Limitations of Pseudogenes in Identifying Gene Losses. - James C. Costello; Mira V. Han; Matthew W. Hahn (RECOMB-CG, 2008)

Identifying Parent-Daughter Relationships Among Duplicated Genes. - Mira V. Han; Matthew W. Hahn (Pacific Symposium on Biocomputing, 2009)

phyloXML: XML for evolutionary biology and comparative genomics. - Mira V. Han; Christian M. Zmasek (BMC Bioinform., 2009)

A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies. - Richard Van; Daniel Alvarez; Travis Mize; Sravani Gannavarapu; Lohitha Chintham Reddy; Fatma Nasoz; Mira V. Han (BMC Bioinform., 2024)

A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection. - Jelard Aquino; Daniel Witoslawski; Steve Park; Jessica Holder; Amei Amei; Mira V. Han (Briefings Bioinform., 2025)