The Geobucket Data Structure for Polynomials. - Thomas Yan (J. Symb. Comput., 1998)

Querying and computing with BioCyc databases. - Markus Krummenacker; Suzanne M. Paley; Lukas A. Mueller; Thomas Yan; Peter D. Karp (Bioinform., 2005)

PatMatch: a program for finding patterns in peptide and nucleotide sequences. - Thomas Yan; Danny Yoo; Tanya Z. Berardini; Lukas A. Mueller; Dan C. Weems; Shuai Weng; J. Michael Cherry; Seung Yon Rhee (Nucleic Acids Res., 2005)

A Social Network Ontology for Semantic Web Enabled Collaboration. - Thomas Yan; Hans-Peter Dommel (SWWS, 2006)

Practical Issues in Ontology Engineering. - Thomas Yan (IC-AI, 2007)