MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. - Chengze Shen; Paul Zaharias; Tandy J. Warnow (Bioinform., 2022)

WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. - Chengze Shen; Minhyuk Park; Tandy J. Warnow (J. Comput. Biol., 2022)

EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract). - Chengze Shen; Baqiao Liu; Kelly P. Williams; Tandy J. Warnow (WABI, 2023)

BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). - Eleanor Wedell; Chengze Shen; Tandy J. Warnow (WABI, 2023)

UPP2: fast and accurate alignment of datasets with fragmentary sequences. - Minhyuk Park; Stefan Ivanovic; Gillian Chu; Chengze Shen; Tandy J. Warnow (Bioinform., 2023)

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment. - Chengze Shen; Baqiao Liu; Kelly P. Williams; Tandy J. Warnow (Algorithms Mol. Biol., 2023)

TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics. - Chengze Shen; Eleanor Wedell; Mihai Pop; Tandy J. Warnow (PLoS Comput. Biol., 2025)