KnotAli: informed energy minimization through the use of evolutionary information. - Mateo Gray; Sean Chester; Hosna Jabbari (BMC Bioinform., 2022)

SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. - Mateo Gray; Sebastian Will; Hosna Jabbari (WABI, 2023)

SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration. - Mateo Gray; Sebastian Will; Hosna Jabbari (Algorithms Mol. Biol., 2024)

Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. - Mateo Gray; Sebastian Will; Hosna Jabbari (WABI, 2025)