Denglab Metagenomic Analysis Pipeline (DMAP)
This analysis pipeline is built and maintained by Deng Lab and it is suitable for high-throughput sequencing data analysis, focusing on amplicon sequencing data (16S rRNA, ITS, 18S rRNA and functional genes).
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iNAP (integrated Network Analysis Pipeline)
This analysis pipeline is built and maintained by Metagenomics for Environmental Microbiology (MEM) (Deng Lab) and it is used to model, analyze and manage the the Molecular Ecological Networks (MENs) for adjacent matrix and Inter-Domain Ecological Networks (IDENs) for bipartite matrix from metagenomic datasets, e.g. GeoChip and Sequencing, and synchronous plant surveys, including Molecular Ecological Network Analysis (MENA) Pipeline and InterDomain Ecological Network Analysis Pipeline (IDENAP).
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Rapid DEgenerate Primer design program
This analysis pipeline is built by Deng Lab. It is used for sequence database management and primer assessment.
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Antibiotic Resistance Gene Analyzer (ARGA)
This pipeline is used for antibiotic resistance genes (ARGs) analysis based on the Sequence Database for ARGs (SDARG).
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Nitrogen Cycling Functional Gene Analyzer (NcycFunGen)
This pipeline is used for nitrogen functional gene analysis based on the Sequence Database for NcycFunGen.
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Reprogrammed Expectation Maximization Iterative Reconstruction of Genes from the Environment (REMIRGE)
It is used for reconstruct full-length functional(or ribosomal) genes from microbial community short read sequencing data.
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Ecological Design of High-Performance Synthetic Microbial Communities: From Theoretical Foundations to Functional Optimization

Zhihan Wang, Shang Wang*, Qing He, Xingsheng Yang, Bo Zhao, Haihan Zhang*, Ye Deng*. ISME Communications, 2025, 5(1): ycaf133
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Latest news

  • 2025-6-9
  • Dr. Deng was was ranked in the "Best Ecology and Evolution Scientists" by Research.com
    as national 13th and global 634th.
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  • 2025-3-25
  • Dr. Deng was honored as a "2024 Highly Cited Chinese Researcher in Ecology" by Elsevier.
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  • 2024-11-19
  • Dr. Deng was honored as a "Highly Cited Researcher 2024" by Clarivate in the cross-field.
    This was the 7th HCR award.
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  • 2024-9-9
  • Dr. Deng was was ranked in the "Best Ecology and Evolution Scientists" by Research.com
    as national 16th and global 949th.
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  • 2024-3-27
  • Dr. Deng was honored as a "2023 Highly Cited Chinese Researcher in Ecology" by Elsevier.
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  • 2023-11-16
  • Dr. Deng was honored as a "Highly Cited Researcher 2023" by Clarivate.
    This was the 6th HCR award.
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  • 2023-5-5
  • Dr. Deng was ranked in the "Best Ecology and Evolution Scientists" by Research.com
    as national 17th and global 1029th.
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  • 2022-11-16
  • Dr. Deng was honored as a "Highly Cited Researcher 2022" by Clarivate.
    This was the 5th HCR award.
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  • 2021-11-15
  • Dr. Deng was honored as a "Highly Cited Researcher 2021" by Clarivate.
    This was the 4th HCR award in the field of Cross-Field for Dr. Deng since 2018.
    According to the Web of Sciences, the major fields of Dr. Deng were classified
    into Microbiology and Environmental Science.
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  • 2021-9-1
  • Dr. Deng started to serve as a senior editor for the ISME Journal,
    which is the flagship journal of the International Scociety of Microbial ecology.
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  • 2021-6-1
  • Dr. Deng started to serve as an associate editor for both Microbiome and
    Environmental Microbiome journals. Besides, Dr. Deng is an editorial board
    member of BMC Microbiology. All these three journals are BMC series journals.
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