A Performance Evaluation of Sequence Alignment Software in Virtualized Environments. - Zachary Estrada; Zachary Stephens; Cuong Manh Pham; Zbigniew Kalbarczyk; Ravishankar K. Iyer (CCGRID, 2014)

Performance Comparison and Tuning of Virtual Machines For Sequence Alignment Software. - Zachary John Estrada; Fei Deng; Zachary Stephens; Cuong Manh Pham; Zbigniew T. Kalbarczyk; Ravishankar K. Iyer (Scalable Comput. Pract. Exp., 2015)

Unraveling complex local genomic rearrangements from long-read data. - Zachary D. Stephens; Ravishankar K. Iyer; Chen Wang 001; Jean-Pierre A. Kocher (BIBM, 2017)

Measuring the Mappability Spectrum of Reference Genome Assemblies. - Zachary D. Stephens; Ravishankar K. Iyer (BCB, 2018)

Detection and visualization of complex structural variants from long reads. - Zachary Stephens; Chen Wang 001; Ravishankar K. Iyer; Jean-Pierre A. Kocher (BMC Bioinform., 2018)

Telogator: a method for reporting chromosome-specific telomere lengths from long reads. - Zachary Stephens; Alejandro Ferrer; Lisa Boardman; Ravishankar K. Iyer; Jean-Pierre A. Kocher (Bioinform., 2022)

Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. - Zachary Stephens; Jean-Pierre A. Kocher (BMC Bioinform., 2024)