The HOMFLY polynomial of links in closed braid form. - Pengyu Liu 003; Yuanan Diao; Gábor Hetyei (Discret. Math., 2019)

A tree distinguishing polynomial. - Pengyu Liu 003 (Discret. Appl. Math., 2021)

Comparing the topology of phylogenetic network generators. - Remie Janssen; Pengyu Liu 003 (J. Bioinform. Comput. Biol., 2021)

Quantifying syntax similarity with a polynomial representation of dependency trees. - Pengyu Liu 003; Tinghao Feng; Rui Liu (Glottometrics, 2022)

Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding. - Pengyu Liu 003; Jacob Lusk; Natasa Jonoska; Mariel Vázquez (PLoS Comput. Biol., 2024)