A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree. - Tanja Stadler; James H. Degnan (Algorithms Mol. Biol., 2012)

A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees. - James H. Degnan; Noah A. Rosenberg; Tanja Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Evaluating Variations on the STAR Algorithm for Relative Efficiency and Sample Sizes Needed to Reconstruct Species Trees. - James H. Degnan (Pacific Symposium on Biocomputing, 2013)

Species Tree Inference by the STAR Method and Its Generalizations. - Elizabeth S. Allman; James H. Degnan; John A. Rhodes (J. Comput. Biol., 2013)

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. - Sha Zhu; James H. Degnan; Sharyn Goldstien; Bjarki Eldon (BMC Bioinform., 2015)

Species Tree Inference from Gene Splits by Unrooted STAR Methods. - Elizabeth S. Allman; James H. Degnan; John A. Rhodes (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

PRANC: ML species tree estimation from the ranked gene trees under coalescence. - Anastasiia Kim; James H. Degnan (Bioinform., 2020)

DiffuScope: inferring post-specific diffusion network. - Md Rashidul Hasan; Dheeman Saha; Farhan Asif Chowdhury; James H. Degnan; Abdullah Mueen (ASONAM, 2021)

Trying out a million genes to find the perfect pair with RTIST. - Gleb Zhelezov; James H. Degnan (Bioinform., 2022)