| 2014 | PAKDD | Constrained-hLDA for Topic Discovery in Chinese Microblogs. | Wei Wang, Hua Xu, Weiwei Yang, Xiaoqiu Huang |
| 2013 | EMNLP | Implicit Feature Detection via a Constrained Topic Model and SVM. | Wei Wang, Hua Xu, Xiaoqiu Huang |
| 2008 | CIKM | Pairwise statistical significance of local sequence alignment using multiple parameter sets. | Ankit Agrawal, Xiaoqiu Huang |
| 2008 | CIT | Pairwise DNA Alignment with Sequence Specific Transition-Transversion Ratio Using Multiple Parameter Sets. | Ankit Agrawal, Xiaoqiu Huang |
| 2008 | CIT | Pairwise Statistical Significance of Local Sequence Alignment Using Substitution Matrices with Sequence-Pair-Specific Distance. | Ankit Agrawal, Xiaoqiu Huang |
| 2004 | BIBE | Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds. | I-Hsuan Yang, Sheng-Ho Wang, Yang-Ho Chen, Pao-Hsian Huang, Liang Ye, Xiaoqiu Huang, Kun-Mao Chao |
| 2004 | SNPD | A Sensitive Sequence Comparison Method. | Xiaoqiu Huang, Liang Ye, I-Hsuan Yang, Kun-Mao Chao |
| 2002 | HiPC | Parallel Syntenic Alignments. | Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang |
| 1994 | CPM | A Context Dependent Method for Comparing Sequences. | Xiaoqiu Huang |
| 1994 | CPM | Parametric Recomuting in Alignment Graphs. | Xiaoqiu Huang, Pavel A. Pevzner, Webb Miller |
| 1990 | ICPP | Computing Local Sequence Similarities on a Hypercube. | Xiaoqiu Huang |