| 2026 | ICDE | RISK: Efficiently Processing Rich Spatial-Keyword Queries on Encrypted Geo-Textual Data. | Zhen Lv, Cong Cao, Hongwei Huo, Jiangtao Cui, Yanguo Peng, Hui Li, Yingfan Liu |
| 2025 | ICDE | Indexing Labeled Property Multidigraphs in Entropy Space, with Applications. | Hongwei Huo, Yongze Yu, Zongtao He, Jeffrey Scott Vitter |
| 2025 | TrustCom | RASKEE: A TEE-Assisted Secure Range Spatial Keyword Query in a Multi-user Setting. | Zhen Lv, Yaorong Tan, Hongwei Huo, Yanguo Peng, Youliang Tian |
| 2018 | DCC | Practical Succinct Text Indexes in External Memory. | Hongwei Huo, Xiaoyang Chen, Yuhao Zhao, Xiaojin Zhu, Jeffrey Scott Vitter |
| 2018 | DCC | Optimal In-Place Suffix Sorting. | Zhize Li, Jian Li, Hongwei Huo |
| 2018 | SPIRE | Optimal In-Place Suffix Sorting. | Zhize Li, Jian Li, Hongwei Huo |
| 2016 | DCC | CS2A: A Compressed Suffix Array-Based Method for Short Read Alignment. | Hongwei Huo, Zhigang Sun, Shuangjiang Li, Jeffrey Scott Vitter, Xinkun Wang, Qiang Yu, Jun Huan |
| 2015 | ALENEX | A Data-Aware FM-index. | Hongwei Huo, Longgang Chen, Heng Zhao, Jeffrey Scott Vitter, Yakov Nekrich, Qiang Yu |
| 2014 | DCC | A Practical Implementation of Compressed Suffix Arrays with Applications to Self-Indexing. | Hongwei Huo, Longgang Chen, Jeffrey Scott Vitter, Yakov Nekrich |
| 2012 | INDIN | A multi-channel MAC protocol design based on IEEE 802.15.4 standard in industry. | Cuimei Wu, Hairong Yan, Hongwei Huo |
| 2007 | BIBE | A Suffix Tree Construction Algorithm for DNA Sequences. | Hongwei Huo, Vojislav Stojkovic |
| 2007 | ICNC | A simulated annealing algorithm for multiple sequence alignment with guaranteed accuracy. | Hongwei Huo, Vojislav Stojkovic |
| 2006 | CIS | Two-Phase Quantum Based Evolutionary Algorithm for Multiple Sequence Alignment. | Hongwei Huo, Vojislav Stojkovic |
| 2006 | CIS | Software Agents Action Securities. | Vojislav Stojkovic, Hongwei Huo |
| 2006 | ICNC | A Maximum Weighted Path Approach to Multiple Alignments for DNA Sequences. | Hongwei Huo, Vojislav Stojkovic, Zhiwei Xiao |
| 2005 | ADMA | HGA-COFFEE : Aligning Multiple Sequences by Hybrid Genetic Algorithm. | Lifang Liu, Hongwei Huo, Bao-Shu Wang |
| 2005 | CIS | Simulated Annealing with Injecting Star-Alignment for Multiple Sequence Alignments. | Hongwei Huo, Hua Ming |
| 2005 | IWANN | A Novel Optimization of Profile HMM by a Hybrid Genetic Algorithm. | Lifang Liu, Hongwei Huo, Bao-Shu Wang |