Yirong Shi
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Author Swipe
View article: Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2026
Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2026 Open
The National Genomics Data Center (NGDC), as part of the China National Center for Bioinformation (CNCB), provides a suite of database resources for worldwide researchers. As multi-omics big data and artificial intelligence reshape the par…
View article: Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP
Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP Open
Dysfunctional mitochondria are implicated in various diseases, while little is known about comprehensive characterization of mitochondrial DNA (mtDNA) in Chinese population. Here, we conducted a systematic analysis of mtDNA from 7331 sampl…
View article: TOAnnoPriDB: an integrative database for trans-omic annotation and prioritization of non-coding variants across human genome
TOAnnoPriDB: an integrative database for trans-omic annotation and prioritization of non-coding variants across human genome Open
View article: Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits
Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits Open
View article: Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population
Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population Open
Characterizing natural selection signatures and relationships with phenotype spectra is important for understanding human evolution and both biological and pathological mechanisms. Here, we identified 24 genetic loci under recent selection…
View article: Characterization of genome-wide STR variation in 6487 human genomes
Characterization of genome-wide STR variation in 6487 human genomes Open
View article: Characterizing mobile element insertions in 5675 genomes
Characterizing mobile element insertions in 5675 genomes Open
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-sca…
View article: NyuWa Genome resource: A deep whole-genome sequencing-based variation profile and reference panel for the Chinese population
NyuWa Genome resource: A deep whole-genome sequencing-based variation profile and reference panel for the Chinese population Open
View article: piRBase: integrating piRNA annotation in all aspects
piRBase: integrating piRNA annotation in all aspects Open
Piwi-interacting RNAs are a type of small noncoding RNA that have various functions. piRBase is a manually curated resource focused on assisting piRNA functional analysis. piRBase release v3.0 is committed to providing more comprehensive p…
View article: Genome-wide analysis of mobile element insertions in human genomes
Genome-wide analysis of mobile element insertions in human genomes Open
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-sca…
View article: A Novel Testing Method for Interrupt Response Time
A Novel Testing Method for Interrupt Response Time Open
Interrupt response time is an important index to measure the real-time performance of real-time operating system.Accurate test data can be the evaluation index for selecting real-time operating system.This paper proposes a test method for …
View article: NyuWa Genome Resource: Deep Whole Genome Sequencing Based Chinese Population Variation Profile and Reference Panel
NyuWa Genome Resource: Deep Whole Genome Sequencing Based Chinese Population Variation Profile and Reference Panel Open
The lack of Chinese population specific haplotype reference panel and whole genome sequencing resources has greatly hindered the genetics studies in the world’s largest population. Here we presented the NyuWa genome resource based on deep …
View article: CD4+ T Cell Count, Sleep, Depression, and Anxiety in People Living With HIV: A Growth Curve Mixture Modeling
CD4+ T Cell Count, Sleep, Depression, and Anxiety in People Living With HIV: A Growth Curve Mixture Modeling Open
We investigated changes in CD 4+ T cell counts related to sleep quality, depression, anxiety, and sociodemographic variables in heterogeneous groups of people living with HIV in a 6-month prospective study. Our longitudinal study involved …
View article: Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
This study presented an example to annotate lncRNA in new species based on model species using transcriptome data. These data and analysis provide information for duck lncRNAs' function in immune response to influenza A virus.
View article: Additional file 3: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 3: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Information of lncRNA annotated with GTF files. (GTF 1785 kb)
View article: Additional file 10: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 10: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Table S8. KEGG analysis of DEGs co-expressed with DElncRNAs. (XLSX 83 kb)
View article: Additional file 6: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 6: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Table S4. List of DEGs used in co-expression analysis. (XLSX 2055 kb)
View article: Additional file 8: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 8: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Table S6. Thirteen co-expression modules were predicted with the WGCNA package. (CSV 2346 kb)
View article: Additional file 4: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 4: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Table S2. DElncRNAs detected between duck infected with DK/49 or GS/65 H5N1 virus and control individuals. (XLSX 176 kb)
View article: Additional file 5: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 5: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Table S3. Protein-coding genes located within 10/100â kb upstream and downstream of duck lncRNAs. (XLSX 642 kb)
View article: Additional file 7: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 7: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Table S5. FPKM value of DElncRNAs and DEGs.(CSV 1273 kb)
View article: Additional file 9: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Additional file 9: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos) Open
Table S7. GO enrichment analysis of DEGs co-expressed with DElncRNAs. (XLSX 135 kb)