Rujiao Li
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View article: Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications
Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications Open
Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems, including the constituent elements within and among species. Through various efforts in genomic data archiving, integrative analysis a…
View article: Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024 Open
The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulatio…
View article: PPGR: a comprehensive perennial plant genomes and regulation database
PPGR: a comprehensive perennial plant genomes and regulation database Open
Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive r…
View article: MethBank 4.0: an updated database of DNA methylation across a variety of species
MethBank 4.0: an updated database of DNA methylation across a variety of species Open
DNA methylation, as the most intensively studied epigenetic mark, regulates gene expression in numerous biological processes including development, aging, and disease. With the rapid accumulation of whole-genome bisulfite sequencing data, …
View article: ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers
ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers Open
Alternative splicing (AS) is a fundamental process that governs almost all aspects of cellular functions, and dysregulation in this process has been implicated in tumor initiation, progression and treatment resistance. With accumulating st…
View article: Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution
Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution Open
Single-cell transcriptome studies have revealed immune dysfunction in COVID-19 patients, including lymphopenia, T cell exhaustion, and increased levels of pro-inflammatory cytokines, while DNA methylation plays an important role in the reg…
View article: GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip
GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip Open
The Illumina HumanMethylation BeadChip is one of the most cost-effective methods to quantify DNA methylation levels at single-base resolution across the human genome, which makes it a routine platform for epigenome-wide association studies…
View article: EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study Open
Epigenome-Wide Association Study (EWAS) has become a standard strategy to discover DNA methylation variation of different phenotypes. Since 2018, we have developed EWAS Atlas and EWAS Data Hub to integrate a growing volume of EWAS knowledg…
View article: scMethBank: a database for single-cell whole genome DNA methylation maps
scMethBank: a database for single-cell whole genome DNA methylation maps Open
Single-cell bisulfite sequencing methods are widely used to assess epigenomic heterogeneity in cell states. Over the past few years, large amounts of data have been generated and facilitated deeper understanding of the epigenetic regulatio…
View article: The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR
The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR Open
On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nC…
View article: The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR
The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR Open
On 22 January 2020, the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), created the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access SARS-CoV-2 information resource. 2019nCoVR f…
View article: EWAS Data Hub: a resource of DNA methylation array data and metadata
EWAS Data Hub: a resource of DNA methylation array data and metadata Open
Epigenome-Wide Association Study (EWAS) has become an effective strategy to explore epigenetic basis of complex traits. Over the past decade, a large amount of epigenetic data, especially those sourced from DNA methylation array, has been …
View article: EWAS Atlas: a curated knowledgebase of epigenome-wide association studies
EWAS Atlas: a curated knowledgebase of epigenome-wide association studies Open
This FAIRsharing record describes: The Epigenome-Wide Association Study Atlas (EWAS) Atlas is a curated knowledgebase of EWAS data. EWAS Atlas focuses on DNA methylation and provides a trait enrichment analysis tool, which is capable of pr…
View article: NucMap: a database of genome-wide nucleosome positioning map across species
NucMap: a database of genome-wide nucleosome positioning map across species Open
This FAIRsharing record describes: NucMap is a database of genome-wide nucleosome positioning across multiple species. Based on raw sequence data from published studies, NucMap integrates, analyzes, and visualizes nucleosome positioning da…
View article: MethBank 3.0: a database of DNA methylomes across a variety of species
MethBank 3.0: a database of DNA methylomes across a variety of species Open
This FAIRsharing record describes: MethBank stores DNA methylome data across a variety of species. MethBank integrates consensus reference methylomes (CRMs) compiled from healthy human samples at different ages, single-base resolution meth…
View article: MarR-Family Transcription Factor HpaR Controls Expression of the <i>vgrR</i>-<i>vgrS</i> Operon of <i>Xanthomonas campestris</i> pv. <i>campestris</i>
MarR-Family Transcription Factor HpaR Controls Expression of the <i>vgrR</i>-<i>vgrS</i> Operon of <i>Xanthomonas campestris</i> pv. <i>campestris</i> Open
MarR (multiple antibiotic resistance regulator)-family transcription factors (TFs), which regulate the expression of virulence factors and other physiological pathways in pathogenic bacteria, are regarded as ideal molecular targets for the…
View article: Database Resources of the BIG Data Center in 2018
Database Resources of the BIG Data Center in 2018 Open
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the …
View article: An Essential Regulatory System Originating from Polygenic Transcriptional Rewiring of PhoP-PhoQ of <i>Xanthomonas campestris</i>
An Essential Regulatory System Originating from Polygenic Transcriptional Rewiring of PhoP-PhoQ of <i>Xanthomonas campestris</i> Open
How essential, regulatory genes originate and evolve is intriguing because mutations of these genes not only lead to lethality in organisms, but also have pleiotropic effects since they control the expression of multiple downstream genes. …
View article: Additional file 5: of Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells
Additional file 5: of Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells Open
Differently expressed target genes between CVA16-infected and CVA16-non-infected cell samples. (XLS 403 kb)
View article: Additional file 2: of Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells
Additional file 2: of Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells Open
Differently expressed genes between CVA16-infected and CVA16-non-infected cell samples. (XLS 584 kb)
View article: Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells
Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells Open
The present study elucidated the changes in 293T cells upon CVA16 infection at transcriptome level, containing highly up-regulated SCARB2 and genes in ECM-receptor interaction and circadian rhythm pathways, and key miRNAs in gene expressio…
View article: Additional file 4: of Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells
Additional file 4: of Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells Open
Differently expressed miRNA between CVA16-infected and CVA16-non-infected cell samples. (XLS 38 kb)
View article: BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data
BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data Open
Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective ex…
View article: Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq
Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq Open
This study establishes a single-base resolution DNA methylation profile of chicken lung and suggests a regulatory role of DNA methylation in controlling gene expression and maintaining genome transcription stability. Furthermore, profiling…
View article: Additional file 10: of Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq
Additional file 10: of Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq Open
Expression levels of DMR-associated genes from RNA-seq data. (XLSX 161 kb)
View article: Additional file 11: of Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq
Additional file 11: of Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq Open
DMR-associated genes that show more than two-fold expression differences between Fayoumi and Leghorn. (XLSX 33 kb)