An efficient exact algorithm for computing all pairwise distances between reconciliations in the duplication-transfer-loss model. - Santi Santichaivekin; Ross Mawhorter; Ran Libeskind-Hadas (BMC Bioinform., 2019)

eMPRess: a systematic cophylogeny reconciliation tool. - Santi Santichaivekin; Qing Yang; Jingyi Liu; Ross Mawhorter; Justin Jiang; Trenton Wesley; Yi-Chieh Wu; Ran Libeskind-Hadas (Bioinform., 2021)

Maximum parsimony reconciliation in the DTLOR model. - Jingyi Liu; Ross Mawhorter; Nuo Liu; Santi Santichaivekin; Eliot C. Bush; Ran Libeskind-Hadas (BMC Bioinform., 2021)

Distance Profiles of Optimal RNA Foldings. - Jingyi Liu; I. Duan; Santi Santichaivekin; Ran Libeskind-Hadas (ISBRA, 2022)