Enrichment of transcriptional regulatory sites in non-coding genomic region. - Wen Xue; Jin Wang; Zhirong Shen; Huaiqiu Zhu (Bioinform., 2004)

Accuracy improvement for identifying translation initiation sites in microbial genomes. - Huaiqiu Zhu; Gang-Qing Hu; Zheng-Qing Ouyang; Jin Wang; Zhen-Su She (Bioinform., 2004)

Multivariate Entropy Distance Method for Prokaryotic Gene Identification. - Zheng-Qing Ouyang; Huaiqiu Zhu; Jin Wang; Zhen-Su She (J. Bioinform. Comput. Biol., 2004)

Tree and rate estimation by local evaluation of heterochronous nucleotide data. - Zhu Yang; John D. O'Brien; Xiaobin Zheng; Huaiqiu Zhu; Zhen-Su She (Bioinform., 2007)

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes. - Huaiqiu Zhu; Gang-Qing Hu; Yi-Fan Yang; Jin Wang; Zhen-Su She (BMC Bioinform., 2007)

Computational evaluation of TIS annotation for prokaryotic genomes. - Gang-Qing Hu; Xiaobin Zheng; Lining Ju; Huaiqiu Zhu; Zhen-Su She (BMC Bioinform., 2008)

A dynamic Bayesian network approach to protein secondary structure prediction. - Xin-Qiu Yao; Huaiqiu Zhu; Zhen-Su She (BMC Bioinform., 2008)

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. - Gang-Qing Hu; Xiaobin Zheng; Yi-Fan Yang; Philippe Ortet; Zhen-Su She; Huaiqiu Zhu (Nucleic Acids Res., 2008)

MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. - Gang-Qing Hu; Jiangtao Guo; Yongchu Liu; Huaiqiu Zhu (Bioinform., 2009)

Prediction of translation initiation site for microbial genomes with TriTISA. - Gang-Qing Hu; Xiaobin Zheng; Huaiqiu Zhu; Zhen-Su She (Bioinform., 2009)

A de novo assembly method for metagenomic DNA reads with mate pairs. - Binbin Lai; Ruogu Ding; Huaiqiu Zhu (BMEI, 2011)

Gene prediction in metagenomic fragments based on the SVM algorithm. - Yongchu Liu; Jiangtao Guo; Huaiqiu Zhu (BMEI, 2011)

A mutation degree model for the identification of transcriptional regulatory elements. - Changqing Zhang; Jin Wang; Xu Hua; Jinggui Fang; Huaiqiu Zhu; Xiang Gao (BMC Bioinform., 2011)

A de novo metagenomic assembly program for shotgun DNA reads. - Binbin Lai; Ruogu Ding; Yang Li; Liping Duan; Huaiqiu Zhu (Bioinform., 2012)

Gene prediction in metagenomic fragments based on the SVM algorithm. - Yongchu Liu; Jiangtao Guo; Gang-Qing Hu; Huaiqiu Zhu (BMC Bioinform., 2013)

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads. - Binbin Lai; Fumeng Wang; Xiaoqi Wang; Liping Duan; Huaiqiu Zhu (BMC Bioinform., 2015)

Examining the neural correlates of depressive and motor symptoms in Parkinson's disease using Frequency Component Analysis (FCA). - Xiaopeng Song; Xiao Hu; Shuqin Zhou; Weiguo Liu; Yijun Liu; Huaiqiu Zhu; Jia-Hong Gao 001 (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2016)

Identifying micro-inversions using high-throughput sequencing reads. - Feifei He; Yang Li; Yu-Hang Tang; Jian Ma 004; Huaiqiu Zhu (BMC Genom., 2016)

MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. - Peng Zhai; Longshu Yang; Xiao Guo; Zhe Wang; Jiangtao Guo; Xiaoqi Wang; Huaiqiu Zhu (BMC Bioinform., 2017)

A Novel Compression Algorithm for High-Throughput DNA Sequence Based on Huffman Coding Method. - Chuan He; Huaiqiu Zhu (CISP-BMEI, 2018)

Micro-Inversions In Human Cancer Genomes. - Li Qu; Huaiqiu Zhu; May D. Wang (EMBC, 2018)

LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning. - Cheng Yang 001; Longshu Yang; Man Zhou; Haoling Xie; Chengjiu Zhang; May D. Wang; Huaiqiu Zhu (Bioinform., 2018)

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes. - Xiaoqing Jiang; Xin Li 060; Longshu Yang; Chunhong Liu; Qi Wang; Weilai Chi; Huaiqiu Zhu (Genom. Proteom. Bioinform., 2019)

An Error Correction Method of Nanopore Sequencing Data Using Deep Learning. - Luotong Wang; Li Qu; Longshu Yang; Yiying Wang; Huaiqiu Zhu (CISP-BMEI, 2020)

PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning. - Zhencheng Fang; Jie Tan; Shufang Wu; Mo Li; Chunhui Wang; Yongchu Liu; Huaiqiu Zhu (Bioinform., 2020)

AI-aided Data Mining in Gut Microbiome: The Road to Precision Medicine. - Xiaoqing Jiang; Congmin Xu; Qian Guo; Huaiqiu Zhu (CISP-BMEI, 2021)

LightCUD: a program for diagnosing IBD based on human gut microbiome data. - Congmin Xu; Man Zhou; Zhongjie Xie; Mo Li; Xi Zhu; Huaiqiu Zhu (BioData Min., 2021)

LncADeep performance on full-length transcripts. - Cheng Yang 001; Man Zhou; Haoling Xie; Huaiqiu Zhu (Nat. Mach. Intell., 2021)

HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes. - Jie Tan; Zhencheng Fang; Shufang Wu; Qian Guo; Xiaoqing Jiang; Huaiqiu Zhu (Bioinform., 2022)

Computer Simulation of Gene Knockout in Bacteria Accelerated by AI. - Peter X. Geng; Jiaheng Hou; Huaiqiu Zhu (CISP-BMEI, 2023)

Predicting Microbial Community Productivity Based-On Genomic Sequences with Graph Neural Network. - Jiaheng Hou; Peter X. Geng; Zhikai Wu; Wenlin Fan; Huaiqiu Zhu (CISP-BMEI, 2024)