A5014554768- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Insect Resistance and Genetics
- RNA Research and Splicing
- Medical Image Segmentation Techniques
- Genomics and Rare Diseases
- Entomopathogenic Microorganisms in Pest Control
- Immune Cell Function and Interaction
- Genomics and Chromatin Dynamics
- Cancer-related gene regulation
- Epigenetics and DNA Methylation
- Forest Insect Ecology and Management
- Machine Learning in Bioinformatics
- T-cell and B-cell Immunology
- Image and Video Stabilization
- Circular RNAs in diseases
- vaccines and immunoinformatics approaches
- Polysaccharides and Plant Cell Walls
- interferon and immune responses
- MicroRNA in disease regulation
- Chromosomal and Genetic Variations
- Genetic Neurodegenerative Diseases
Institute of Biophysics
2017-2024
Chinese Academy of Sciences
2017-2024
University of Chinese Academy of Sciences
2017-2024
Anhui University
2024
Czech Academy of Sciences, Institute of Biophysics
2017-2020
NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long (lncRNAs). Since 2016 was released two years ago, amount novel identified ncRNAs has been enlarged by reduced cost next-generation sequencing, which produced an explosion newly data. The third-generation sequencing revolution also offered longer more accurate annotations. Moreover, accumulating evidence...
Small proteins is the general term for with length shorter than 100 amino acids. Identification and functional studies of small have advanced rapidly in recent years, several shown that play important roles diverse functions including development, muscle contraction DNA repair. characterization previously unrecognized may contribute ways to cell biology human health. Current databases are generally somewhat deficient they either not collected systematically, or contain only predictions a...
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%....
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...
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, various cancers. However, MEI resources from large-scale genome sequencing still lacking compared those for SNPs SVs. Here, we report comprehensive map 36 699 non-reference MEIs constructed 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) 2677 the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that...
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 Background Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related host plant specialization, reproductive isolation, ecological speciation. To further evolutionary studies in this interesting group, here we present draft genome of representative specialist, viridicyanea , the first Alticinae reported thus far. Results The 864.8 Mb consists 4490 scaffolds with N50 size 557 kb, which...
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 Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, various cancers. However, MEI resources from large-scale genome sequencing still lacking compared those for SNPs SVs. Here, we report comprehensive map 36,699 non-reference MEIs constructed 5,675 genomes, comprising 2,998 Chinese samples (∼26.2X, NyuWa) 2,677 the 1000 Genomes Project (∼7.4X, 1KGP). We...
Abstract Lycium barbarum, a member of the Solanaceae family, represents an important eudicot lineage with homology food and medicine. barbarum pectin polysaccharides (LBPPs) are key bioactive ingredients among few both biocompatibility biomedical activity. While previous studies have primarily focused on functional properties LBPPs, mechanisms biosynthesis transport by enzymes remain poorly understood. Here, we reported completion 2.18-gigabase reference genome reconstructed first entire...
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....
Abstract Background Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used as model system in which to address questions related host plant specialization, reproductive isolation, ecological speciation. To further evolutionary studies this important group, here we present high-quality draft genome of representative specialist, viridicyanea , the first Alticinae fourth chrysomelid reported thus far. Results The 864.8 Mb...
Biological processes, especially developmental are often dynamic. Previous BodyMap projects for human and mouse have provided researchers with portals to tissue-specific gene expression, but these efforts not included dynamic expression patterns. Over the past few years, substantial progress in our understanding of molecular mechanisms protein-coding long noncoding RNA (lncRNA) genes development processes has been achieved through numerous time series sequencing (RNA-seq) studies. However,...
Abstract Whole genome sequencing technology has facilitated the discovery of a large number somatic mutations in enhancers (SMEs), whereas utility SMEs tumorigenesis not been fully explored. Here we present Ennet, method to comprehensively investigate enriched networks (SME-networks) cancer by integrating SMEs, enhancer-gene interactions and gene-gene interactions. Using performed pan-cancer analysis 2004 samples from 8 types found many well-known drivers were involved SME-networks,...
Abstract Background: Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related host plant specialization, reproductive isolation, ecological speciation. To further evolutionary studies in this interesting group, here we present draft genome of representative specialist, viridicyanea , the first Alticinae fifth chrysomelid reported thus far. Results: The 864.8 Mb consists 4,490 scaffolds with N50 size...