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Biography

The focus of my lab at HUST is to identify genes and/or microbial species that are of clinical significance by computational methods and multi-omics data integration, and develop novel methods to manipulate them for the purpose of real-life applications. The lab is currently working on the following three topics:
 gut- and intra-tumor- microbiota and their association with disease progression and impact on treatment
 genetic modification of bacteria and phages for the purpose of drug delivery, cancer treatment and diagnosis
 gut virome (phage and human viruses) profiling and association with diseases
The lab is mostly computational, with close collaborations with experimental microbiologists, clinicians, hospitals and entrepreneurs.

Activities

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Employment (1)

Huazhong University of Science and Technology: Wuhan, Hubei, CN

2016-10-01 to present | Professor (College of Life Science and Technology)
Employment
Source: Self-asserted source
Wei-Hua Chen

Works (22)

Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts

Science Advances
2024-08-16 | Journal article
DOI: 10.1126/sciadv.adn3316
Contributors: Senying Lai; Huarui Wang; Peer Bork; Wei-Hua Chen; Xing-Ming Zhao
Source: check_circle
Crossref

Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial

Gut
2024-07 | Journal article
DOI: 10.1136/gutjnl-2023-330168
Contributors: Jiaying Zhu; Chuqing Sun; Min Li; Guoru Hu; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers

Gut Microbes
2023-12-31 | Journal article
DOI: 10.1080/19490976.2023.2205386
Contributors: Min Li; Jinxin Liu; Jiaying Zhu; Huarui Wang; Chuqing Sun; Na L. Gao; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

Cross-Platform Transcriptomic Data Integration, Profiling, and Mining in Vibrio cholerae

Microbiology Spectrum
2023-06-15 | Journal article
DOI: 10.1128/spectrum.05369-22
Contributors: Zi-Xin Qin; Guo-Zhong Chen; Qian-Qian Yang; Ying-Jian Wu; Chu-Qing Sun; Xiao-Man Yang; Mei Luo; Chun-Rong Yi; Jun Zhu; Wei-Hua Chen et al.
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Crossref

Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces

Microbiology Spectrum
2023-06-15 | Journal article
DOI: 10.1128/spectrum.04340-22
Contributors: Xueyang Zhao; Chuqing Sun; Menglu Jin; Jingchao Chen; Lulu Xing; Jin Yan; Hailei Wang; Zhi Liu; Wei-Hua Chen; Junhua Li
Source: check_circle
Crossref

scBrainMap: a landscape for cell types and associated genetic markers in the brain

Database
2023-05-17 | Journal article
DOI: 10.1093/database/baad035
Contributors: Yuhao Chi; Ruicheng Qi; Yue Zhou; Huige Tong; Hanbo Jin; Christoph W Turck; Wei-Hua Chen; Guang-Zhong Wang
Source: check_circle
Crossref

An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli

Microbiology Spectrum
2022-08-31 | Journal article
DOI: 10.1128/spectrum.01271-22
Contributors: Menglu Jin; Jingchao Chen; Xueyang Zhao; Guoru Hu; Hailei Wang; Zhi Liu; Wei-Hua Chen; Jinxin Liu; Jinhu Huang
Source: check_circle
Crossref

Efficient recovery of complete gut phage genomes by combined short- and long-sequencing

2022-07-04 | Preprint
DOI: 10.1101/2022.07.03.498593
Contributors: Wei-Hua Chen; Jingchao Chen; Chuqing Sun; Yanqi Dong; Menglu Jin; Senying Lai; Longhao Jia; Xueyang Zhao; Na L Gao; Zhi Liu et al.
Source: check_circle
Crossref

Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-Free Mice

Genomics, Proteomics & Bioinformatics
2022-04-01 | Journal article
DOI: 10.1016/j.gpb.2020.06.024
Contributors: Yanze Li; Wenming Cao; Na L Gao; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison

Nucleic Acids Research
2022-01-07 | Journal article
DOI: 10.1093/nar/gkab1019
Contributors: Die Dai; Jiaying Zhu; Chuqing Sun; Min Li; Jinxin Liu; Sicheng Wu; Kang Ning; Li-jie He; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

mBodyMap: a curated database for microbes across human body and their associations with health and diseases

Nucleic Acids Research
2022-01-07 | Journal article
DOI: 10.1093/nar/gkab973
Contributors: Hanbo Jin; Guoru Hu; Chuqing Sun; Yiqian Duan; Zhenmo Zhang; Zhi Liu; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes

Genomics, Proteomics & Bioinformatics
2021-12 | Journal article
DOI: 10.1016/j.gpb.2021.03.002
Contributors: Na L. Gao; Zilong He; Qianhui Zhu; Puzi Jiang; Songnian Hu; Wei-Hua Chen
Source: check_circle
Crossref

Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models

mSystems
2021-06-29 | Journal article
DOI: 10.1128/mSystems.00112-21
Contributors: Puzi Jiang; Sicheng Wu; Qibin Luo; Xing-ming Zhao; Wei-Hua Chen; Vanni Bucci
Source: check_circle
Crossref

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

Nucleic Acids Research
2021-01-08 | Journal article
DOI: 10.1093/nar/gkaa869
Contributors: Senying Lai; Longhao Jia; Balakrishnan Subramanian; Shaojun Pan; Jinglong Zhang; Yanqi Dong; Wei-Hua Chen; Xing-Ming Zhao
Source: check_circle
Crossref

STAB: a spatio-temporal cell atlas of the human brain

Nucleic Acids Research
2021-01-08 | Journal article
DOI: 10.1093/nar/gkaa762
Contributors: Liting Song; Shaojun Pan; Zichao Zhang; Longhao Jia; Wei-Hua Chen; Xing-Ming Zhao
Source: check_circle
Crossref

Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment

BMC Genomics
2020-12 | Journal article
DOI: 10.1186/s12864-020-6749-z
Contributors: Puzi Jiang; Senying Lai; Sicheng Wu; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment

2020-04-20 | Preprint
DOI: 10.21203/rs.3.rs-17100/v2
Contributors: Puzi Jiang; Senying Lai; Sicheng Wu; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment

2020-03-13 | Preprint
DOI: 10.21203/rs.3.rs-17100/v1
Contributors: Puzi Jiang; Senying Lai; Sicheng Wu; Xing-Ming Zhao; Wei-Hua Chen
Source: check_circle
Crossref

Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees

Nucleic Acids Research
2019-07-02 | Journal article
DOI: 10.1093/nar/gkz357
Contributors: Balakrishnan Subramanian; Shenghan Gao; Martin J Lercher; Songnian Hu; Wei-Hua Chen
Source: check_circle
Crossref

GAAD: A Gene and Autoimmiune Disease Association Database

Genomics, Proteomics & Bioinformatics
2018-08-01 | Journal article
DOI: 10.1016/j.gpb.2018.05.001
Contributors: Guanting Lu; Xiaowen Hao; Wei-Hua Chen; Shijie Mu
Source: check_circle
Crossref

MVP: a microbe–phage interaction database

Nucleic Acids Research
2018-01-04 | Journal article
DOI: 10.1093/nar/gkx1124
Contributors: Na L Gao; Chengwei Zhang; Zhanbing Zhang; Songnian Hu; Martin J Lercher; Xing-Ming Zhao; Peer Bork; Zhi Liu; Wei-Hua Chen
Source: check_circle
Crossref

Energy efficiency trade-offs drive nucleotide usage in transcribed regions

Nature Communications
2016-04-21 | Journal article
DOI: 10.1038/ncomms11334
Contributors: Wei-Hua Chen; Guanting Lu; Peer Bork; Songnian Hu; Martin J. Lercher
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Crossref

Peer review (5 reviews for 2 publications/grants)

Review activity for Biosafety and health. (2)
Review activity for BMC bioinformatics (3)
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