer. - Yen-Yi Lin; Alexander Gawronski; Faraz Hach; Sujun Li; Ibrahim Numanagic; Iman Sarrafi; Swati Mishra 006; Andrew W. McPherson; Colin C. Collins; Milan Radovich; Haixu Tang; Süleyman Cenk Sahinalp (Bioinform., 2018)

CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme. - Hossein Asghari; Yen-Yi Lin; Yang Xu; Ehsan Haghshenas; Colin C. Collins; Faraz Hach (Bioinform., 2020)

Phenotype prediction from single-cell RNA-seq data using attention-based neural networks. - Yuzhen Mao; Yen-Yi Lin; Nelson K. Y. Wong; Stanislav Volik; Funda Sar; Colin C. Collins; Martin Ester (Bioinform., 2024)