A5040023716- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Immune Cell Function and Interaction
- Enzyme Structure and Function
- Protein Structure and Dynamics
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- interferon and immune responses
- Molecular Biology Techniques and Applications
- Chromosomal and Genetic Variations
- T-cell and B-cell Immunology
- vaccines and immunoinformatics approaches
- Single-cell and spatial transcriptomics
- Microbial Community Ecology and Physiology
- Genetics and Neurodevelopmental Disorders
- Genomics and Chromatin Dynamics
- Influenza Virus Research Studies
- Gene expression and cancer classification
- Ionic liquids properties and applications
- Genomic variations and chromosomal abnormalities
- Genetic Neurodegenerative Diseases
- Genomics and Rare Diseases
- Polydiacetylene-based materials and applications
- Genetic Mapping and Diversity in Plants and Animals
Chinese Academy of Sciences
2014-2025
Czech Academy of Sciences, Institute of Biophysics
2024-2025
Institute of Biophysics
2014-2024
University of Chinese Academy of Sciences
2014
Chonnam National University Hospital
2009
Abstract NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 dedicated to providing the full scope lncRNAs across plants The number has increased from 548 640 644 510 since last update 2017. human 172 216 173 112. mouse 131 697 974. plant 94 697. relationship between cancer were updated with transcriptome sequencing profiles. Three important new features also introduced...
The lack of haplotype reference panels and whole-genome sequencing resources specific to the Chinese population has greatly hindered genetic studies in world's largest population. Here, we present NyuWa genome resource, based on deep (26.2×) 2,999 individuals, construct a panel 5,804 haplotypes 19.3 million variants, which is high-quality publicly available population-specific with thousands samples. Compared other panels, reduces Han imputation error rate by margin ranging from 30% 51%....
Piwi-interacting RNAs are a type of small noncoding RNA that have various functions. piRBase is manually curated resource focused on assisting piRNA functional analysis. release v3.0 committed to providing more comprehensive related information. The latest covers >181 million unique sequences, including 440 datasets from 44 species. More disease-related piRNAs and targets been collected displayed. regulatory relationships between visualized. In addition the reuse expansion content in...
Abstract Small proteins specifically refer to consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance has been revealed current years, along with the discovery their diverse functions. However, systematic annotation is still insufficient. SmProt was specially developed provide valuable information on for scientific community. Here we present update SmProt, emphasizes reliability...
Short tandem repeats (STRs) are abundant and highly mutagenic in the human genome. Many STR loci have been associated with a range of genetic disorders. However, most population-scale studies on variation humans focused European ancestry cohorts or limited by sequencing depth. Here, we depicted comprehensive map 366,013 polymorphic STRs (pSTRs) constructed from 6487 deeply sequenced genomes, comprising 3983 Chinese samples (~31.5x, NyuWa) 2504 1000 Genomes Project (~33.3x, 1KGP). We found...
Characterizing natural selection signatures and relationships with phenotype spectra is important for understanding human evolution both biological pathological mechanisms. Here, we identified 24 genetic loci under recent by analyzing rare singletons in 3946 high-depth whole-genome sequencing data of Han Chinese. The include immune-related gene regions (MHC cluster, IGH STING1, PSG), alcohol metabolism-related (ADH1B, ALDH2, ALDH3B2), the olfactory perception OR4C16, which MHC ADH1B ALDH2...
Abstract Cis-regulatory elements have an important role in human adaptation to the living environment. However, lag population genomic cohort studies and epigenomic studies, hinders research adaptive analysis of cis-regulatory populations. In this study, we collected 4,013 unrelated individuals performed a comprehensive selection genome-wide Han Chinese. total, 12.34% regions are under influence selection, where 1.00% enhancers 2.06% promoters positive 0.06% 0.02% balancing selection. Gene...
Abstract Human leukocyte antigen (HLA) genes play a crucial role in the adaptation of human populations to dynamic pathogenic environment. Despite their significance, investigating pathogen-driven evolution HLAs and implications for autoimmune diseases presents considerable challenges. Here, we genotyped over twenty HLA at 3-field resolution 8278 individuals from diverse ethnic backgrounds, including 4013 unrelated Han Chinese. We focused on Chinese by analyzing binding affinity various...
Influenza virus can rapidly change its antigenicity, via mutation in the hemagglutinin (HA) protein, to evade host immunity. The emergence of novel human-infecting avian H7N9 China has caused widespread concern. However, evolution antigenicity this is not well understood. Here, we inferred antigenic epitopes HA protein from all H7 viruses, based on five well-characterized human H3N2 virus. By comparing two major phylogenetic lineages, i.e., Eurasian lineage and North American lineage, found...
Many template-based modeling (TBM) methods have been developed over the recent years that allow for protein structure prediction and study of structure-function relationships proteins. One major problem all TBM algorithms face, however, is their unsatisfactory performance when proteins under consideration are low-homology. To improve such targets, a novel model evaluation method was here, named MEFTop. Our focuses on evaluating topology by using two groups features. These features included...
Abstract The lack of Chinese population specific haplotype reference panel and whole genome sequencing resources has greatly hindered the genetics studies in world’s largest population. Here we presented NyuWa resource based on deep (26.2X) 2,999 individuals, constructed 5,804 haplotypes 19.3M variants, which is first publicly available with thousands samples. Compared other panels, reduces Han imputation error rate by range 30% to 51%. Population structure simulation tests supported...
Abstract Small proteins specifically refer to consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance has been revealed current years, along with the discovery their diverse functions. However, systematic annotation is still insufficient. SmProt was specially developed provide valuable information on for scientific community. Here we present update SmProt, emphasizes reliability...
The brain is the central hub of entire nervous system. Its development a lifelong process guided by genetic blueprint. Understanding how genes influence critical for deciphering formation human cognitive functions and underlying mechanisms neurological disorders. Recent advances in multi-omics techniques have now made it possible to explore these aspects comprehensively. However, integrating analyzing extensive data presents significant challenges. Here, we introduced MAPbrain...
Human leukocyte antigen (HLA) genes play a crucial role in the adaptation of human populations to dynamic pathogenic environment. Despite their significance, investigating pathogen-driven evolution HLAs and implications for autoimmune diseases presents considerable challenges. Here, we genotyped over twenty HLA at 3-field resolution 8278 individuals from diverse ethnic backgrounds, including 4013 unrelated Han Chinese. We focused on Chinese by analysing binding affinity various pathogens,...
Variable number tandem repeat (VNTR) is a pervasive and highly mutable genetic feature that varies in both length sequence. Despite the well-studied copy-number variants, functional impacts of motif polymorphisms remain unknown. Here, we present largest genome-wide VNTR polymorphism map to date, with over 2.5 million (VNTR-LPs) 11 (VNTR-MPs) detected 8,222 high-coverage genomes. Leveraging large-scale NyuWa cohort, identified 2,982,456 (31.8%) NyuWa-specific VNTR-MPs, which 95.3% were rare....
Motivation: Protein domains are fundamental units of protein structure, function and evolution; thus, it is critical to gain a deep understanding domain organization. Previous works have attempted identify key residues involved in organization architecture. Because one the most important characteristics architecture arrangement secondary structure elements (SSEs), here we present picture through an integrated consideration SSE arrangements residue contact networks. Results: In this work, by...
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may allow more definitive diagnosis of holoprosencephaly, and the outcome affected fetuses often have other major structural abnormalities nearly always fatal.