Xiuqing Zhang

Summary

Affiliation: Chinese Academy of Sciences
Country: China

Publications

  1. pmc Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
    Ying Hui Li
    Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement NFCRI Key Lab of Germplasm Utilization MOA, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
    BMC Genomics 14:579. 2013
  2. pmc A systematic analysis on DNA methylation and the expression of both mRNA and microRNA in bladder cancer
    Jialou Zhu
    Beijing Genomics Institute at Shenzhen, Shenzhen, China
    PLoS ONE 6:e28223. 2011
  3. pmc Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma
    Liang Zhou
    The Key Laboratory of Stem Cell Biology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU HKUST Medical Center, Shenzhen, China
    PLoS ONE 5:e15224. 2010
  4. pmc Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events
    Xianxin Li
    Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
    PLoS ONE 6:e22570. 2011
  5. pmc The DNA methylome of human peripheral blood mononuclear cells
    Yingrui Li
    BGI Shenzhen, Shenzhen, Guangdong, China
    PLoS Biol 8:e1000533. 2010
  6. pmc Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing
    Shan Dan
    Department of Perinatal Medicine, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Beijing, China
    PLoS ONE 7:e27835. 2012
  7. pmc Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies
    Fuman Jiang
    BGI Shenzhen, Shenzhen, China
    BMC Med Genomics 5:57. 2012
  8. pmc Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
    Qi Zhou
    CAS Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
    BMC Genomics 13:109. 2012
  9. pmc Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method
    Ye Du
    BGI_shenzhen, Shenzhen 518000, China
    BMC Genomics 13:77. 2012
  10. pmc Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
    Andrew Adey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Genome Biol 11:R119. 2010

Collaborators

  • Jun Wang
  • Yingrui Li
  • Hui Jiang
  • Chang Yu
  • Fang Chen
  • Wei Wang
  • Xiao Liu
  • Xun Xu
  • Yi Huang
  • Geng Tian
  • Ping Hu
  • Shan Dan
  • Jian Xu
  • Lei Zhang
  • Lee M Butcher
  • Liang Sun
  • Ning Li
  • Fei Gao
  • Gabor Vajta
  • Yong Wang
  • Ying Chen
  • Huanming Yang
  • Songgang Li
  • Karsten Kristiansen
  • Shengpei Chen
  • XueDa Hu
  • Chunlei Zhang
  • Yaoting Gui
  • Xianxin Li
  • Xuchao Li
  • Ruiqiang Li
  • Guangwu Guo
  • Zhiming Cai
  • Liang Zhou
  • Lars Bolund
  • Xiaoyu Pan
  • Hongzhi Cao
  • Xiaokun Zhao
  • Chaozhao Liang
  • Jing Chen
  • Hancheng Zheng
  • Weiwei Xie
  • Song Wu
  • Fangjian Zhou
  • Zhimao Jiang
  • Renhua Wu
  • Qibin Li
  • Tao Jiang
  • - Asan
  • Jingxiang Li
  • Junjie Qin
  • Yueqiu Tan
  • Xuyang Yin
  • Ge Lin
  • Fuman Jiang
  • Peide Huang
  • Zesong Li
  • Shengjie Gao
  • Rui Ye
  • Wenlong Jia
  • Aifa Tang
  • Xiaojuan Sun
  • Shengqing Wan
  • Chao Chen
  • Meiru Zhao
  • Jialou Zhu
  • Chen Ye
  • Xin Yi
  • Ruilin Yang
  • Xiaodong Fang
  • Zhongfu Zhang
  • Jing Zou
  • Min Jian
  • Honglong Wu
  • Jiahao Chen
  • Maoshan Chen
  • Zujing Han
  • Jian Li
  • Guojie Zhang
  • Hongmei Zhu
  • Huisong Zheng
  • Huiqing Liang
  • Zhengfeng Xu
  • Chunsheng Zhang
  • Guangxiu Lu
  • Ke Tan
  • Weiyang Li
  • Jingxiao Lu
  • Fan Fan
  • Huanhuan Peng

Detail Information

Publications44

  1. pmc Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
    Ying Hui Li
    Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement NFCRI Key Lab of Germplasm Utilization MOA, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
    BMC Genomics 14:579. 2013
    ....
  2. pmc A systematic analysis on DNA methylation and the expression of both mRNA and microRNA in bladder cancer
    Jialou Zhu
    Beijing Genomics Institute at Shenzhen, Shenzhen, China
    PLoS ONE 6:e28223. 2011
    ..DNA methylation aberration and microRNA (miRNA) deregulation have been observed in many types of cancers. A systematic study of methylome and transcriptome in bladder urothelial carcinoma has never been reported...
  3. pmc Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma
    Liang Zhou
    The Key Laboratory of Stem Cell Biology, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU HKUST Medical Center, Shenzhen, China
    PLoS ONE 5:e15224. 2010
    ..The purpose of this study was to systematically profile the expression of both mRNA and miRNA genes in clear cell renal cell carcinoma (ccRCC) using massively parallel sequencing technology...
  4. pmc Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events
    Xianxin Li
    Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
    PLoS ONE 6:e22570. 2011
    ..Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA) in a single type of cancer...
  5. pmc The DNA methylome of human peripheral blood mononuclear cells
    Yingrui Li
    BGI Shenzhen, Shenzhen, Guangdong, China
    PLoS Biol 8:e1000533. 2010
    ..Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies...
  6. pmc Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing
    Shan Dan
    Department of Perinatal Medicine, Beijing Obstetrics and Gynecology Hospital Capital Medical University, Beijing, China
    PLoS ONE 7:e27835. 2012
    ..4 Mb to 37.3 Mb of 5 samples from chorionic villus sampling (CVS) using SeqSeq algorithm. Our work demonstrated MPS is a robust and accurate approach to detect aneuploidy and imbalanced chromosomal arrangements in prenatal samples...
  7. pmc Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies
    Fuman Jiang
    BGI Shenzhen, Shenzhen, China
    BMC Med Genomics 5:57. 2012
    ..Conventional prenatal screening tests, such as maternal serum tests and ultrasound scan, have limited resolution and accuracy...
  8. pmc Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
    Qi Zhou
    CAS Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
    BMC Genomics 13:109. 2012
    ..12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility...
  9. pmc Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method
    Ye Du
    BGI_shenzhen, Shenzhen 518000, China
    BMC Genomics 13:77. 2012
    ..It has remarkable advantage of reducing the complexity of the genome by orders of magnitude. However, comprehensive evaluation for actual efficacy of SNP identification by this method is still unavailable...
  10. pmc Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
    Andrew Adey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Genome Biol 11:R119. 2010
    ..We also extend its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 ng of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing...
  11. pmc Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP
    Bjørn A Nexø
    Institute of Human Genetics, University of Aarhus, DK 8000 Aarhus C, Denmark
    BMC Med Genet 9:56. 2008
    ..The study groups included 434 postmenopausal breast cancer cases and an identical number of individually matched controls...
  12. pmc An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines
    Jian Li
    Institute of Human Genetics, University of Aarhus, The Bartholin Building, Aarhus C, Denmark
    BMC Genomics 10:223. 2009
    ..DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of particular importance...
  13. ncbi Massively parallel sequencing for chromosomal abnormality testing in trophectoderm cells of human blastocysts
    Xuyang Yin
    BGI Shenzhen, Shenzhen, China
    Biol Reprod 88:69. 2013
    ..Our study demonstrated MPS could be applied to accurately detect embryonic chromosomal abnormality with a flexible and cost-effective strategy and higher potential accuracy...
  14. ncbi Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies
    Li Wang
    BGI Shenzhen, Shenzhen, Guangdong, China
    J Biotechnol 157:1-6. 2012
    ....
  15. pmc High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing
    Junwen Wang
    Beijing Genomics Institute at Shenzhen, Beishan Road, Shenzhen 518000, China
    BMC Genomics 12:597. 2011
    ..Thus, they are not practical for researchers to study multiple clinical samples in biomarker research...
  16. ncbi Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
    Yingrui Li
    BGI Shenzhen, Shenzhen, China
    Nat Biotechnol 29:723-30. 2011
    ..These findings demonstrate that whole-genome de novo assembly is a feasible approach to deriving more comprehensive maps of genetic variation...
  17. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  18. pmc Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer
    Yingrui Li
    BGI Shenzhen, BeiShan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People s Republic of China
    Gigascience 1:12. 2012
    ....
  19. pmc Sequencing of 50 human exomes reveals adaptation to high altitude
    Xin Yi
    BGI Shenzhen, Shenzhen 518083, China
    Science 329:75-8. 2010
    ..This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude...
  20. ncbi A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing
    Shengpei Chen
    BGI Shenzhen, Shenzhen, China
    Prenat Diagn 33:584-90. 2013
    ..To report the feasibility of fetal chromosomal deletion/duplication detection using a novel bioinformatic method of low coverage whole genome sequencing of maternal plasma...
  21. ncbi Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor
    Xun Xu
    BGI Shenzhen, Shenzhen, China
    Cell 148:886-95. 2012
    ....
  22. pmc Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing
    Junwen Wang
    Science and Technology Department, BGI Shenzhen, no 11, Bei Shan Industrial Zone, Yantian District, Shenzhen, China
    BMC Genomics 14:11. 2013
    ..This method could be improved to generate a more comprehensive representation...
  23. ncbi Multilayered molecular profiling supported the monoclonal origin of metastatic renal cell carcinoma
    Yi Huang
    Shenzhen Second People s Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China National Regional Key Technology Engineering Laboratory for Clinical Application of Cancer Genomics, Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen, China
    Int J Cancer 135:78-87. 2014
    ..Thus, there was a broad window for early detection of circulating tumor cells and future targeted treatments for patients with mRCCs should rely on the molecular profiles of metastases. ..
  24. ncbi Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma
    Guangwu Guo
    Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Shenzhen, Shenzhen, China
    Nat Genet 44:17-9. 2012
    ..01 and 0.04, respectively). Our findings highlight the potential contribution of UMPP to ccRCC tumorigenesis through the activation of the hypoxia regulatory network...
  25. ncbi Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation
    Guangwu Guo
    1 Department of Urological Surgery, Shenzhen Second People s Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China 2 BGI Shenzhen, Shenzhen, China 3
    Nat Genet 45:1459-63. 2013
    ..Our analysis provides evidence that genetic alterations affecting the SCCS process may be involved in bladder tumorigenesis and identifies a new therapeutic possibility for bladder cancer. ..
  26. ncbi Building the sequence map of the human pan-genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nat Biotechnol 28:57-63. 2010
    ..The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly...
  27. ncbi Rapid detection of aneuploidies on a benchtop sequencing platform
    Weiwei Xie
    BGI Shenzhen, Shenzhen, China
    Prenat Diagn 33:232-7. 2013
    ..To report a novel method of rapidly detecting fetal aneuploidies for spontaneous abortion using ultra-low whole genome sequencing data on a benchtop sequencing platform...
  28. ncbi Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells
    Fei Gao
    Science and Technology Department, BGI Shenzhen, Shenzhen, 518083, China Electronic address
    Genomics 103:204-10. 2014
    ..These works support the association between H3K27me3 and DNA methylation marks for specific cancer genes and will spur future work on combined histone and DNA methylation that could define cancer's epigenetic abnormalities. ..
  29. ncbi Whole genome DNA methylation analysis based on high throughput sequencing technology
    Ning Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Methods 52:203-12. 2010
    ....
  30. pmc The diploid genome sequence of an Asian individual
    Jun Wang
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Nature 456:60-5. 2008
    ..These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics...
  31. pmc Paired-end sequencing of long-range DNA fragments for de novo assembly of large, complex Mammalian genomes by direct intra-molecule ligation
    - Asan
    BGI Shenzhen, Shenzhen, Guangdong, China
    PLoS ONE 7:e46211. 2012
    ..Here, we characterize and extend a long-range PE library construction method based on direct intra-molecule ligation (or molecular linker-free circularization) for NGS...
  32. ncbi Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder
    Yaoting Gui
    Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU HKUST Medical Center, Shenzhen, China
    Nat Genet 43:875-8. 2011
    ..Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer...
  33. pmc PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing
    Xuchao Li
    BGI Shenzhen, Shenzhen, China
    PLoS ONE 9:e85096. 2014
    ..In this study, using low coverage whole-genome sequencing (LCS) we have developed an effective population-scale CNV calling (PSCC) method...
  34. ncbi High-performance single-chip exon capture allows accurate whole exome sequencing using the Illumina Genome Analyzer
    Tao Jiang
    Beijing Genomics Institute, Shenzhen 518000, China
    Sci China Life Sci 54:945-52. 2011
    ..The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach...
  35. ncbi Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants
    Yingrui Li
    BGI Shenzhen, Shenzhen, China
    Nat Genet 42:969-72. 2010
    ..This excess was more pronounced for X-linked SNPs, suggesting that deleterious substitutions are primarily recessive...
  36. ncbi Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors
    Shan Dan
    BGI Shenzhen, Shenzhen, China
    Prenat Diagn 32:1225-32. 2012
    ..To report the performance of massively parallel sequencing (MPS) based prenatal noninvasive fetal trisomy test based on cell-free DNA sequencing from maternal plasma in a routine clinical setting in China...
  37. pmc Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
    Guojie Zhang
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Genome Res 20:646-54. 2010
    ..Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed...
  38. pmc A human gut microbial gene catalogue established by metagenomic sequencing
    Junjie Qin
    BGI Shenzhen, Shenzhen 518083, China
    Nature 464:59-65. 2010
    ..We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively...
  39. pmc A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing
    Chunlei Zhang
    Science and Technology, BGI Shenzhen, Shenzhen, China
    PLoS ONE 8:e54236. 2013
    ....
  40. pmc Sequencing bias: comparison of different protocols of microRNA library construction
    Geng Tian
    Beijing Genomics Institute, Shenzhen 518000, China
    BMC Biotechnol 10:64. 2010
    ..However, the possible bias between the relative expression levels and sequences introduced by different protocols of library preparation have rarely been explored...
  41. ncbi A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies
    Hongzhi Cao
    BGI Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
    Hum Mutat 34:1715-20. 2013
    ..We thus demonstrate RCHSBT to be a genotyping method comparable to Sanger sequencing-based typing in quality, while being more cost-effective, and higher throughput. ..
  42. ncbi HIVID: an efficient method to detect HBV integration using low coverage sequencing
    Weiyang Li
    BGI Shenzhen, Shenzhen, 518083, China School of Bioscience and Bioengineering, South China University of Technology, China
    Genomics 102:338-44. 2013
    ..7% (10/15) of validation rate. Our study shows HIVID is a cost-effective methodology with high specificity and sensitivity to identify viral integration in human genome. ..
  43. ncbi Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm
    Yong Hou
    BGI Shenzhen, Shenzhen, China
    Cell 148:873-85. 2012
    ..Further, we established a single-cell sequencing method that opens the way for detailed analyses of a variety of tumor types, including those with high genetic complex between patients...
  44. pmc Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing
    Chang Yu
    BGI Shenzhen, Shenzhen, Guangdong 518083, China
    Cell Res 24:701-12. 2014
    ....