Explanipedia

A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron Open

Xiaoyuan Lin, Zhou Sha, Chunlin Zhang, Julia M. Adler, Ricardo Martin Vidal , et al. · 2025

Advancing osteoarthritis research: the role of AI in clinical, imaging and omics fields Open

Junwen Ou, Jin Zhang, Momen Alswadeh, Zhenglin Zhu, Jijun Tang , et al. · 2025

The Induction of Disease Resistance by Scopolamine and the Application of Datura Extract Against Potato (Solanum tuberosum L.) Late Blight Open

Zhiming Zhu, Shicheng Liu, Yi Liu, Xinze Zhang, Zhiwen Shi , et al. · 2024

Late blight, caused by Phytophthora infestans, is a devastating disease of potato. Our previous work illustrated that scopolamine, the main bioactive substance of Datura extract, exerts direct inhibitory effects on P. infestans, but it is …

Identifying the HIV-Resistance-Related Factors and Regulatory Network via Multi-Omics Analyses Open

Xueyan Long, Gexin Liu, Xinyi Liu, Chunlin Zhang, Lei Shi , et al. · 2024

For research on HIV/AIDS, it is important to elucidate the complex viral–host interaction, host dependency factors (HDFs), and restriction factors. However, the regulatory network of HIV-resistance-related factors remains not well understo…

Phenotypic, Metabolic and Genetic Adaptations of the Ficus Species to Abiotic Stress Response: A Comprehensive Review Open

Shengyun Yuan, T. M. Yin, huteng he, Xinyi Liu, Xueyan Long , et al. · 2024

The Ficus genus, having radiated from the tropics and subtropics to the temperate zone worldwide, is the largest genus among woody plants, comprising over 800 species. Evolution of the Ficus species results in genetic diversity, global rad…

NSP4 mutation T492I drives rapid evolution of SARS-CoV-2 toward Omicron Open

Xiaoyuan Lin, Zhou Sha, Chunlin Zhang, Julia M. Adler, Ricardo Martin Vidal , et al. · 2024

T492I, a mutation encountered in SARS-CoV-2 nonstructural protein 4 (NSP4), enhances viral replication and alters nonstructural protein cleavage, causing potential evolutionary impacts. Through comprehensive comparative analyses based on e…

Quantization of extraoral free flap monitoring for venous congestion with deep learning integrated iOS applications on smartphones Open

Chunyan Li, Wei Liu, Zhenglin Zhu, Xing Wang, Yanbin Zhang · 2023

aDepartment of Clinical Laboratory, Beijing Jishuitan Hospital, Capital Medical University, Fourth Clinical College of Peking University, Beijing, 100035, China bDepartment of Laboratory Medicine, Beijing Jishuitan Hospital, Capital Medica…

The NSP4 T492I mutation increases SARS-CoV-2 infectivity by altering non-structural protein cleavage Open

Xiaoyuan Lin, Zhou Sha, Jakob Trimpert, Dušan Kunec, Chen Jiang , et al. · 2023

T492I mutation alters SARS-CoV-2 properties via modulating viral non-structural proteins Open

Xiaoyuan Lin, Zhou Sha, Jakob Trimpert, Dušan Kunec, Chen Jiang , et al. · 2023

The historically dominant SARS-CoV-2 Delta variants and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on a combination of in silico analyses, we predicted that the T492…

Applying the digital data and the bioinformatics tools in SARS-CoV-2 research Open

Meng How Tan, Jiaxin Xia, Haitao Luo, Geng Meng, Zhenglin Zhu · 2023

Bioinformatics has been playing a crucial role in the scientific progress to fight against the pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The advances in …

Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion Open

Xiaoyuan Lin, Weiwei Xue, Yueping Zhang, Beibei Fu, Jakob Trimpert , et al. · 2021

Previous work indicated that the nucleocapsid 203 mutation increase the virulence and transmission of the SARS-CoV-2 Alpha variant. However, Delta later outcompeted Alpha and other lineages, promoting a new wave of infections. Delta also p…

Author Correction: Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2 Open

Zhenglin Zhu, Kaiwen Meng, Geng Meng · 2021

as follows.

Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2 Open

Haibo Wu, Na Xing, Kaiwen Meng, Beibei Fu, Weiwei Xue , et al. · 2021

Solitary Living Brings a Decreased Weight and an Increased Agility to the Domestic Silkworm, Bombyx mori Open

Zhenglin Zhu, Yuting Tan, Siyu Xiao, Zhufen Guan, Wen Zhao , et al. · 2021

The domestic silkworms, Bombyx mori, always live in groups and little is known of the outcomes of solitary living. We bred solitary silkworms and performed a comprehensive investigation of the difference between solitary and group-living s…

Nucleocapsid mutation R203K/G204R increases the infectivity, fitness and virulence of SARS-CoV-2 Open

Haibo Wu, Na Xing, Kaiwen Meng, Beibei Fu, Weiwei Xue , et al. · 2021

In addition to the mutations on the spike protein (S), co-occurring mutations on nucleocapsid (N) protein are also emerging in SARS-CoV-2 world widely. Mutations R203K/G204R on N, carried by high transmissibility SARS-CoV-2 lineages includ…

Identification of regulatory networks associated with anti-HIV/AIDS genes via integrated transcriptome, epigenome and proteome analyses Open

Gexin Liu, Chunlin Zhang, Lei Shi, Zhenglin Zhu · 2021

There are individuals naturally resistant to HIV. To identify anti-HIV genes and regulatory networks that enable the native ability to resist HIV, we reanalyzed the transcriptome of HIV resistant and susceptible individuals based on previo…

A CRISPR-Cas9 based shuffle system for endogenous histone H3 and H4 combinatorial mutagenesis Open

Yu Fu, Zhenglin Zhu, Geng Meng, Rijun Zhang, Yueping Zhang · 2021

Post-translational modifications of histone proteins greatly impact gene expression and cell fate decisions in eukaryotes. To study these, it is important to develop a convenient, multiplex, and efficient method to precisely introduce muta…

Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis Open

Zhenglin Zhu, Gexin Liu, Kaiwen Meng, Liuqing Yang, Di Liu , et al. · 2021

The novel coronavirus (SARS-CoV-2) has become a pandemic and is threatening human health globally. Here, we report nine newly evolved SARS-CoV-2 single nucleotide polymorphism (SNP) alleles those underwent a rapid increase (seven cases) or…

Nucleocapsid Mutations R203K/G204R Increase the Infectivity, Fitness and Virulence of SARS-CoV-2 Open

Haibo Wu, Na Xing, Kaiwen Meng, Beibei Fu, Weiwei Xue , et al. · 2021

Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2 Open

Zhenglin Zhu, Kaiwen Meng, Geng Meng · 2020

Rapid spread of mutant alleles in worldwide COVID-19 strains revealed by genome-wide SNP analysis Open

Zhenglin Zhu, Gexin Liu, Kaiwen Meng, Liuqing Yang, Geng Meng · 2020

The novel coronavirus (COVID-19) has become a pandemic and is threatening human health globally. Here, we report 14 newly evolved COVID-19 single nucleotide polymorphism (SNP) alleles those underwent a rapid increase (12 cases) or decrease…

The genomic recombination events may reveal the evolution of coronavirus and the origination of 2019-nCoV Open

Zhenglin Zhu, Kaiwen Meng, Geng Meng · 2020

To trace the evolution of coronavirus and reveal the possible origination of the novel pneumonia coronavirus (2019-nCoV), we collected and thoroughly analyzed 2966 publicly available coronavirus genomes, including 182 2019-nCoVs strains. W…

A database resource for Genome-wide dynamics analysis of Coronaviruses on a historical and global scale Open

Zhenglin Zhu, Kaiwen Meng, Geng Meng · 2020

The recent outbreak of a new zoonotic origin Coronavirus has ring the bell for the potential spread of epidemic Coronavirus crossing the species. With the urgent needs to assist the control of the Coronavirus spread and to provide valuable…

SWAV: a web-based visualization browser for sliding window analysis Open

Zhenglin Zhu, Ya-Wang Wang, Xichuan Zhou, Liuqing Yang, Geng Meng , et al. · 2020

Sliding window analysis has been extensively applied in evolutionary biology. With the development of the high-throughput DNA sequencing of organisms at the population level, an application that is dedicated to visualizing population genet…

ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus Open

Zhenglin Zhu, Geng Meng · 2020

The recent outbreaks of African swine fever (ASF) in China and Europe have threatened the swine industry globally. To control the transmission of ASF virus (ASFV), we developed the African swine fever virus database (ASFVdb), an online dat…

A database resource and online analysis tools for coronaviruses on a historical and global scale Open

Zhenglin Zhu, Kaiwen Meng, Gexin Liu, Geng Meng · 2020

The recent outbreak of COVID-19 caused by a new zoonotic origin coronavirus (SARS-CoV-2 or 2019-nCoV) has sound the alarm for the potential spread of epidemic coronavirus crossing species. With the urgent needs to assist disease control an…

SGID: a comprehensive and interactive database of the silkworm Open

Zhenglin Zhu, Zhufen Guan, Gexin Liu, Ya-Wang Wang, Ze Zhang · 2019

Although the domestic silkworm ( Bombyx mori ) is an important model and economic animal, there is a lack of comprehensive database for this organism. Here, we developed the silkworm genome informatics database, SGID. It aims to bring toge…

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes Open

Yi Shao, Chunyan Chen, Hao Shen, Bin He, Daqi Yu , et al. · 2019

The origination of new genes contributes to phenotypic evolution in humans. Two major challenges in the study of new genes are the inference of gene ages and annotation of their protein-coding potential. To tackle these challenges, we crea…

SGID: a comprehensive and interactive database of the silkworm Open

Zhenglin Zhu, Zhufen Guan, Gexin Liu, Ya-Wang Wang, Ze Zhang · 2019

Although the domestic silkworm (Bombyx mori) is an important model and economic animal, there is a lack of comprehensive database for this organism. Here, we developed the silkworm genome informatics database (SGID). It aims to bring toget…

LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots Open

Zhenglin Zhu, Shengjun Tan, Yaqiong Zhang, Yong E. Zhang · 2016

RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons…

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