A5008030545- Plant biochemistry and biosynthesis
- Traditional Chinese Medicine Analysis
- Gut microbiota and health
- Microbial Natural Products and Biosynthesis
- Wood and Agarwood Research
- Tea Polyphenols and Effects
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Medicinal Plant Pharmacodynamics Research
- Medicinal Plants and Neuroprotection
- Microbial Community Ecology and Physiology
- Ginseng Biological Effects and Applications
- Plant Gene Expression Analysis
- Natural product bioactivities and synthesis
- Phytochemicals and Antioxidant Activities
- Bioinformatics and Genomic Networks
- Pharmacological Effects of Natural Compounds
- Biological and pharmacological studies of plants
- Plant tissue culture and regeneration
- Sesquiterpenes and Asteraceae Studies
- GABA and Rice Research
- Gene expression and cancer classification
- Bioactive Natural Diterpenoids Research
- CRISPR and Genetic Engineering
- Berberine and alkaloids research
Chinese Academy of Medical Sciences & Peking Union Medical College
2017-2025
Shanghai Institute of Materia Medica
2024
Nanjing University of Chinese Medicine
2024
Chinese Academy of Sciences
2024
Shanghai First People's Hospital
2024
Agriculture Victoria
2024
Shanghai Jiao Tong University
2024
China Academy of Chinese Medical Sciences
2024
Guang’anmen Hospital
2022
Bozhou People's Hospital
2020
Traditional Chinese medicine (TCM) is not only an effective solution for primary health care, but also a great resource drug innovation and discovery. To meet the increasing needs TCM-related data resources, we developed ETCM, Encyclopedia of Medicine. ETCM includes comprehensive standardized information commonly used herbs formulas TCM, as well their ingredients. The herb basic property quality control standard, formula composition, ingredient drug-likeness, many other provided by can serve...
Abstract Data visualization plays a crucial role in illustrating results and sharing knowledge among researchers. Though many types of tools are widely used, most them require enough coding experience or designed for specialized usages, not free. Here, we present ImageGP, platform biology chemistry data illustration. ImageGP could generate generalized plots like lines, bars, scatters, boxes, sets, heatmaps, histograms with the common input content user‐friendly interface. Normally plotting...
Marine organisms are expected to be an important source of inspiration for drug discovery after terrestrial plants and microorganisms. Despite the remarkable progress in field marine natural products (MNPs) chemistry, there only a few open access databases dedicated MNPs research. To meet growing demand mining sharing MNPs-related data resources, we developed CMNPD, comprehensive database based on manually curated data. CMNPD currently contains more than 31 000 chemical entities with various...
Abstract Tanshinones are the bioactive nor -diterpenoid constituents of Chinese medicinal herb Danshen ( Salvia miltiorrhiza ). These groups chemicals have characteristic furan D-ring, which differentiates them from phenolic abietane-type diterpenoids frequently found in Lamiaceae family. However, how 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly using a highly homozygous genotype. We identify cytochrome P450 (CYP71D) tandem gene array through...
It is difficult for beginners to learn and use amplicon analysis software because there are so many tools choose from, all of them need multiple steps operation. Herein, we provide a cross-platform, open-source, community-supported pipeline EasyAmplicon. EasyAmplicon has most the modules needed an analysis, including data quality control, merging paired-end reads, dereplication, clustering or denoising, chimera detection, generation feature tables, taxonomic diversity compositional biomarker...
With the gradual maturity of sequencing technology, many microbiome studies have published, driving emergence and advance related analysis tools. R language is widely used platform for data powerful functions. However, tens thousands packages numerous similar tools brought major challenges researchers to explore data. How choose suitable, efficient, convenient, easy-to-learn from has become a problem researchers. We organized 324 common classified them according application categories...
Existing traditional Chinese medicine (TCM)-related databases are still insufficient in data standardization, integrity and precision, need to be updated urgently. Herein, an Encyclopedia of Traditional Medicine version 2.0 (ETCM v2.0, http://www.tcmip.cn/ETCM2/front/#/) was constructed as the latest curated database hosting 48,442 TCM formulas recorded by ancient medical books, 9872 patent drugs, 2079 medicinal materials 38,298 ingredients. To facilitate mechanistic research new drug...
Abstract Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in‐depth analysis of microbial communities at both the high‐resolution taxonomic and functional levels. This approach provides valuable insights diversity, interactions, their roles health disease. However, complexity data processing need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, user‐friendly pipeline that supports...
Abstract ImageGP is an extensively utilized, open‐access platform for online data visualization and analysis. Over the past 7 years, it has catered to more than 700,000 usages globally, garnering substantial user feedback. The updated version, 2 (available at https://www.bic.ac.cn/BIC ), introduces a redesigned interface leveraging cutting‐edge web technologies enhance functionality interaction. Key enhancements include following: (i) Addition of modules format transformation, facilitating...
The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. first edition, launched 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend sincere invitation to researchers participate the upcoming 2nd version of MPB, contributing their valuable advance research. is research area that focuses on studying omics microbe [1] with rapid development past few decades,...
Abstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration microbial communities through amplicon sequencing. widespread adoption across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility many...
Ent-kaurene diterpenoids are the largest group of known Isodon diterpenoids. Among them, oridonin is accumulated in leaves, and most frequently studied compound because its antitumor antibacterial activities. We have identified five copalyl diphosphate synthase (CPS) six kaurene synthase-like (KSL) genes by transcriptome profiling rubescens leaves. An vitro assay assigns ten them to different diterpene biosynthesis pathways, except IrCPS3 that has a mutation catalytic motif. The...
Aporphine alkaloids have diverse pharmacological activities; however, our understanding of their biosynthesis is relatively limited. Previous studies classified aporphine into two categories based on the configuration and number substituents D-ring proposed preliminary biosynthetic pathways for each category. In this study, we identified specific cytochrome P450 enzymes (CYP80G6 CYP80Q5) with distinct activities toward (S)-configured (R)-configured substrates from herbaceous perennial vine...
The dry root and rhizome of Salvia miltiorrhiza Bunge, or Danshen, is a well-known, traditional Chinese medicine. Tanshinones are active compounds that accumulate in the periderm, resulting red-colored roots. However, lines with orange roots have been observed cultivated fields. Here, we performed metabolome transcriptome analyses to investigate changes orange-rooted Danshen.Metabolome analysis was by ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry...
Cytochrome P450s (CYPs) are important enzymes in the secondary metabolism of plants and have been recognized as key players bioengineering synthetic biology. Previously reported CYP76AH1 CYP76AH3, having greater than 80% sequence homology, played a continuous catalytic role biosynthesis tanshinones Salvia miltiorrhiza. Homology modeling indicates that four sites might be responsible for differences activity between two enzymes. A series modeling-based mutational variants were designed to...
Abstract Medicinal plants have garnered significant attention in ethnomedicine and traditional medicine due to their potential antitumor, anti-inflammatory antioxidant properties. Recent advancements genome sequencing synthetic biology revitalized interest natural products. Despite the availability of sequenced genomes transcriptomes these plants, absence publicly accessible gene annotations tabular formatted expression data has hindered effective utilization. To address this pressing issue,...