A5045423389- Forensic and Genetic Research
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- Genetic diversity and population structure
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Forensic Anthropology and Bioarchaeology Studies
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Archaeology and ancient environmental studies
- Epigenetics and DNA Methylation
- Forest Insect Ecology and Management
- Genetic Mapping and Diversity in Plants and Animals
- Pleistocene-Era Hominins and Archaeology
- Quantum Dots Synthesis And Properties
- melanin and skin pigmentation
- CRISPR and Genetic Engineering
- Insect Pest Control Strategies
- Entomopathogenic Microorganisms in Pest Control
- Genomic variations and chromosomal abnormalities
- Molecular Biology Techniques and Applications
- Chalcogenide Semiconductor Thin Films
- Linguistics and Cultural Studies
- Rangeland Management and Livestock Ecology
- Paleopathology and ancient diseases
Shanghai Institute of Nutrition and Health
2019-2025
University of Chinese Academy of Sciences
2019-2025
University of Science and Technology of China
2023-2024
Shanghai Institutes for Biological Sciences
2019-2024
Chinese Academy of Sciences
2019-2024
The First Affiliated Hospital, Sun Yat-sen University
2024
Sun Yat-sen University
2024
Space Engineering University
2024
Experimental Center of Forestry in North China
2022
Anhui Polytechnic University
2015
Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to pangenome form, but populations of Asian ancestry are underrepresented. Here we present data the first phase Chinese Pangenome Consortium, including collection 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority ethnic groups. With average 30.65× high-fidelity long-read coverage, contiguity N50 more than 35.63 megabases total size 3.01 gigabases,...
Abstract As the largest ethnic group in world, Han Chinese population is nonetheless underrepresented global efforts to catalogue genomic variability of natural populations. Here, we developed PGG.Han, a genome database serve as central repository for data Genome Initiative (Phase I). In its current version, PGG.Han archives whole-genome sequences or high-density genome-wide single-nucleotide variants (SNVs) 114 783 individuals (a.k.a. Han100K), representing geographical sub-populations...
Population admixture results in genome-wide combinations of genetic variants derived from different ancestral populations distinct ancestry, thus providing a unique opportunity for understanding the determinants phenotypic variation humans. Here, we used whole-genome sequencing 92 individuals with high coverage (30-60×) to systematically investigate genomic diversity Uyghurs living Xinjiang, China (XJU), an admixed population both European-like and East-Asian-like ancestry. The XJU shows...
Abstract Human genetic adaptation to high altitudes (>2500 m) has been extensively studied over the last few years, but functional adaptive variants have identified, largely owing lack of deep-genome sequencing data available previous studies. Here, we build a list putative variants, including 63 missense, 7 loss-of-function, 1,298 evolutionarily conserved and 509 expression quantitative traits loci. Notably, top signal selection is located in TMEM247, transmembrane protein-coding...
Abstract It remains unknown and debatable how European-Asian–differentiated alleles affect individual phenotypes. Here, we made the first effort to analyze expression profiles of highly differentiated genes with eastern western origins in 90 Uyghurs using whole-genome (30× 60×) transcriptome data. We screened 921 872 east–west genetic variants, which ∼4.32% were quantitative trait loci (eQTLs), ∼0.12% alternative splicing (sQTLs), showed allele-specific (ASE). The 8305 eQTLs strong effects...
Automatic mitochondrial segmentation enjoys great popularity with the development of deep learning. However, coarse prediction raised by presence regular 3D grids in previous methods regardless CNN or vision transformers suggest a possibly sub-optimal feature arrangement. To mitigate this limitation, we attempt to interpret EM image stacks as set interrelated fragments for better solution. it is non-trivial model without introducing excessive computational overhead. In paper, design coherent...
Abstract We developed a method, ArchaicSeeker 2.0 , to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us discern two waves of introgression from both Denisovan-like Neanderthal-like hominins in present-day Eurasian populations an ancient Siberian individual. estimated that early occurred Eurasia around 118.8–94.0 thousand years ago (kya). In contrast, we detected only one single episode admixture indigenous peoples eastern the Wallace-Line....
The Angiotensin-Converting Enzyme-2 (ACE2) gene, located on Xp22.2, attracts a great deal of attention because the protein it encodes is believed to be functional cellular receptor for new coronavirus (SARS-CoV-2). However, recent studies are controversial, especially concerning intrinsic link between ACE2 diversity and COVID-19 susceptibility. Here, we conduct population genetic study in 6354 individuals representing 210 present-day populations 5329 ancient or archaic groups. We dissected...
Abstract Population admixture results in the combinations of genetic components derived from distinct ancestral populations, which may impact diversity at genetic, transcriptomic, and phenotypic levels, as well postadmixture adaptive evolution. Here, we systematically investigated genomic transcriptomic Kazaks, Uyghurs, Huis—three admixed populations various Eurasian ancestries living Xinjiang, China. All three showed elevated closer distance compared with reference across continent....
Abstract Despite the tremendous growth of DNA sequencing data in last decade, our understanding human genome is still its infancy. To understand implications genetic variants light population genetics and molecular evolution, we developed a database, PGG .SNV ( https://www.pggsnv.org ), which gives much higher weight to previously under-investigated indigenous populations Asia. archives 265 million SNVs across 220,147 present-day genomes 1018 ancient genomes, including 1009 newly sequenced...
Abstract The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han (HAN) but practice Islam. However, second-largest minority group China numbering well over 10 million, Huis under-represented both global and regional genomic studies. Here, we present first whole-genome sequencing effort of 234 individuals (NXH) aged 60 who have been living Ningxia, where mostly concentrated. NXH genetically more similar to East Asian than any other populations. In...
Mitochondria, as tiny structures within the cell, are of significant importance in studying cell functions for biological and clinical analysis. And exploring how to automatically segment mitochondria electron microscopy (EM) images has attracted increasing attention. However, most existing methods struggle adapt different scales appearances input due inherent limitations traditional CNN architecture. To mitigate these limitations, we propose a novel adaptive template transformer (ATFormer)...
Abstract The LopNur people are an ethnic group living on the edge of Taklamakan Desert, and they believed to demonstrate a unique genetic makeup due their isolation limited contact with neighboring populations. However, lack studies has resulted in knowledge about ancestral origins demographic history. Here, we conducted first whole-genome sequencing study 164 individuals (LOP) gain insight into history adaptive evolution isolated desert area. Our analysis revealed that present-day LOP have...
Kazakh people, like many other populations that settled in Central Asia, demonstrate an array of mixed anthropological features East Eurasian (EEA) and West (WEA) populations, indicating a possible scenario biological admixture between already differentiated EEA WEA populations. However, their complex origin, genomic makeup, genetic interaction with surrounding are not well understood. To decipher structure population history, we conducted, to our knowledge, the first whole-genome sequencing...
Cervical cancer (CCa) patients with lymph node (LN) metastasis face poor prognoses and have limited treatment options. Aberrant N6-methyladenosine (m
WEE1 has emerged as an attractive target in epithelial ovarian cancer (EOC), but how EOC cells may alter their sensitivity to inhibition remains unclear. Here, through a cell cycle machinery-related gene RNAi screen, we found that targeting outer dense fiber of sperm tails 2-like (ODF2L) was synthetic lethal partner with kinase cells. Knockdown ODF2L robustly sensitized treatment the inhibitor AZD1775 lines vitro well xenografts vivo. Mechanistically, increased upon loss accompanied by...
Abstract The tiger shrimp ( Penaeus monodon ) is an important marine crustacean in terms of biological diversity and aquaculture resource. widespread across the Indo‐Pacific region shows apparent genetic differentiation among geographical populations. It common practice to transport female brooders between different countries seed farms, posing potential problems unwanted population admixture. We developed 23 polymorphic microsatellites for P. (average H E = 0.936) these were applicable...
Streptococcus sanguis comprises a heterogeneous group of oral streptococci indigenous to the cavity humans. A total 289 isolates from an infant population ( n =37) were tentatively identified as S. on basis distinctive colony morphology shown MM10‐sucrose non‐selective medium. These divided into four biovars determined by extended panel biochemical attributes. Chromosomal DNA was extracted each isolate, and AP‐PCR fingerprint profile obtained allow study diversity within among infants. In...
Abstract Sex-biased gene expression differs across human populations; however, the underlying genetic basis and molecular mechanisms remain largely unknown. Here, we explore influence of ancestry on sex differences in transcriptome its effects a Eurasian admixed population: Uyghurs living Xinjiang (XJU), by analyzing whole-genome sequencing data 90 XJU 40 unrelated Han Chinese individuals. We identified 302 sex-biased expressed genes 174 cis-expression quantitative loci (sb-cis-eQTLs) XJU,...
Abstract The earlier version of AncestryPainter is a Perl program that displays the ancestry composition numerous individuals using rounded graph. Motivated by requests users in practical applications, we updated to 2.0 coding an R package and improving layout, providing more options compatible statistical functions for graphing. Apart from visualization per se this update, added extra graphing module visualize genetic distance through radial bars varying lengths surrounding core. Notably,...
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the distinction connection of broad geographical TIAs. Despite diverse makeup large interarea differentiation between TIA groups, we identified basal Asian ancestry (bASN) specifically shared by these populations. The bASN was relatively enriched ancient human genomes dated as early...
Abstract Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to pangenome form but populations of Asian ancestry are underrepresented. Here, we present the first effort (Phase I) Chinese Pangenome Consortium (CPC) with collection 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority ethnic groups. With > 30.65× High-Fidelity long-reads coverage, average contiguity N50 35.63 Mb, total size 3.01 Gb, CPC...