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Weizhong Li is a professor at the J. Craig Venter Institute working in the informatics group. Dr. Li’s research is focused on the development of algorithms and computational resources in solving data analysis problems in genomics, metagenomics, RNA-seq and other next generation sequencing data and other omics data. He is currently focused on using his expertise to better quantify and understand the human microbiome in the gut and oral cavities.
Prior to joining JCVI, Dr. Li was a senior principal scientist at Human Longevity Inc., a research scientist and investigator at University of California San Diego, a staff scientist at Sanford Burnham Prebys Medical Discovery Institute and a senior research scientist at Quorex Pharmaceuticals. He received his PhD and his BS in computational chemistry from the Nankai University in China.
Research Priorities
Computational tool development
- Ultra-fast and robust algorithms in biological sequence clustering analysis (CD-HIT), applications using clustering algorithms in various areas such as 16S rRNA analysis and improving NGS data analysis.
- Algorithms, methods and integrated pipelines for metagenomics including mapping, assembly, visualization, taxonomy identification and functional annotation.
- Computer cloud-based workflows and web portal for end-to-end RNA-seq sequence data analysis.
Metagenomics and microbiome
- Microbiome disease association through large-scale metagenomic sequencing projects for various disease types, such as IBD, liver disease, diabetes, infection and so on.
- Host-microbiome study for human and animals using multi-omics approach involving host genomics data, RNA-seq, 16S and metagenomics data.
Publications
Antibiotics at birth and later antibiotic courses: effects on gut microbiota.
Pediatric research. 2021-04-06;
PMID: 33824448
Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.
Microbial ecology. 2021-01-07;
PMID: 33410935
Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.
Microbial ecology. 2020-11-20;
PMID: 33219400
Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.
Microbial ecology. 2020-11-06;
PMID: 33155101
Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth.
The Journal of infectious diseases. 2020-04-02;
PMID: 32239170
Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis.
Frontiers in immunology. 2019-11-12; 10.2602.
PMID: 31781106
Interplay between the human gut microbiome and host metabolism.
Nature communications. 2019-10-03; 10.1: 4505.
PMID: 31582752
Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.
Cell metabolism. 2019-09-03; 30.3: 607.
PMID: 31484056
Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.
Cell metabolism. 2017-05-02; 25.5: 1054-1062.e5.
PMID: 28467925
Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.
BMC genomics. 2017-04-13; 18.1: 296.
PMID: 28407798
Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species.
BMC genomics. 2016-09-27; 17.1: 761.
PMID: 27678198
A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.
Scientific reports. 2016-08-25; 6.31731.
PMID: 27558918
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data.
Bioinformatics (Oxford, England). 2013-01-01; 29.1: 122-3.
PMID: 23044549
CD-HIT: accelerated for clustering the next-generation sequencing data.
Bioinformatics (Oxford, England). 2012-12-01; 28.23: 3150-2.
PMID: 23060610
Ultrafast clustering algorithms for metagenomic sequence analysis.
Briefings in bioinformatics. 2012-11-01; 13.6: 656-68.
PMID: 22772836
WebMGA: a customizable web server for fast metagenomic sequence analysis.
BMC genomics. 2011-09-07; 12.444.
PMID: 21899761
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.
Bioinformatics (Oxford, England). 2011-06-15; 27.12: 1704-5.
PMID: 21505035
Artificial and natural duplicates in pyrosequencing reads of metagenomic data.
BMC bioinformatics. 2010-04-13; 11.187.
PMID: 20388221
CD-HIT Suite: a web server for clustering and comparing biological sequences.
Bioinformatics (Oxford, England). 2010-03-01; 26.5: 680-2.
PMID: 20053844
Analysis and comparison of very large metagenomes with fast clustering and functional annotation.
BMC bioinformatics. 2009-10-28; 10.359.
PMID: 19863816
Identification of ribosomal RNA genes in metagenomic fragments.
Bioinformatics (Oxford, England). 2009-05-15; 25.10: 1338-40.
PMID: 19346323
Probing metagenomics by rapid cluster analysis of very large datasets.
PloS one. 2008-01-01; 3.12: e3375.
PMID: 18846219
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Bioinformatics (Oxford, England). 2006-07-01; 22.13: 1658-9.
PMID: 16731699
Research Priorities
Computational tool development
- Ultra-fast and robust algorithms in biological sequence clustering analysis (CD-HIT), applications using clustering algorithms in various areas such as 16S rRNA analysis and improving NGS data analysis.
- Algorithms, methods and integrated pipelines for metagenomics including mapping, assembly, visualization, taxonomy identification and functional annotation.
- Computer cloud-based workflows and web portal for end-to-end RNA-seq sequence data analysis.
Metagenomics and microbiome
- Microbiome disease association through large-scale metagenomic sequencing projects for various disease types, such as IBD, liver disease, diabetes, infection and so on.
- Host-microbiome study for human and animals using multi-omics approach involving host genomics data, RNA-seq, 16S and metagenomics data.