HGA-COFFEE : Aligning Multiple Sequences by Hybrid Genetic Algorithm. - Lifang Liu 001; Hongwei Huo; Bao-Shu Wang (ADMA, 2005)

Simulated Annealing with Injecting Star-Alignment for Multiple Sequence Alignments. - Hongwei Huo; Hua Ming (CIS (1), 2005)

A Novel Optimization of Profile HMM by a Hybrid Genetic Algorithm. - Lifang Liu 001; Hongwei Huo; Bao-Shu Wang (IWANN, 2005)

Two-Phase Quantum Based Evolutionary Algorithm for Multiple Sequence Alignment. - Hongwei Huo; Vojislav Stojkovic (CIS, 2006)

Software Agents Action Securities. - Vojislav Stojkovic; Hongwei Huo (CIS, 2006)

A Maximum Weighted Path Approach to Multiple Alignments for DNA Sequences. - Hongwei Huo; Vojislav Stojkovic; Zhiwei Xiao (ICNC (2), 2006)

A Suffix Tree Construction Algorithm for DNA Sequences. - Hongwei Huo; Vojislav Stojkovic (BIBE, 2007)

A simulated annealing algorithm for multiple sequence alignment with guaranteed accuracy. - Hongwei Huo; Vojislav Stojkovic (ICNC (2), 2007)

An Energy Efficient Communication Protocol Based on Data Equilibrium in Mobile Wireless Sensor Network. - Shuai Gao; Yanchao Niu; Hongwei Huo; Hongke Zhang (MSN, 2007)

ASDP: An Action-Based Service Discovery Protocol Using Ant Colony Algorithm in Wireless Sensor Networks. - Hongwei Huo; Deyun Gao; Yanchao Niu; Shuai Gao (MSN, 2007)

An Enhanced DV-hop Localization Algorithm for Irregularly Shaped Sensor Networks. - Yanchao Niu; Sidong Zhang; Xiaoyu Xu; Hongwei Huo; Shuai Gao (MSN, 2007)

A Greedy Two-stage Gibbs Sampling Method for Motif Discovery in Biological Sequences. - Lifang Liu 001; Licheng Jiao; Hongwei Huo (BMEI (1), 2008)

An Adaptive Suffix Tree Based Algorithm for Repeats Recognition in a DNA Sequence. - Hongwei Huo; Xiaowu Wang; Vojislav Stojkovic (IJCBS, 2009)

Repeats identification using improved suffix trees. - Hongwei Huo; Xiaowu Wang; Vojislav Stojkovic (Int. J. Comput. Biol. Drug Des., 2009)

A Quantum-Inspired Genetic Algorithm Based on Probabilistic Coding for Multiple Sequence Alignment. - Hongwei Huo; Vojislav Stojkovic; Qiao-Luan Xie (J. Bioinform. Comput. Biol., 2010)

Optimizing genetic algorithm for motif discovery. - Hongwei Huo; Zhenhua Zhao; Vojislav Stojkovic; Lifang Liu 001 (Math. Comput. Model., 2010)

Wireless sensor network based E-health system ?? implementation and experimental results. - Hairong Yan; Hongwei Huo; Youzhi Xu; Mikael Gidlund (IEEE Trans. Consumer Electron., 2010)

Wireless-Sensor-Networks-based healthcare system: a survey on the view of communication paradigms. - Hongwei Huo; Youzhi Xu; Hongke Zhang; Yu Hsiu Chuang; Tzong-Chen Wu (Int. J. Ad Hoc Ubiquitous Comput., 2011)

A multi-channel MAC protocol design based on IEEE 802.15.4 standard in industry. - Cuimei Wu; Hairong Yan; Hongwei Huo (INDIN, 2012)

A MapReduce-based Algorithm for Motif Search. - Hongwei Huo; Shuai Lin; Qiang Yu 003; Yipu Zhang; Vojislav Stojkovic (IPDPS Workshops, 2012)

StemFinder: An efficient algorithm for searching motif stems over large alphabets. - Qiang Yu 003; Hongwei Huo; Jeffrey Scott Vitter; Jun Huan; Yakov Nekrich (BIBM, 2013)

A Heuristic Cluster-Based EM Algorithm for the Planted (L, d) Problem. - Yipu Zhang; Hongwei Huo; Qiang Yu 003 (J. Bioinform. Comput. Biol., 2013)

An efficient motif finding algorithm for large DNA data sets. - Qiang Yu 003; Hongwei Huo; Xiaoyang Chen; Haitao Guo; Jeffrey Scott Vitter; Jun Huan (BIBM, 2014)

A Practical Implementation of Compressed Suffix Arrays with Applications to Self-Indexing. - Hongwei Huo; Longgang Chen; Jeffrey Scott Vitter; Yakov Nekrich (DCC, 2014)

A Data-Aware FM-index. - Hongwei Huo; Longgang Chen; Heng Zhao; Jeffrey Scott Vitter; Yakov Nekrich; Qiang Yu 003 (ALENEX, 2015)

Reference sequence selection for motif searches. - Qiang Yu 003; Hongwei Huo; Ruixing Zhao; Dazheng Feng; Jeffrey Scott Vitter; Jun Huan (BIBM, 2015)

A dynamic energy-saving strategy for green cellular railway communication network. - Jiying Huang; Zhangdui Zhong; Hongwei Huo (EURASIP J. Wirel. Commun. Netw., 2015)

An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets. - Qiang Yu 003; Hongwei Huo; Jeffrey Scott Vitter; Jun Huan; Yakov Nekrich (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

CS2A: A Compressed Suffix Array-Based Method for Short Read Alignment. - Hongwei Huo; Zhigang Sun; Shuangjiang Li; Jeffrey Scott Vitter; Xinkun Wang; Qiang Yu 003; Jun Huan (DCC, 2016)

RefSelect: a reference sequence selection algorithm for planted (l, d) motif search. - Qiang Yu 003; Hongwei Huo; Ruixing Zhao; Dazheng Feng; Jeffrey Scott Vitter; Jun Huan (BMC Bioinform., 2016)

MSQ-Index: A Succinct Index for Fast Graph Similarity Search. - Xiaoyang Chen; Hongwei Huo; Jun Huan; Jeffrey Scott Vitter (CoRR, 2016)

Efficient Graph Similarity Search in External Memory. - Xiaoyang Chen; Hongwei Huo; Jun Huan; Jeffrey Scott Vitter (IEEE Access, 2017)

Fast Computation of Graph Edit Distance. - Xiaoyang Chen; Hongwei Huo; Jun Huan; Jeffrey Scott Vitter (CoRR, 2017)

Practical Succinct Text Indexes in External Memory. - Hongwei Huo; Xiaoyang Chen; Yuhao Zhao; Xiaojin Zhu 004; Jeffrey Scott Vitter (DCC, 2018)

Fast Top-K Graph Similarity Search Via Representative Matrices. - Zhigang Sun; Hongwei Huo; Xiaoyang Chen (IEEE Access, 2018)

SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets. - Qiang Yu 003; Dingbang Wei; Hongwei Huo (BMC Bioinform., 2018)

A new algorithm for DNA motif discovery using multiple sample sequence sets. - Qiang Yu 003; Xiang Zhao; Hongwei Huo (J. Bioinform. Comput. Biol., 2019)

An efficient algorithm for graph edit distance computation. - Xiaoyang Chen; Hongwei Huo; Jun Huan; Jeffrey Scott Vitter (Knowl. Based Syst., 2019)

Feature reduction based on semantic similarity for graph classification. - Zhigang Sun; Hongwei Huo; Jun Huan; Jeffrey Scott Vitter (Neurocomputing, 2020)

Efficient Compression and Indexing for Highly Repetitive DNA Sequence Collections. - Hongwei Huo; Xiaoyang Chen; Xu Guo; Jeffrey Scott Vitter (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

MSQ-Index: A Succinct Index for Fast Graph Similarity Search. - Xiaoyang Chen; Hongwei Huo; Jun Huan; Jeffrey Scott Vitter; Weiguo Zheng; Lei Zou 001 (IEEE Trans. Knowl. Data Eng., 2021)

CIndex: compressed indexes for fast retrieval of FASTQ files. - Hongwei Huo; Pengfei Liu; Chenhui Wang; Hongbo Jiang; Jeffrey Scott Vitter (Bioinform., 2022)

Optimal in-place suffix sorting. - Zhize Li; Jian Li 015; Hongwei Huo (Inf. Comput., 2022)

RASK: Range Spatial Keyword Queries on Massive Encrypted Geo-Textual Data. - Zhen Lv 001; Kaiyu Shang; Hongwei Huo; Ximeng Liu; Yanguo Peng; Xiangyu Wang 010; Yaorong Tan (IEEE Trans. Serv. Comput., 2023)

Practical High-Order Entropy-Compressed Text Self-Indexing. - Hongwei Huo; Peng Long; Jeffrey Scott Vitter (IEEE Trans. Knowl. Data Eng., 2023)

An efficient Burrows-Wheeler transform-based aligner for short read mapping. - Lilu Guo; Hongwei Huo (Comput. Biol. Chem., 2024)

An Efficient Heuristic for Graph Edit Distance. - Xiaoyang Chen; Yujia Wang; Hongwei Huo; Jeffrey Scott Vitter (From Strings to Graphs, and Back Again, 2025)

FM-Adaptive: A Practical Data-Aware FM-Index. - Hongwei Huo; Zongtao He; Pengfei Liu; Jeffrey Scott Vitter (The Expanding World of Compressed Data, 2025)