Jun Wang

Summary

Affiliation: Chinese Academy of Sciences
Country: China

Publications

  1. pmc Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication
    Hui Xiang
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East JiaoChang Road, Kunming, Yunnan Province 650223, China
    BMC Genomics 14:646. 2013
  2. 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
  3. pmc State of the art de novo assembly of human genomes from massively parallel sequencing data
    Yingrui Li
    BGI Shenzhen, Shenzhen, Guangdong, China
    Hum Genomics 4:271-7. 2010
  4. pmc The sequence and analysis of a Chinese pig genome
    Xiaodong Fang
    BGI Shenzhen, Bei Shan Road, Yantian, Shenzhen, 518083, China
    Gigascience 1:16. 2012
  5. pmc SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
    Ruibang Luo
    BGI HK Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong
    Gigascience 1:18. 2012
  6. pmc Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns
    Joachim Weischenfeldt
    The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark
    Genome Biol 13:R35. 2012
  7. pmc Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
    A Albrechtsen
    Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
    Diabetologia 56:298-310. 2013
  8. pmc Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation
    Guoqing Pan
    State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
    BMC Genomics 14:186. 2013
  9. doi request reprint Exome sequencing identifies a COL14A1 mutation in a large Chinese pedigree with punctate palmoplantar keratoderma
    Bi Rong Guo
    Institute of Dermatology and Department of Dermatology, No 1 Hospital, Anhui Medical University, Hefei, Anhui, China
    J Med Genet 49:563-8. 2012
  10. pmc A genome triplication associated with early diversification of the core eudicots
    Yuannian Jiao
    Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 13:R3. 2012

Collaborators

  • Xiuqing Zhang
  • Jun Yu
  • Wen Wang
  • Gane Ka Shu Wong
  • Guojie Zhang
  • Jun Li
  • Jianguo Zhang
  • Yong Zhang
  • Yingrui Li
  • Huanming Yang
  • Ruiqiang Li
  • Karsten Kristiansen
  • Lars Bolund
  • Songgang Li
  • Xun Xu
  • Rasmus Nielsen
  • Geng Tian
  • Chang Yu
  • Xiao Liu
  • Xiaodong Fang
  • Hancheng Zheng
  • Xin Li
  • Dong Li
  • Ruibang Luo
  • Honglong Wu
  • Deyin Hou
  • Weiming He
  • Hui Jiang
  • Junjie Qin
  • Hongmei Zhu
  • Heng Li
  • Shancen Zhao
  • Yang Dong
  • Guangwu Guo
  • Bo Wang
  • Hui Xiang
  • Xiaosen Guo
  • Renhua Wu
  • Anders Albrechtsen
  • Quan Chen
  • Tao Jiang
  • Bo Li
  • Shengting Li
  • Chen Ye
  • Hongzhi Cao
  • Yan Zhou
  • Qibin Li
  • Zhaokun Luan
  • Søren Brunak
  • Xin Liu
  • Aifa Tang
  • Jiumeng Min
  • Xiaojuan Sun
  • Zesong Li
  • Zhiming Cai
  • Binghang Liu
  • Haojing Shao
  • Thorfinn Korneliussen
  • Fang Chen
  • Qingyou Xia
  • Wei Fan
  • Jie Chen
  • Quanfei Huang
  • XueDa Hu
  • Torben Hansen
  • Oluf Pedersen
  • Mingzhi Ye
  • Ning Li
  • Min Jian
  • Jing Zhao
  • - Asan
  • Jue Ruan
  • Xin Jin
  • Peixiang Ni
  • Qi Zhou
  • Huisong Zheng
  • Changwei Zhao
  • Huiqing Liang
  • Wubin Qian
  • Xiaojing Ren
  • Lijia Ma
  • Yiran Guo
  • Lin Fang
  • Mikkel H Schierup
  • Li Juan Qiu
  • Chi Zhang
  • Yong Tao
  • Shengkai Pan
  • Yong Hou
  • Fengyi Hu

Detail Information

Publications127 found, 100 shown here

  1. pmc Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication
    Hui Xiang
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East JiaoChang Road, Kunming, Yunnan Province 650223, China
    BMC Genomics 14:646. 2013
    ..The silkworm is still an enigma in that it has two DNA methyltransferases (DNMT1 and DNMT2) but their functionality is unknown. Even in particular the functionality of the widely distributed DNMT1 remains unknown in insects in general...
  2. 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
    ....
  3. pmc State of the art de novo assembly of human genomes from massively parallel sequencing data
    Yingrui Li
    BGI Shenzhen, Shenzhen, Guangdong, China
    Hum Genomics 4:271-7. 2010
    ..This review describes two public short-read de novo assembly applications that can handle human genomes, ABySS and SOAPdenovo. It also discusses the technical aspects and future challenges of human genome de novo assembly by short reads...
  4. pmc The sequence and analysis of a Chinese pig genome
    Xiaodong Fang
    BGI Shenzhen, Bei Shan Road, Yantian, Shenzhen, 518083, China
    Gigascience 1:16. 2012
    ..WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome...
  5. pmc SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
    Ruibang Luo
    BGI HK Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong
    Gigascience 1:18. 2012
    ..SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions...
  6. pmc Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns
    Joachim Weischenfeldt
    The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark
    Genome Biol 13:R35. 2012
    ..Here, we combine mouse genetics and RNA-seq to provide the first in vivo analysis of the global impact of NMD on splicing patterns in two primary mouse tissues ablated for the NMD factor UPF2...
  7. pmc Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
    A Albrechtsen
    Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
    Diabetologia 56:298-310. 2013
    ..Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) >1% with common metabolic phenotypes...
  8. pmc Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation
    Guoqing Pan
    State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
    BMC Genomics 14:186. 2013
    ..bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees)...
  9. doi request reprint Exome sequencing identifies a COL14A1 mutation in a large Chinese pedigree with punctate palmoplantar keratoderma
    Bi Rong Guo
    Institute of Dermatology and Department of Dermatology, No 1 Hospital, Anhui Medical University, Hefei, Anhui, China
    J Med Genet 49:563-8. 2012
    ..To date, no causal gene for this disease has been identified...
  10. pmc A genome triplication associated with early diversification of the core eudicots
    Yuannian Jiao
    Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 13:R3. 2012
    ..Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear...
  11. pmc Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture
    Lei Li
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Genome Biol 6:R52. 2005
    ..Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes...
  12. pmc Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes
    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, People s Republic of China
    Genome Biol 9:R98. 2008
    ..The regular mammalian X and Y chromosomes diverged from each other at least 166 to 148 million years ago, leaving few traces of their early evolution, including degeneration of the Y chromosome and evolution of dosage compensation...
  13. pmc Identification and characterization of novel amphioxus microRNAs by Solexa sequencing
    Xi Chen
    Jiangsu Diabetes Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Hankou Road, Nanjing, Jiangsu 210093, PR China
    Genome Biol 10:R78. 2009
    ..While the number of known human and murine miRNAs is continuously increasing, information regarding miRNAs from other species such as amphioxus remains limited...
  14. pmc Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
    Jan Gorodkin
    Division of Genetics and Bioinformatics, IBHV, Grønnegårdsvej 3, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark
    Genome Biol 8:R45. 2007
    ..The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages...
  15. pmc Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups
    Mikkel H Schierup
    Institute of Human Genetics, University of Aarhus, DK 8000 Aarhus C, Denmark
    BMC Med Genet 10:20. 2009
    ..The whole region seems related to the cellular response to external damaging agents and markers in it are associated with risk of several cancers...
  16. pmc Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
    Rasmus Wernersson
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    BMC Genomics 6:70. 2005
    ..Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls...
  17. pmc Gene conversion in the rice genome
    Shuqing Xu
    Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China
    BMC Genomics 9:93. 2008
    ..Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes increases opportunities for gene conversion...
  18. pmc Identification and characterization of insect-specific proteins by genome data analysis
    Guojie Zhang
    State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology Chinese Academy of Sciences, Haidian Beijing 100080, China
    BMC Genomics 8:93. 2007
    ..Here we present results from a computational method that uses genome analysis to characterize insect and eukaryote proteomes as an approximation complementary to experimental approaches...
  19. pmc Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes
    Dong Li
    The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
    BMC Evol Biol 10:81. 2010
    ....
  20. pmc Estimation of allele frequency and association mapping using next-generation sequencing data
    Su Yeon Kim
    Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA 94720, USA
    BMC Bioinformatics 12:231. 2011
    ..g., < 15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates...
  21. pmc A cross-species alignment tool (CAT)
    Heng Li
    Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
    BMC Bioinformatics 8:349. 2007
    ..The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sensitive methods which are usually applied in aligning inter-species sequences...
  22. 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...
  23. doi request reprint Evolutionary transients in the rice transcriptome
    Jun Wang
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 8:211-28. 2010
    ..Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots...
  24. pmc RePS: a sequence assembler that masks exact repeats identified from the shotgun data
    Jun Wang
    Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China
    Genome Res 12:824-31. 2002
    ..We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2% in exact repeats...
  25. ncbi request reprint Genome organization of the SARS-CoV
    Jing Xu
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 1:226-35. 2003
    ..The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs...
  26. doi request reprint The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  27. ncbi request reprint Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs
    Jun Wang
    James D Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310007, China
    Nature 431:1 p following 757; discussion following 757. 2004
  28. ncbi request reprint Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome
    Yan Zhou
    Hangzhou Genomics Institute Institute of Bioinformatics of Zhejiang University Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China
    Genomics Proteomics Bioinformatics 1:26-42. 2003
    ..We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development...
  29. pmc SNP detection for massively parallel whole-genome resequencing
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Genome Res 19:1124-32. 2009
    ..Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth...
  30. pmc Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
    Xin Li
    CAS Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    BMC Genomics 13:300. 2012
    ..japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara...
  31. ncbi request reprint The R protein of SARS-CoV: analyses of structure and function based on four complete genome sequences of isolates BJ01-BJ04
    Zuyuan Xu
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 1:155-65. 2003
    ..Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS...
  32. pmc Origin and evolution of new exons in rodents
    Wen Wang
    CAS Max Planck Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
    Genome Res 15:1258-64. 2005
    ..Most of the new exons appear to be alternative exons that are expressed at low levels...
  33. pmc SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data
    Rasmus Nielsen
    BGI Shenzhen, Shenzhen, China
    PLoS ONE 7:e37558. 2012
    ..We evaluate the statistical properties of the methods using simulations and by application to a real data set...
  34. doi request reprint 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
    ....
  35. doi request reprint Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage
    Jun Li
    Beijing Genomics Institute, Shenzhen, Building Complex, BeiShan Industrial Zone, Yantian District, Shenzhen, 518083, China
    J Mol Evol 68:414-23. 2009
    ..Our results indicated that currently used algorithms for Ka and Ks calculations are flawed and need improvements...
  36. 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...
  37. pmc Analysis of elite variety tag SNPs reveals an important allele in upland rice
    Jun Lyu
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
    Nat Commun 4:2138. 2013
    ..This report provides a potential strategy to mine rare, agronomically important alleles. ..
  38. doi request reprint Draft genome of the wheat A-genome progenitor Triticum urartu
    Hong Qing Ling
    State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Nature 496:87-90. 2013
    ..Our T. urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat...
  39. doi request reprint The genome of the cucumber, Cucumis sativus L
    Sanwen Huang
    Key Laboratory of Horticultural Crops Genetic Improvement of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
    Nat Genet 41:1275-81. 2009
    ..We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system...
  40. doi request reprint 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...
  41. pmc High rate of chimeric gene origination by retroposition in plant genomes
    Wen Wang
    CAS Max Plank Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    Plant Cell 18:1791-802. 2006
    ..These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species...
  42. ncbi request reprint A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
    Jun Yu
    Beijing Genomics Institute Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China
    Science 296:79-92. 2002
    ..4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences...
  43. pmc A comparison of rice chloroplast genomes
    Jiabin Tang
    Institute of Genetics and Developmental Biology and Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Plant Physiol 135:412-20. 2004
    ..Based on the total number of nucleotide substitutions between the two chloroplast genomes, we dated the divergence of indica and japonica chloroplast genomes as occurring approximately 86,000 to 200,000 years ago...
  44. 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...
  45. doi request reprint Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential
    Gengyun Zhang
    BGI Shenzhen, Shenzhen, China
    Nat Biotechnol 30:549-54. 2012
    ..Rearrangements in the C(4) photosynthesis pathway were also identified...
  46. doi request reprint Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor
    Xun Xu
    BGI Shenzhen, Shenzhen, China
    Cell 148:886-95. 2012
    ....
  47. pmc Transcriptome and network changes in climbers at extreme altitudes
    Fang Chen
    BGI Shenzhen, Shenzhen, China
    PLoS ONE 7:e31645. 2012
    ..Our approach established a new framework for analyzing the transcriptional regulatory network from a very limited number of samples...
  48. doi request reprint Boron removal from aqueous solution by direct contact membrane distillation
    Deyin Hou
    State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco Environmental Sciences, Chinese Academy of Sciences, PO Box 2871, Beijing 100085, China
    J Hazard Mater 177:613-9. 2010
    ..All the experimental results indicated that DCMD could be efficiently used for boron removal from aqueous solution...
  49. doi request reprint Genome sequence and analysis of the tuber crop potato
    Xun Xu
    BGI Shenzhen, Chinese Ministry of Agricultural, Key Lab of Genomics, BeiShan Industrial Zone, Yantian District, Shenzhen 518083, China
    Nature 475:189-95. 2011
    ..Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop...
  50. ncbi request reprint Vertebrate gene predictions and the problem of large genes
    Jun Wang
    Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    Nat Rev Genet 4:741-9. 2003
    ..The crucial variable is gene size (including introns)--genes of the most extreme sizes, especially very large genes, are most likely to be incorrectly predicted...
  51. pmc Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution
    Jinfeng Chen
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No 1 West Beichen Road, Chaoyang District, Beijing 100101, China
    Nat Commun 4:1595. 2013
    ..The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza...
  52. pmc Accelerated evolution of the pituitary adenylate cyclase-activating polypeptide precursor gene during human origin
    Yin Qiu Wang
    Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan
    Genetics 170:801-6. 2005
    ..Our data suggested that the PACAP precursor gene underwent adaptive changes during human origin and may have contributed to the formation of human cognition...
  53. pmc De novo assembly of human genomes with massively parallel short read sequencing
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
    Genome Res 20:265-72. 2010
    ..3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way...
  54. ncbi request reprint KaKs_Calculator: calculating Ka and Ks through model selection and model averaging
    Zhang Zhang
    Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
    Genomics Proteomics Bioinformatics 4:259-63. 2006
    ..In addition, several existing methods for calculating Ka and Ks are also incorporated into this software...
  55. pmc Compositional gradients in Gramineae genes
    Gane Ka Shu Wong
    Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China
    Genome Res 12:851-6. 2002
    ..The magnitudes of these gradients are large enough to hinder the annotation of the rice genome and to confound the detection of protein homologies across the monocot-eudicot divide...
  56. ncbi request reprint The E protein is a multifunctional membrane protein of SARS-CoV
    Qingfa Wu
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 1:131-44. 2003
    ..Our phylogenetic analyses of the E protein sequences in all published coronaviruses place SARS-CoV in an independent group in Coronaviridae and suggest a non-human animal origin...
  57. doi request reprint Ancient human genome sequence of an extinct Palaeo-Eskimo
    Morten Rasmussen
    Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
    Nature 463:757-62. 2010
    ..This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit...
  58. 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...
  59. doi request reprint A metagenome-wide association study of gut microbiota in type 2 diabetes
    Junjie Qin
    BGI Shenzhen, Shenzhen 518083, China
    Nature 490:55-60. 2012
    ..An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes...
  60. doi request reprint Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nature 499:74-8. 2013
    ..Such regions could correspond to loci selected early during domestication...
  61. 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
    ....
  62. doi request reprint SOAP2: an improved ultrafast tool for short read alignment
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen, 518083, China
    Bioinformatics 25:1966-7. 2009
    ..Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome...
  63. doi request reprint Single base-resolution methylome of the silkworm reveals a sparse epigenomic map
    Hui Xiang
    CAS Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
    Nat Biotechnol 28:516-20. 2010
    ....
  64. ncbi request reprint Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup
    Xiao Jing Yu
    Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
    Genomics 88:745-51. 2006
    ..We also demonstrated that rhesus macaque performed much better than mouse as an outgroup in identifying lineage-specific selection in humans...
  65. doi request reprint Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
    Xun Xu
    CAS Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences CAS, Kunming, China
    Nat Biotechnol 30:105-11. 2012
    ..The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice...
  66. ncbi request reprint BGI-RIS V2
    Ximiao He
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China
    Methods Mol Biol 406:275-99. 2007
    ..This database is available through the web server (http://rise.genomics.org.cn or http://rice.genomics.org.cn) and the File Transfer Protocol (FTP) server (ftp://ftp.genomics.org.cn/pub/database/rice)...
  67. doi request reprint 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...
  68. doi request reprint Preparation, structural analysis and bioactivity of ribonuclease A-albumin conjugate: tetra-conjugation or PEG as the linker
    Chunju Li
    National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
    J Biotechnol 162:283-8. 2012
    ..In addition, the slow release of BSA from R-HDA-B may increase the enzymatic activity of R-HDA-B. Our study is expected to provide strategies to develop protein-albumin conjugate with high therapeutic potential...
  69. ncbi request reprint The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes
    Zuogang Peng
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, 7th Donghu South Road, Wuhan 430072, China
    Gene 376:290-7. 2006
    ..In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed...
  70. doi request reprint 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...
  71. ncbi request reprint The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate
    Xuzhen Wang
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Gene 399:11-9. 2007
    ..Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny...
  72. pmc The analysis of large-scale gene expression correlated to the phase changes of the migratory locust
    Le Kang
    National Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
    Proc Natl Acad Sci U S A 101:17611-5. 2004
    ..This study provides ample molecular markers and genomic information on hemimetabolous insects and insights into the genetic and molecular mechanisms of phase changes in locusts...
  73. pmc A platform for soybean molecular breeding: the utilization of core collections for food security
    Li Juan Qiu
    The National Key Facility for Crop Gene Resources and Genetic Improvement NFCRI, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    Plant Mol Biol 83:41-50. 2013
    ..The efficient utilization of this platform in the future is relying on accurate phenotyping methods, abundant functional markers, high-throughput genotyping platforms, and effective breeding programs. ..
  74. doi request reprint Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
    Jizeng Jia
    National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    Nature 496:91-5. 2013
    ..This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species...
  75. doi request reprint 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
    ....
  76. doi request reprint Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)
    Yang Zheng
    Beijing Institute of Genomics, Chinese Academy of Sciences CAS, Beijing, China
    Sci China Life Sci 53:107-11. 2010
    ..Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda...
  77. doi request reprint 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...
  78. 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...
  79. doi request reprint Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)
    Yang Dong
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
    Nat Biotechnol 31:135-41. 2013
    ..This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes...
  80. pmc Insights into salt tolerance from the genome of Thellungiella salsuginea
    Hua Jun Wu
    State Key Laboratory of Plant Genomics, National Center for Plant Gene Research Beijing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    Proc Natl Acad Sci U S A 109:12219-24. 2012
    ..Comparative genomics and experimental analyses identified genes related to cation transport, abscisic acid signaling, and wax production prominent in T. salsuginea as possible contributors to its success in stressful environments...
  81. pmc Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque
    Xiaodong Fang
    Beijing Genomics Institute Shenzhen, Chinese Academy of Sciences, Shenzhen 518083, China
    Genome Biol 12:R63. 2011
    ..Rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate animal in biomedical research. A global map of genetic variations in rhesus macaque is valuable for both evolutionary and functional studies...
  82. ncbi request reprint Fabrication of asymmetric poly (m-phenylene isophthalamide) nanofiltration membrane for chromium (VI) removal
    Xiaojing Ren
    State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
    J Environ Sci (China) 22:1335-41. 2010
    ..It is concluded that chromium(VI) could be effectively removed from chromium-containing wastewater by the PMIA nanofiltration membranes while maintaining their pollution resistance under alkaline condition...
  83. pmc SOAPindel: efficient identification of indels from short paired reads
    Shengting Li
    BGI Shenzhen, Shenzhen 518000, China
    Genome Res 23:195-200. 2013
    ..A validation experiment suggests that SOAPindel has a false-positive rate of ∼10% for long indels (>5 bp), while still providing many more candidate indels than other approaches...
  84. pmc Comprehensive comparison of three commercial human whole-exome capture platforms
    - Asan
    Beijing Institute of Genomics, Chinese Academy of Sciences, No 7 Beitucheng West Road, Chaoyang District, Beijing 100029, China
    Genome Biol 12:R95. 2011
    ..Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study...
  85. doi request reprint Propylbenzmethylation at Val-1(α) markedly increases the tetramer stability of the PEGylated hemoglobin: a comparison with propylation at Val-1(α)
    Tao Hu
    Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
    Biochim Biophys Acta 1820:2044-51. 2012
    ..Thus, it is necessary to increase the tetramer stability of the PEGylated Hb...
  86. ncbi request reprint A mitochondrial genome sequence of the Tibetan antelope (Pantholops hodgsonii)
    Shu Qing Xu
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 3:5-17. 2005
    ....
  87. pmc A population model for genotyping indels from next-generation sequence data
    Haojing Shao
    BGI Shenzhen, Shenzhen 518083, China
    Nucleic Acids Res 41:e46. 2013
    ..Compared with existing methods, we report a 4-fold reduction in overall indel genotype error rates with a 9-fold reduction in low coverage regions...
  88. doi request reprint SOAP: short oligonucleotide alignment program
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
    Bioinformatics 24:713-4. 2008
    ..SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets...
  89. ncbi request reprint Fluoride removal from brackish groundwater by direct contact membrane distillation
    Deyin Hou
    State Key Laboratory of Environmental Aquatic Chemistry Research Center for Eco Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
    J Environ Sci (China) 22:1860-7. 2010
    ..In addition, a 300 hr continuous fluoride removal experiment of acidified groundwater was carried out with concentration factor at 4.0, the permeate flux kept stable and the permeate fluoride was not detected...
  90. ncbi request reprint Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei): A new insight
    Zuogang Peng
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, 7 Donghu South Road, Wuhan 430072, China
    Gene 370:113-24. 2006
    ..The origin of the Otocephala is estimated as having occurred about 282 Mya, with the origin of the Otophysi being estimated at about 251 Mya...
  91. pmc Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences
    Zhen Yu Gao
    State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, Zhejiang Province, China
    Proc Natl Acad Sci U S A 110:14492-7. 2013
    ..The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice. ..
  92. 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...
  93. ncbi request reprint Genomic organization, transcript variants and comparative analysis of the human nucleoporin 155 (NUP155) gene
    Xiuqing Zhang
    Human Genome Center, Institute of Genetics, Chinese Academy of Sciences, Datun Road, Beijing 100101, China
    Gene 288:9-18. 2002
    ..Different gene orders in the human and Fugu genomic regions harboring the Nup155 orthologs advocate cautious interpretation of synteny in comparative genomic analysis even within the vertebrate lineage...
  94. doi request reprint Effect of urbanization on the structure and functional traits of remnant subtropical evergreen broad-leaved forests in South China
    Liujing Huang
    Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
    Environ Monit Assess 185:5003-18. 2013
    ..Urbanization affects the structure and functional traits of remnant subtropical evergreen broad-leaved forests...
  95. doi request reprint Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation
    Shancen Zhao
    Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Nat Genet 45:67-71. 2013
    ..We identified three distinct panda populations that show genetic adaptation to their environments. However, in all three populations, anthropogenic activities have negatively affected pandas for 3,000 years...
  96. doi request reprint The oyster genome reveals stress adaptation and complexity of shell formation
    Guofan Zhang
    Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
    Nature 490:49-54. 2012
    ..The oyster genome sequence fills a void in our understanding of the Lophotrochozoa...
  97. pmc Permian vegetational Pompeii from Inner Mongolia and its implications for landscape paleoecology and paleobiogeography of Cathaysia
    Jun Wang
    State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
    Proc Natl Acad Sci U S A 109:4927-32. 2012
    ..Therefore, this flora will serve as a baseline for the study of other fossil floras in East Asia and the early Permian globally that will be needed for a better understanding of paleoclimate evolution through time...
  98. doi request reprint Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells
    Lei Liu
    The State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Nat Cell Biol 14:177-85. 2012
    ..Mechanistic studies further revealed that hypoxia induced dephosphorylation of FUNDC1 and enhanced its interaction with LC3 for selective mitophagy. Our findings thus offer insights into mitochondrial quality control in mammalian cells...
  99. ncbi request reprint [Effects of litter coverage and watering frequency on seed germination and seedling survival of Castanopsis fissa]
    Jun Wang
    National Field Research Station of Forestry Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
    Ying Yong Sheng Tai Xue Bao 19:2097-102. 2008
    ..fissa seedlings was enhanced significantly by litter covering. It was suggested that keeping a litter layer on soil surface could benefit the seed germination and seedling survival of C. fissa to restore subtropical shrub land...
  100. doi request reprint Pathways and determinants of early spontaneous vegetation succession in degraded lowland of South China
    Wen Jun Duan
    Heshan Hilly Land Interdisciplinary Experimental Station, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
    J Integr Plant Biol 50:147-56. 2008
    ..Our results showed that the environmental variables changed in diverse directions, and that soil bulk density, soil water capacity and soil acidity were the most important factors...
  101. ncbi request reprint The M protein of SARS-CoV: basic structural and immunological properties
    Yongwu Hu
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 1:118-30. 2003
    ..2% of the entire ORF and screened them by using ELISA (enzyme-linked immunosorbent assay) with sera from SARS patients. The results confirmed our predictions on antigenic sites...