Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors. - Leah L. Weber; Mohammed El-Kebir (WABI, 2020)

PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. - Leah L. Weber; Nuraini Aguse; Nicholas Chia; Mohammed El-Kebir (PLoS Comput. Biol., 2020)

Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors. - Leah L. Weber; Mohammed El-Kebir (Algorithms Mol. Biol., 2021)

doubletD: detecting doublets in single-cell DNA sequencing data. - Leah L. Weber; Palash Sashittal; Mohammed El-Kebir (Bioinform., 2021)

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. - Leah L. Weber; Chuanyi Zhang; Idoia Ochoa; Mohammed El-Kebir (PLoS Comput. Biol., 2023)

TRIBAL: Tree Inference of B Cell Clonal Lineages. - Leah L. Weber; Derek Reiman; Mrinmoy Saha Roddur; Yuanyuan Qi; Mohammed El-Kebir; Aly A. Khan (RECOMB, 2024)

Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors. - Leah L. Weber; Anna Hart; Idoia Ochoa; Mohammed El-Kebir (RECOMB, 2025)