Zhewen Zhang

Chinese Academy of Sciences

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Jingfa Xiao

Beijing Institute of Genomics

Jiayan Wu

Sun Yat-sen University

Yadong Zhang

Sun Yat-sen University

Meili Chen

Beijing Institute of Genomics

Zaichao Zhang

Huaiyin Normal University

Yongbing Zhao

National Institute of Arthritis and Musculoskeletal and Skin Diseases

Jinyue Wang

Beijing Institute of Genomics

Zhang Zhang

Chinese Academy of Sciences

Jun Yu

Chinese Academy of Sciences

Jingyao Zeng

Beijing Institute of Genomics

Cooperative Institutions

Chinese Academy of Sciences

165

Beijing Institute of Genomics

113

University of Chinese Academy of Sciences

110

Shanghai Center For Bioinformation Technology

Sun Yat-sen University

Zhejiang University

Huazhong University of Science and Technology

Central South University

Jilin University

Peking University

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

Genomics Proteomics & Bioinformatics (2021)

Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang

The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.

Data Sharing

Data set

Data access

10.1016/j.gpb.2021.08.001

Cite

Citations (974)

The C-Terminal Repeat Units of SpaA Mediate Adhesion of Erysipelothrix rhusiopathiae to Host Cells and Regulate Its Virulence

Biology (2022)

Chao Wu Zhewen Zhang Chao Kang Qiang Zhang Weifeng Zhu

Erysipelothrix rhusiopathiae is a causative agent of erysipelas in animals and erysipeloid in humans. However, current information regarding E. rhusiopathiae pathogenesis remains limited. Previously, we identified two E. rhusiopathiae strains, SE38 and G4T10, which were virulent and avirulent in pigs, respectively. Here, to further study the pathogenic mechanism of E. rhusiopathiae, we sequenced and assembled the genomes of strains SE38 and G4T10, and performed a comparative genomic analysis to identify differences or mutations in virulence-associated genes. Next, we comparatively analyzed 25 E. rhusiopathiae virulence-associated genes in SE38 and G4T10. Compared with that of SE38, the spaA gene of the G4T10 strain lacked 120 bp, encoding repeat units at the C-terminal of SpaA. To examine whether these deletions or splits influence E. rhusiopathiae virulence, these 120 bp were successfully deleted from the spaA gene in strain SE38 by homologous recombination. The mutant strain ΔspaA displayed attenuated virulence in mice and decreased adhesion to porcine iliac artery endothelial cells, which was also observed using the corresponding mutant protein SpaA'. Our results demonstrate that SpaA-mediated adhesion between E. rhusiopathiae and host cells is dependent on its C-terminal repeat units.

Erysipelothrix rhusiopathiae

Strain (injury)

10.3390/biology11071010

Cite

Citations (2)

Laparoscopy Training in Surgical Education: The Utility of Incorporating a Structured Preclinical Laparoscopy Course into the Traditional Apprenticeship Method

Journal of surgical education (2013)

Gunter De Win Siska Van Bruwaene Rajesh Aggarwal Nicola Crea Zhewen Zhang

Apprenticeship

Trainer

10.1016/j.jsurg.2013.04.001

Cite

Citations (34)

The Genome Sequence Archive Family: Towards Explosive Data Growth and Diverse Data Types

bioRxiv (Cold Spring Harbor Laboratory) (2021)

Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang

Abstract The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storing and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA ( https://ngdc.cncb.ac.cn/gsa/ ), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/ ), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/ ). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accept data submissions from all over the world and provide free open access to all publicly available data in support of worldwide research activities.

Data Sharing

Data set

Data access

10.1101/2021.06.29.449849

Cite

Citations (10)

Characteristic cytokine profile of the aqueous humor in eyes with congenital cataract and pre-existing posterior capsule dysfunction

Frontiers in Medicine (2024)

Yinying Zhao Qihui Zhao Hongfang Zhang Zhewen Zhang Dandan Wang

Objectives To investigate the characteristic cytokine profile of the aqueous humor in eyes with congenital cataract and pre-existing posterior capsule dysfunction (PCD). Methods In this cross-sectional study, the enrolled eyes with congenital cataract and PCD were included in the PCD group, while those with an intact posterior capsule were included in the control group. Demographic data and biometric parameters were recorded. The levels of 17 inflammatory factors in the aqueous humor collected from the enrolled eyes were detected using Luminex xMAP technology, and intergroup differences in the collected data were analyzed. Results The PCD group comprised 41 eyes from 31 patients with congenital cataract and PCD, whereas the control group comprised 42 eyes from 27 patients with congenital cataract and an intact posterior capsule. Lens thickness was significantly thinner in the PCD group than in the control group. However, the levels of monocyte chemoattractant protein-1 (MCP-1), transforming growth factor-β2 (TGF-β2), and vascular endothelial growth factor (VEGF) were significantly higher in the PCD group than in the control group. Multivariate logistic regression confirmed that lens thickness and TGF-β2 level were independent risk factors for PCD. Conclusion A thinner lens thickness in eyes with congenital cataract and PCD could serve as a biometric feature of these eyes. The higher levels of MCP-1, TGF-β2, and VEGF in eyes with PCD indicated a change in their intraocular inflammatory microenvironment, which possibly led to cataract progression. Lens thickness and TGF-β2 level are independent risk factors for PCD.

Capsule

10.3389/fmed.2024.1301588

Cite

Citations (0)

Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

Frontiers in Microbiology (2016)

Xinpeng Tian Zhewen Zhang Tingting Yang Meili Chen Jie Li

Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.

Phylogenetic diversity

Comparative Genomics

10.3389/fmicb.2016.00998

Cite

Citations (68)

ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics

Nucleic Acids Research (2022)

Yadong Zhang Hao Zhang Zaichao Zhang Qiheng Qian Zhewen Zhang

Compared with conventional comparative genomics, the recent studies in pan-genomics have provided further insights into species genomic dynamics, taxonomy and identification, pathogenicity and environmental adaptation. To better understand genome characteristics of species of interest and to fully excavate key metabolic and resistant genes and their conservations and variations, here we present ProPan (https://ngdc.cncb.ac.cn/propan), a public database covering 23 archaeal species and 1,481 bacterial species (in a total of 51,882 strains) for comprehensively profiling prokaryotic pan-genome dynamics. By analyzing and integrating these massive datasets, ProPan offers three major aspects for the pan-genome dynamics of the species of interest: 1) the evaluations of various species' characteristics and composition in pan-genome dynamics; 2) the visualization of map association, the functional annotation and presence/absence variation for all contained species' gene clusters; 3) the typical characteristics of the environmental adaptation, including resistance genes prediction of 126 substances (biocide, antimicrobial drug and metal) and evaluation of 31 metabolic cycle processes. Besides, ProPan develops a very user-friendly interface, flexible retrieval and multi-level real-time statistical visualization. Taken together, ProPan will serve as a weighty resource for the studies of prokaryotic pan-genome dynamics, taxonomy and identification as well as environmental adaptation.

Comparative Genomics

10.1093/nar/gkac832

Cite

Citations (13)

TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies

Nucleic Acids Research (2022)

Mingming Lu Yadong Zhang Fengchun Yang Jialin Mai Qianwen Gao

Abstract Transcriptome-wide association studies (TWASs), as a practical and prevalent approach for detecting the associations between genetically regulated genes and traits, are now leading to a better understanding of the complex mechanisms of genetic variants in regulating various diseases and traits. Despite the ever-increasing TWAS outputs, there is still a lack of databases curating massive public TWAS information and knowledge. To fill this gap, here we present TWAS Atlas (https://ngdc.cncb.ac.cn/twas/), an integrated knowledgebase of TWAS findings manually curated from extensive literature. In the current implementation, TWAS Atlas collects 401,266 high-quality human gene–trait associations from 200 publications, covering 22,247 genes and 257 traits across 135 tissue types. In particular, an interactive knowledge graph of the collected gene–trait associations is constructed together with single nucleotide polymorphism (SNP)–gene associations to build up comprehensive regulatory networks at multi-omics levels. In addition, TWAS Atlas, as a user-friendly web interface, efficiently enables users to browse, search and download all association information, relevant research metadata and annotation information of interest. Taken together, TWAS Atlas is of great value for promoting the utility and availability of TWAS results in explaining the complex genetic basis as well as providing new insights for human health and disease research.

Association (psychology)

10.1093/nar/gkac821

Cite

Citations (38)

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Archives of Microbiology (2016)

Guoxiang Shi Mingming Su Junrong Liang Ran Duan Wenpeng Gu

Yersinia enterocolitica

Yersinia

Homology

10.1007/s00203-016-1229-1

Cite

Citations (7)

A Novel Resveratrol-Arsenic Trioxide Combination Treatment Synergistically Induces Apoptosis of Adriamycin-Selected Drug-Resistant Leukemia K562 Cells

Journal of Cancer (2019)

Jing Chen Baoying Tian Cunmin Zhou Jingjing Sun Lin Li

Leukemia cells can develop resistance to apoptosis induced by chemotherapeutic agents. Concomitant multidrug resistance of cells remains the greatest clinical obstacle in the effective treatment of blood and solid tumors. Natural products have been identified that possess the capacity to modulate chemotherapeutic resistance and induce apopotosis. In this study, we generated adriamycin-resistant K562 leukemia (K562/RA) cells and compared the responses of sensitive and resistant leukemia cells to the natural products arsenic trioxide (ATO) and resveratrol (Rsv), with a view to determining whether Rsv potentiates the sensitivity of drug-resistant cells to ATO-induced apoptosis and the associated molecular mechanisms. Our results showed that resistance of K562/RA cells induced by adriamycin treatment was significantly higher (115.81-fold) than that of parental K562 cells. Simultaneously, K562/RA cells were cross-resistant to multiple agents, with the exception of ATO. Rsv enhanced the sensitivity of K562/RA cells to ATO and reduced the required dose of ATO as well as associated adverse reactions by promoting the proliferation inhibitory and apoptosis-inducing effects of ATO, which may be associated with reduced expression of the drug resistance genes mdr1/P-gp, mrp1/MRP1 and bcrp/BCRP, as well as the apoptotic inhibitory genes bcl-2, NF-κB and P53, and conversely, activation of caspase-3. Our collective findings indicate that ATO and Rsv synergistically enhance the sensitivity of drug-resistant leukemia cells to apoptosis.

Arsenic Trioxide

K562 cells

10.7150/jca.34506

Cite

Citations (11)