EST clustering error evaluation and correction. - Ji-Ping Z. Wang; Bruce G. Lindsay 002; James H. Leebens-Mack; Liying Cui; P. Kerr Wall; Webb Colby Miller; Claude W. dePamphilis (Bioinform., 2004)

ChloroplastDB: the Chloroplast Genome Database. - Liying Cui; Narayanan Veeraraghavan; Alexander Richter; P. Kerr Wall; Robert K. Jansen; James H. Leebens-Mack; Izabela Makalowska; Claude W. dePamphilis (Nucleic Acids Res., 2006)

Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny. - David Sankoff; Chunfang Zheng; P. Kerr Wall; Claude W. dePamphilis; James H. Leebens-Mack; Victor A. Albert (RECOMB-CG, 2008)

PlantTribes: a gene and gene family resource for comparative genomics in plants. - P. Kerr Wall; James H. Leebens-Mack; Kai F. Müller; Dawn Field; Naomi S. Altman; Claude W. dePamphilis (Nucleic Acids Res., 2008)

Gene Loss under Neighborhood Selection Following Whole genome Duplication and the Reconstruction of the Ancestral Populus genome. - Chunfang Zheng; P. Kerr Wall; James H. Leebens-Mack; Claude de Pamphilis; Victor A. Albert; David Sankoff (J. Bioinform. Comput. Biol., 2009)

Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny. - David Sankoff; Chunfang Zheng; P. Kerr Wall; Claude de Pamphilis; James H. Leebens-Mack; Victor A. Albert (J. Comput. Biol., 2009)

Phylogenomic Analysis of the Phenylalanine Ammonia Lyase Gene Family in Loblolly Pine (Pinus Taeda L.). - Ujwal R. Bagal; James H. Leebens-Mack; W. Walter Lorenz; Jeffrey F. D. Dean (BIBM, 2011)

The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. - Li-San Wang; James H. Leebens-Mack; P. Kerr Wall; Kevin Beckmann; Claude W. dePamphilis; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

PhylOnt: A domain-specific ontology for phylogeny analysis. - Maryam Panahiazar; Ajith Ranabahu; Vahid Taslimi; Hima Yalamanchili; Arlin Stoltzfus; Jim Leebens-Mack; Amit P. Sheth (BIBM, 2012)

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)