Gene Hunting without Sequencing Genomis Clones: the "Twenty Questions" game with genes. - Guorong Xu; Sing-Hoi Sze; Cheng-Pin Liu; Pavel A. Pevzner; Norman Arnheim (German Conference on Bioinformatics, 1997)

Las Vegas Algorithms for Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment. - Sing-Hoi Sze; Pavel A. Pevzner (J. Comput. Biol., 1997)

Algorithms and software for support of gene identification experiments. - Sing-Hoi Sze; Mikhail A. Roytberg; Mikhail S. Gelfand; Andrey A. Mironov; Tatiana V. Astakhova; Pavel A. Pevzner (Bioinform., 1998)

Combinatorial Approaches to Finding Subtle Signals in DNA Sequences. - Pavel A. Pevzner; Sing-Hoi Sze (ISMB, 2000)

Splicing graphs and EST assembly problem. - Steffen Heber; Max A. Alekseyev; Sing-Hoi Sze; Haixu Tang; Pavel A. Pevzner (ISMB, 2002)

Finding Weak Motifs in DNA Sequences. - Sing-Hoi Sze; Mikhail S. Gelfand; Pavel A. Pevzner (Pacific Symposium on Biocomputing, 2002)

Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding. - Sing-Hoi Sze; Songjian Lu; Jianer Chen (WABI, 2004)

Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences. - Sing-Hoi Sze; Xiaoyan Zhao (Systems Biology and Regulatory Genomics, 2005)

Greedy Localization and Color-Coding: Improved Matching and Packing Algorithms. - Yang Liu 002; Songjian Lu; Jianer Chen; Sing-Hoi Sze (IWPEC, 2006)

A Polynomial Time Solvable Formulation of Multiple Sequence Alignment. - Sing-Hoi Sze; Yue Lu; Qingwu Yang (J. Comput. Biol., 2006)

Improved algorithms for path, matching, and packing problems. - Jianer Chen; Songjian Lu; Sing-Hoi Sze; Fenghui Zhang (SODA, 2007)

Finding Pathway Structures in Protein Interaction Networks. - Songjian Lu; Fenghui Zhang; Jianer Chen; Sing-Hoi Sze (Algorithmica, 2007)

Identifying clusters of functionally related genes in genomes. - Gangman Yi; Sing-Hoi Sze; Michael R. Thon (Bioinform., 2007)

Path Matching and Graph Matching in Biological Networks. - Qingwu Yang; Sing-Hoi Sze (J. Comput. Biol., 2007)

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. - Qingwu Yang; Sing-Hoi Sze (BMC Bioinform., 2008)

Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. - Yue Lu; Sing-Hoi Sze (J. Comput. Biol., 2008)

Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models. - Xiaoning Qian; Sing-Hoi Sze; Byung-Jun Yoon (J. Comput. Biol., 2009)

Graphlet alignment in protein interaction networks. - Mu-Fen Hsieh; Sing-Hoi Sze (GENSiPS, 2010)

Identifying Gene Clusters within Localized Regions in Multiple Genomes. - Qingwu Yang; Gangman Yi; Fenghui Zhang; Michael R. Thon; Sing-Hoi Sze (J. Comput. Biol., 2010)

Motif Finding in DNA Sequences Based on Skipping Nonconserved Positions in Background Markov Chains. - Xiaoyan Zhao; Sing-Hoi Sze (J. Comput. Biol., 2011)

Identifying Complexes from Protein Interaction Networks According to Different Types of Neighborhood Density. - Jia-Hao Fan; Jianer Chen; Sing-Hoi Sze (J. Comput. Biol., 2012)

Supervised Protein Family Classification and New Family Construction. - Gangman Yi; Michael R. Thon; Sing-Hoi Sze (J. Comput. Biol., 2012)

Iterative Expansion and Color Coding: An Improved Algorithm for 3D-Matching. - Jianer Chen; Yang Liu 002; Songjian Lu; Sing-Hoi Sze; Fenghui Zhang (ACM Trans. Algorithms, 2012)

A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-seq data. - Sing-Hoi Sze; Aaron M. Tarone (ICCABS, 2013)

Parameterized and Approximation Algorithms for the MAF Problem in Multifurcating Trees. - Jianer Chen; Jia-Hao Fan; Sing-Hoi Sze (WG, 2013)

Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. - Shuhua Fu; Aaron M. Tarone; Sing-Hoi Sze (ICCABS, 2014)

Finding Alignments of Conserved Graphlets in Protein Interaction Networks. - Mu-Fen Hsieh; Sing-Hoi Sze (J. Comput. Biol., 2014)

Parameterized and approximation algorithms for maximum agreement forest in multifurcating trees. - Jianer Chen; Jia-Hao Fan; Sing-Hoi Sze (Theor. Comput. Sci., 2015)

A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms. - Sing-Hoi Sze; Jonathan J. Parrott; Aaron M. Tarone (ICCABS, 2016)

Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in melilotus. - Shuhua Fu; Peter L. Chang; Maren L. Friesen; Natasha L. Teakle; Aaron M. Tarone; Sing-Hoi Sze (ICCABS, 2017)

Codon-Based Sequence Alignment for Mutation Analysis by High-Throughput Sequencing. - Sing-Hoi Sze; Craig D. Kaplan (ICCABS, 2018)

An Exact Matching Method for 16S rRNA Taxonomy Classification. - Sing-Hoi Sze (J. Comput. Biol., 2025)