MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. - Glen Stecher; Li Liu 035; Maxwell D. Sanderford; Daniel Peterson; Koichiro Tamura; Sudhir Kumar 001 (Bioinform., 2014)

PathFinder: Bayesian inference of clone migration histories in cancer. - Sudhir Kumar 001; Antonia Chroni; Koichiro Tamura; Maxwell D. Sanderford; Olumide Oladeinde; Vivian Aly; Tracy Vu; Sayaka Miura (Bioinform., 2020)

TreeMap: a structured approach to fine mapping of eQTL variants. - Li Liu 035; Pramod Chandrashekar; Biao Zeng; Maxwell D. Sanderford; Sudhir Kumar 001; Greg Gibson (Bioinform., 2021)

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. - Marcos A. Caraballo-Ortiz; Sayaka Miura; Maxwell D. Sanderford; Tenzin Dolker; Qiqing Tao; Steven Weaver; Sergei L. Kosakovsky Pond; Sudhir Kumar 001 (Bioinform., 2022)

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. - Nicholas J. Ose; Brandon M. Butler; Avishek Kumar; I. Can Kazan; Maxwell D. Sanderford; Sudhir Kumar 001; S. Banu Ozkan (PLoS Comput. Biol., 2022)

Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. - Jared Huzar; Madelyn Shenoy; Maxwell D. Sanderford; Sudhir Kumar 001; Sayaka Miura (Frontiers Bioinform., 2023)