RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences. - Qiaoji Xu; Lingling Jin; Chunfang Zheng; James H. Leebens-Mack; David Sankoff (ICCABS, 2020)

Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order. - Qiaoji Xu; Lingling Jin; James H. Leebens-Mack; David Sankoff (Algorithms, 2021)

The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny. - Qiaoji Xu; Xiaomeng Zhang; Yue Zhang; Chunfang Zheng; James H. Leebens-Mack; Lingling Jin; David Sankoff (J. Bioinform. Comput. Biol., 2021)

Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences. - Qiaoji Xu; Lingling Jin; Yue Zhang; Xiaomeng Zhang; Chunfang Zheng; James H. Leebens-Mack; David Sankoff (J. Comput. Biol., 2021)

Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo. - Qiaoji Xu; David Sankoff (RECOMB-CG, 2023)