Publications by authors named "Hongwei Huo"

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Panaln: indexing pangenome for read alignment.
Lilu Guo, Zongtao He, Hongwei Huo

Bioinformatics· September 2025

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An efficient Burrows-Wheeler transform-based aligner for short read mapping.
Lilu Guo, Hongwei Huo

Comput Biol Chem· June 2024

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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· January 2022

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CIndex: compressed indexes for fast retrieval of FASTQ files.
Hongwei Huo, Pengfei Liu, Chenhui Wang, Hongbo Jiang, Jeffrey Scott Vitter

Bioinformatics· January 2022

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A new algorithm for DNA motif discovery using multiple sample sequence sets.
Qiang Yu, Xiang Zhao, Hongwei Huo

J Bioinform Comput Biol· August 2019

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SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets.
Qiang Yu, Dingbang Wei, Hongwei Huo

BMC Bioinformatics· June 2018

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A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model.
Haitao Guo, Hongwei Huo

Biomed Res Int· February 2018

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SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules.
Haitao Guo, Hongwei Huo, Qiang Yu

PLoS One· August 2017

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PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets.
Qiang Yu, Hongwei Huo, Dazheng Feng

Biomed Res Int· February 2017

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RefSelect: a reference sequence selection algorithm for planted (l, d) motif search.
Qiang Yu, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter

BMC Bioinformatics· July 2016

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An Affinity Propagation-Based DNA Motif Discovery Algorithm.
Chunxiao Sun, Hongwei Huo, Qiang Yu, Haitao Guo, Zhigang Sun

Biomed Res Int· June 2016

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An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets.
Qiang Yu, Hongwei Huo, Jeffrey Scott Vitter, Jun Huan, Yakov Nekrich

IEEE/ACM Trans Comput Biol Bioinform· June 2016

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The components of rice and watermelon root exudates and their effects on pathogenic fungus and watermelon defense.
Lixuan Ren, Hongwei Huo, Fang Zhang, Wenya Hao, Liang Xiao

Plant Signal Behav· June 2016

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An Efficient Algorithm for Discovering Motifs in Large DNA Data Sets.
Qiang Yu, Hongwei Huo, Xiaoyang Chen, Haitao Guo, Jeffrey Scott Vitter

IEEE Trans Nanobioscience· July 2015

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PairMotif+: a fast and effective algorithm for de novo motif discovery in DNA sequences.
Qiang Yu, Hongwei Huo, Yipu Zhang, Hongzhi Guo, Haitao Guo

Int J Biol Sci· September 2013

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A heuristic cluster-based EM algorithm for the planted (l, d) problem.
Yipu Zhang, Hongwei Huo, Qiang Yu

J Bioinform Comput Biol· August 2013

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PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
Qiang Yu, Hongwei Huo, Yipu Zhang, Hongzhi Guo

PLoS One· April 2013

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Repeats identification using improved suffix trees.
Hongwei Huo, Xiaowu Wang, Vojislav Stojkovic

Int J Comput Biol Drug Des· March 2010

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A quantum-inspired genetic algorithm based on probabilistic coding for multiple sequence alignment.
Hong-Wei Huo, Vojislav Stojkovic, Qiao-Luan Xie

J Bioinform Comput Biol· February 2010

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A probabilistic coding based quantum genetic algorithm for multiple sequence alignment.
Hongwei Huo, Qiaoluan Xie, Xubang Shen, Vojislav Stojkovic

Comput Syst Bioinformatics Conf· August 2009

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