Ze Zhang

[ZZ* is (co-)corresponding author. ZZ† is (co-)first author.]

1. 

   Chromosome-level genome assembly and annotation of the moon jellyfish Aurelia coerulea

   Xinyue Hu† ,  Yang Guo† ,  Ze Zhang†* ,  Liyuan Wang ,  Duoyuan Chen ,  Zhenkun Zhuang ,  Minxiao Wang ,  Shiping Liu ,  and  Song Feng*

   Scientific Data, Apr 2026

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   Aurelia coerulea (moon jellyfish), a radially symmetrical metazoan in the phylum Cnidaria, possesses key features pertinent to understanding the evolutionary origins of nervous systems. Here, we employed a combination of long-read sequencing, short-read sequencing, and Hi-C chromatin conformation capture techniques to generate a chromosome-level assembly of the A. coerulea genome. The final assembly comprises approximately 554.10 Mb distributed across 21 chromosomes, achieving a scaffold N50 of 24.06 Mb and demonstrating high completeness (protein BUSCO score: 93.0%). Approximately 71.48% of the genome consists of transposable elements. We identified 26,777 protein-coding genes, of which approximately 72.28% have been functionally annotated. This chromosome-level genome provides an essential resource for elucidating early neural evolution and advancing our understanding of cnidarian biology.

   @article{10.1038/s41597-026-07102-9,
     author = {Hu†, Xinyue and Guo†, Yang and Zhang†*, Ze and Wang, Liyuan and Chen, Duoyuan and Zhuang, Zhenkun and Wang, Minxiao and Liu, Shiping and Feng*, Song},
     title = {Chromosome-level genome assembly and annotation of the moon jellyfish Aurelia coerulea},
     journal = {Scientific Data},
     year = {2026},
     month = apr,
     day = {10},
     pages = {854},
     volume = {13},
     number = {1},
     doi = {10.1038/s41597-026-07102-9},
     url = {https://www.nature.com/articles/s41597-026-07102-9},
     eprint = {https://www.nature.com/articles/s41597-026-07102-9},
   }

2. 

   一种高含水量样本的空间转录组制备方法及其应用

   张泽 ,  冯春露 ,  庄镇堃 ,  陈成 ,  胡馨月 ,  and  陈铎元

   CN Patent, Nov 2025

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   本发明公开了一种高含水量样本的空间转录组制备方法及其应用。所述制备方法包括以下步骤：对高含水量生物样本依次进行固定液固定、明胶置换、包埋、切片处理，得到切片样本。本发明高含水量生物的空间转录组样本的制备方法通过优化组织处理、包埋和切片流程，确保切片形态完整性和RNA完整性，满足空间转录组测序的要求，且本发明的制备方法具有广泛的适用性，为空间转录组测序在高含水量样本中的应用提供了可靠的技术支持。

   @article{CN120275136B,
     author = {张泽 and 冯春露 and 庄镇堃 and 陈成 and 胡馨月 and 陈铎元},
     title = {一种高含水量样本的空间转录组制备方法及其应用},
     journal = {CN Patent},
     year = {2025},
     month = nov,
     day = {04},
     pages = {},
     volume = {G01N1/28; G01N1/30; G01N1/36; G01N1/42; G01N1/34; C12Q1/6806; C12Q1/6869; G01N21/64},
     number = {},
     doi = {},
     url = {https://www.patentguru.com/cn/search?q=CN120275136B},
     eprint = {https://www.patentguru.com/cn/search?q=CN120275136B},
   }

3. 

   FACdb: a comprehensive resource for genes, gut microbiota, and metabolites in farm animals

   Ze Zhang† ,  Yang Li† ,  Di Zhang† ,  Shuai Chen* ,  Sien Lu ,  Kang Wang ,  Miao Zhou ,  Zehe Song ,  Qingcui Li* ,  Jie Yin* ,  and  Xiaoping Liu*

   Frontiers in Microbiology, Mar 2025

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   Farm animals, including livestock and poultry, play essential economic, social, and cultural roles and are indispensable in human welfare. Farm Animal Connectome database (FACdb) is a comprehensive resource that includes the association networks among gene expression, gut microbiota, and metabolites in farm animals. Although some databases present the relationship between gut microbes, metabolites, and gene expression, these databases are limited to human and mouse species, with limited data for farm animals. In this database, we calculate the associations and summarize the connections among gene expression, gut microbiota, and metabolites in farm animals using six correlation or distance calculation (including Pearson, Spearman, Cosine, Euclidean, Bray–Curtis, and Mahalanobis). FACdb contains over 55 million potential interactions of 73,571 genes, 11,046 gut microbiota, and 4,540 metabolites. It provides an easy-to-use interface for browsing and searching the association information. Additionally, FACdb offers interactive visualization tools to effectively investigate the relationship among the genes, gut microbiota, and metabolites in farm animals. Overall, FACdb is a valuable resource for understanding interactions among gut microbiota, metabolites, and gene expression. It contributes to the further utilization of microbes in animal products and welfare promotion. Compared to mice, pigs or other farm animals share more similarities with humans in molecular, cellular, and organ-level responses, indicating that our database may offer new insights into the relationship among gut microbiota, metabolites, and gene expression in humans.

   @article{10.3389/fmicb.2025.1557285,
     author = {Zhang†, Ze and Li†, Yang and Zhang†, Di and Chen*, Shuai and Lu, Sien and Wang, Kang and Zhou, Miao and Song, Zehe and Li*, Qingcui and Yin*, Jie and Liu*, Xiaoping},
     title = {FACdb: a comprehensive resource for genes, gut microbiota, and metabolites in farm animals},
     journal = {Frontiers in Microbiology},
     year = {2025},
     month = mar,
     day = {21},
     pages = {},
     volume = {16},
     number = {},
     doi = {10.3389/fmicb.2025.1557285},
     url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1557285/full},
     eprint = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1557285/full},
   }

4. 

   TeCD: The eccDNA Collection Database for extrachromosomal circular DNA

   Jing Guo† ,  Ze Zhang† ,  Qingcui Li ,  Xiao Chang* ,  and  Xiaoping Liu*

   BMC Genomics, Jan 2023

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   Background  Extrachromosomal circular DNA (eccDNA) is a kind of DNA that widely exists in eukaryotic cells. Studies in recent years have shown that eccDNA is often enriched during tumors and aging, and participates in the development of cell physiological activities in a special way, so people have paid more and more attention to the eccDNA, and it has also become a critical new topic in modern biological research. Description  We built a database to collect eccDNA, including animals, plants and fungi, and provide researchers with an eccDNA retrieval platform. The collected eccDNAs were processed in a uniform format and classified according to the species to which it belongs and the chromosome of the source. Each eccDNA record contained sequence length, start and end sites on the corresponding chromosome, order of the bases, genomic elements such as genes and transposons, and other information in the respective sequencing experiment. All the data were stored into the TeCD (The eccDNA Collection Database) and the BLAST (Basic Local Alignment Search Tool) sequence alignment function was also added into the database for analyzing the potential eccDNA sequences. Conclusion  We built TeCD, a platform for users to search and obtain eccDNA data, and analyzed the possible potential functions of eccDNA. These findings may provide a basis and direction for researchers to further explore the biological significance of eccDNA in the future.

   @article{doi:10.1186/s12864-023-09135-5,
     author = {Guo†, Jing and Zhang†, Ze and Li, Qingcui and Chang*, Xiao and Liu*, Xiaoping},
     title = {TeCD: The eccDNA Collection Database for extrachromosomal circular DNA},
     journal = {BMC Genomics},
     volume = {24},
     number = {1},
     pages = {47},
     year = {2023},
     month = jan,
     day = {27},
     doi = {10.1186/s12864-023-09135-5},
     url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09135-5},
     eprint = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09135-5},
   }