Xiuqing Zhang
A5101566986- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Prenatal Screening and Diagnostics
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Cancer-related gene regulation
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
- Molecular Biology Techniques and Applications
- Fetal and Pediatric Neurological Disorders
- Ferroptosis and cancer prognosis
- Gene expression and cancer classification
- Advanced biosensing and bioanalysis techniques
- Immune Cell Function and Interaction
- Reproductive Biology and Fertility
- Polysaccharides and Plant Cell Walls
- Plant Molecular Biology Research
- Protein Degradation and Inhibitors
Shandong University
2011-2025
BGI Group (China)
2015-2024
University of Chinese Academy of Sciences
2018-2024
China Agricultural University
2012-2024
Guangzhou Institutes of Biomedicine and Health
2024
Chinese Academy of Sciences
2002-2024
BGI Research
2023-2024
China National GeneBank
2017-2022
Zhejiang Cancer Hospital
2021-2022
Fourth People's Hospital of Liaocheng
2008-2022
Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, highly scalable acceleration. In this article, we demonstrate SOAPnuke as tool abundant functions "QC-Preprocess-QC" workflow MapReduce acceleration framework. Four modules different designed processing datasets from genomic, small RNA, Digital Gene...
No Genetic Vertigo Peoples living in high altitudes have adapted to their situation (see the Perspective by Storz ). To identify gene regions that might contributed high-altitude adaptation Tibetans, Simonson et al. (p. 72 , published online 13 May) conducted a genome scan of nucleotide polymorphism comparing Han Chinese, and Japanese, while Yi 75 ) performed comparable analyses on coding all genes—their exomes. Both studies converged gene, endothelial Per-Arnt-Sim domain protein 1 (also...
Here we present the first diploid genome sequence of an Asian individual. The was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned short reads onto NCBI human reference 99.97% coverage, and guided by genome, used uniquely mapped assemble a high-quality consensus for 92% individual’s genome. identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, which 13.6% were not in dbSNP database. Genotyping analysis...
We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, represents a male individual first known culture to settle in Greenland. Sequenced average depth 20×, we recover 79% diploid genome, amount close practical limit current sequencing technologies. identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), which 6.8% have not been reported previously. estimate raw read contamination be no higher than 0.8%. use...
High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental populations and present an approach for combining complementary aspects whole-genome, low-coverage data targeted high-coverage data. We apply this to generated by pilot phase Thousand Genomes Project, including whole-genome 2–4× coverage 179 samples from HapMap European, Asian, African panels as well target exons 800...
Abstract We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes vitro DNA fragmentation adaptor incorporation simultaneously. apply this to sequencing human genome find that coverage biases are comparable those of conventional protocols. also its capabilities by developing protocols sub-nanogram library construction, exome capture from 50 ng input DNA, PCR-free colony PCR 96-plex sample indexing.
WEGO (Web Gene Ontology Annotation Plot), created in 2006, is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. Owing largely to the rapid development of high-throughput sequencing increasing acceptance GO, has benefitted from outstanding performance regarding number users citations recent years, which motivated us update version 2.0. uses results as input. Based on GO's standardized DAG (Directed Acyclic Graph) structured vocabulary...
Understanding the dynamics of eukaryotic transcriptome is essential for studying complexity transcriptional regulation and its impact on phenotype. However, comprehensive studies transcriptomes at single base resolution are rare, even modern organisms, lacking rice. Here, we present first atlas eight organs cultivated Using high-throughput paired-end RNA-seq, unambiguously detected transcripts expressing an extremely low level, as well a substantial number novel transcripts, exons,...
DNA methylation plays an important role in biological processes human health and disease. Recent technological advances allow unbiased whole-genome (methylome) analysis to be carried out on cells. Using bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome of the unique sequences peripheral blood mononuclear cells (PBMC) from same Asian individual whose genome was deciphered YH project. PBMC constitute source for clinical tests...
Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and fourth lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little mutational processes responsible. To identify genome-wide signatures, performed either whole-genome sequencing (WGS) or whole-exome (WES) on 104 ESCC individuals combined our data those 88 previously reported samples. An APOBEC-mediated signature 47% 192 tumors suggests...
The cynomolgus and Chinese rhesus macaques are used as animal models in biomedical research. Yan et al. sequence their genomes compare the sequences to that of Indian macaque, providing a genetic foundation for interpreting research results. nonhuman primates most commonly medical from genus Macaca1. To better understand differences between these models, we present high-quality draft genome two macaque species, cynomolgus/crab-eating macaque. Comparison with previously sequenced reveals all...
Massively parallel sequencing of DNA molecules in the plasma pregnant women has been shown to allow accurate and noninvasive prenatal detection fetal trisomy 21. However, whether approach is as for diagnosis 13 18 unclear due lack data from a large sample set. We studied 392 pregnancies, among which 25 involved fetus 37 fetus, by massively sequencing. By using our previously reported standard z-score approach, we demonstrated that this could identify 36.0% 73.0% at specificities 92.4% 97.2%,...
Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with discovery of molecular signatures stress, some which include alterations an individual's somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between stress-related disease, major depression, and amount mtDNA (p = 9.00 × 10(-42), odds ratio 1.33 [95% confidence interval [CI] 1.29-1.37]) telomere length 2.84 10(-14), 0.85 CI...
To report the performance of massively parallel sequencing (MPS) based prenatal noninvasive fetal trisomy test on cell-free DNA from maternal plasma in a routine clinical setting China.The MPS-based was offered as screening for trisomies 21 and 18 to pregnant women 49 medical centers over 2 years. A total 11,263 participants were recruited performed 11,105 pregnancies. Fetal outcome data obtained after expected date confinement.One hundred ninety cases classified positive, including 143 47...
Biological age (BA) has been proposed to evaluate the aging status instead of chronological (CA). Our study shows evidence that there might be multiple "clocks" within whole-body system: systemic drivers/clocks overlaid with organ/tissue-specific counterparts. We utilize multi-omics data, including clinical tests, immune repertoire, targeted metabolomic molecules, gut microbiomes, physical fitness examinations, and facial skin estimate BA different organs (e.g., liver, kidney) systems...
Abstract The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation for 10,592 SpCas9 gRNAs. Integrating these with complementary published data, train a deep learning model, CRISPRon, 23,902 Compared to existing tools, CRISPRon exhibits significantly higher prediction performances four test datasets not overlapping training used development tools....