A5013319494- Genomics and Phylogenetic Studies
- Acoustic Wave Phenomena Research
- Speech and Audio Processing
- Cancer-related molecular mechanisms research
- Advanced Adaptive Filtering Techniques
- Aquaculture disease management and microbiota
- Circular RNAs in diseases
- MicroRNA in disease regulation
- Invertebrate Immune Response Mechanisms
- Single-cell and spatial transcriptomics
- Fish Biology and Ecology Studies
- Identification and Quantification in Food
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- Gut microbiota and health
- Blind Source Separation Techniques
- Genetic diversity and population structure
- Polyamine Metabolism and Applications
- Animal Genetics and Reproduction
- Molecular Biology Techniques and Applications
- Flow Measurement and Analysis
- Aerodynamics and Acoustics in Jet Flows
- Physiological and biochemical adaptations
- interferon and immune responses
- Microbial Community Ecology and Physiology
Institute of Acoustics
2008-2025
Chinese Academy of Sciences
2016-2025
Institute of Zoology
2024-2025
University of Chinese Academy of Sciences
2021-2025
Beijing Institute of Genomics
2015-2024
Chinese Academy of Fishery Sciences
2011-2016
Jimei University
2008-2011
Xiaowen Sun and colleagues report the whole-genome sequencing of common carp, Cyprinus carpio. They also resequenced 33 representative accessions from a worldwide collection provide insights into population structure evolution. The carpio, is one most important cyprinid species globally accounts for 10% freshwater aquaculture production. Here we present draft genome domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes approximately 92.3%...
Objective The initial colonisation of the human microbiota and impact maternal health on neonatal at birth remain largely unknown. aim our study is to investigate possible dysbiosis associated with gestational diabetes mellitus (GDM) estimate potential risks microbial shift neonates. Design Pregnant women neonates suffering from GDM were enrolled 581 (oral, intestinal vaginal) 248 pharyngeal, meconium amniotic fluid) samples collected. To avoid vaginal bacteria contaminations, included...
Abstract Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable mining in-depth information candidate circRNA prioritization. To address this, we integrate transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected from 19 normal tissues across six vertebrate species. This contains 1,007,087 highly reliable circRNAs, of which over 81.3% been assembled into full-length sequences. We profile their...
Abstract Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome Saccharina japonica , one most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98.5% estimated genome, 18,733 protein-coding genes predicted annotated. Gene families related to cell wall synthesis, halogen concentration, development defence systems were expanded. Functional diversification mannuronan C-5-epimerase...
Circular RNAs (circRNAs) are emerging as essential regulators of various biological and disease processes. To comprehensively understand the diversity circRNAs prioritize their importance, we present a large-scale study circRNA repertoires from multiple tissues human, macaque, mouse. We discovered totals 104,388, 96,675, 82,321 three species, respectively, with an average 72.6% being successfully assembled into full-length transcripts for each species. Using these circRNAs, identified...
Currently, circRNA studies are shifting from the identification of circular transcripts to understanding their biological functions. However, such endeavors have been limited by large-scale determination full-length sequences and also inability accurate quantification at isoform level. Here, we propose a new feature, reverse overlap (RO), for detection, which outperforms back-splice junction (BSJ)-based methods in identifying low-abundance circRNAs. By combining RO BSJ features, present...
Despite recent advances in imaging- and antibody-based methods, achieving in-depth, high-resolution protein mapping across entire tissues remains a significant challenge spatial proteomics. Here, we present parallel-flow projection transfer learning omics data (PLATO), an integrated framework combining microfluidics with deep to enable of thousands proteins whole tissue sections. We validated the PLATO by profiling proteome mouse cerebellum, identifying 2,564 groups single run. then applied...
Emerging research underscores the gut microbiome's impact on nervous system via microbiota-gut-brain axis, yet comprehensive insights remain limited. Using a CHD8-haploinsufficient model for autism spectrum disorder (ASD), we explored host-gut microbiota interactions by constructing single-cell transcriptome atlas of brain and intestinal tissues in wild-type mutant mice across three developmental stages. CHD8 haploinsufficiency caused delayed development radial glial precursors excitatory...
Background Common carp (Cyprinus carpio) is one of the most important aquaculture species Cyprinidae with an annual global production 3.4 million tons, accounting for nearly 14% freshwater in world. Due to economical and ecological importance common carp, genomic data are eagerly needed genetic improvement purpose. However, there still no sufficient transcriptome available. The objective project sequence deeply provide well-assembled sequences research community. Result Transcriptome...
Autism spectrum disorder (ASD), a group of neurodevelopmental disorders characterized by social communication deficits and stereotyped behaviors, may be associated with changes to the gut microbiota. However, how commensal bacteria modulate brain function in ASD remains unclear. Here, we used chromodomain helicase DNA-binding protein 8 (CHD8) haploinsufficient mice as model elucidate pathways through which host microbiota interact each other. We found that increased levels amino acid...
Parametric array loudspeakers (PALs) produce highly directional sounds due to the parametric process in air. Its application creating personal audio zones requires simple modeling of audible sound field near PAL, which is crucial for subsequent designs reduce inherent nonlinear distortion. However, current accurate methods describing field, reliant on numerical solutions wave equations, are computationally intensive. To achieve both effectiveness and simplicity, this paper proposes a...
The Amur ide (Leuciscus waleckii) is a cyprinid fish that widely distributed in Northeast Asia. Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50 mmol/L (pH 9.6), thus providing exceptional model which characterize mechanisms genomic evolution underlying adaptation environments. Here, we developed reference genome assembly for L. waleckii from Nur. Intriguingly, identified unusual expanded long terminal repeats (LTRs) higher...
Background Single nucleotide polymorphisms (SNPs) have been used as genetic marker for genome-wide association studies in many species. Gene-associated SNPs could offer sufficient coverage trait related research and further more themselves be causative traits. Common carp (Cyprinus carpio) is one of the most important aquaculture species world accounting nearly 14% freshwater production. There are various strains common with different economic traits, however, mechanism underlying traits not...
Background Amur ide (Leuciscus waleckii) is an economically and ecologically important species in Northern Asia. The Dali Nor population inhabiting Lake, a typical saline-alkaline lake Inner Mongolia, well-known for its adaptation to extremely high alkalinity. Genome information needed conservation aquaculture purposes, as well gain further understanding into the genetics of stress tolerance. objective study sequence transcriptome obtain well-assembled ide. Results was sequenced using...
Abstract Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of databases and de novo metagenome assembly from complex remains a great challenge. Here we present novel experimental bioinformatic framework, metaSort, for effective construction bacterial genomes samples. MetaSort provides sorted mini-metagenome approach based flow cytometry single-cell sequencing methodologies, employs new computational...
Small extracellular vesicles (sEVs) are emerging as pivotal players in a wide range of physiological and pathological processes. However, pressing challenge has been the lack high-throughput techniques capable unraveling intricate heterogeneity sEVs decoding underlying cellular behaviors governing sEV secretion. Here we leverage droplet-based single-cell RNA sequencing (scRNA-seq) introduce an algorithm, SEVtras, to identify sEV-containing droplets estimate secretion activity (ESAI)...
Recently, a multiband-structured subband adaptive filter (MSAF) algorithm was proposed to speed up the convergence of normalized least-mean-square (NLMS) algorithm. In this letter, we extend work and propose an improved (IMSAF) increase MSAF, which can also be regarded as unifying framework for NLMS, affine projection (AP) algorithms. The optimization criterion is based on principle minimal disturbance, canceling most recent <i xmlns:mml="http://www.w3.org/1998/Math/MathML"...