Jun Wang

Summary

Affiliation: Chinese Academy of Sciences
Country: China

Publications

  1. pmc WEGO: a web tool for plotting GO annotations
    Jia Ye
    James D Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310008, China
    Nucleic Acids Res 34:W293-7. 2006
  2. 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
  3. pmc Transcriptome and network changes in climbers at extreme altitudes
    Fang Chen
    BGI Shenzhen, Shenzhen, China
    PLoS ONE 7:e31645. 2012
  4. 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
  5. pmc PigGIS: Pig Genomic Informatics System
    Jue Ruan
    Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
    Nucleic Acids Res 35:D654-7. 2007
  6. pmc The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
    Xun Xu
    BGI Shenzhen, Shenzhen, People s Republic of China
    Nat Biotechnol 29:735-41. 2011
  7. pmc Snap: an integrated SNP annotation platform
    Shengting Li
    The Institute of Human Genetics, University of Aarhus, DK 8000 Aarhus C, Denmark
    Nucleic Acids Res 35:D707-10. 2007
  8. pmc FGF: a web tool for Fishing Gene Family in a whole genome database
    Hongkun Zheng
    Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
    Nucleic Acids Res 35:W121-5. 2007
  9. pmc An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis
    Lachlan J M Coin
    BGI Shenzhen, Shenzhen, 518083, China
    Bioinformatics 28:i370-i374. 2012
  10. pmc ChickVD: a sequence variation database for the chicken genome
    Jing Wang
    College of Life Sciences, Peking University, Beijing 100871, China
    Nucleic Acids Res 33:D438-41. 2005

Collaborators

  • Jun Yu
  • Xiuqing Zhang
  • Wen Wang
  • Yingrui Li
  • Huanming Yang
  • Ruiqiang Li
  • Karsten Kristiansen
  • Songgang Li
  • Lars Bolund
  • Guojie Zhang
  • Xun Xu
  • Rasmus Nielsen
  • Xiaodong Fang
  • Gane Ka Shu Wong
  • Heng Li
  • Chang Yu
  • Geng Tian
  • Dong Li
  • Xiao Liu
  • Jun Li
  • Jue Ruan
  • Yong Zhang
  • Ruibang Luo
  • Qingyou Xia
  • Hancheng Zheng
  • Xin Li
  • Shengting Li
  • Hui Jiang
  • Chen Ye
  • Honglong Wu
  • Peixiang Ni
  • Junjie Qin
  • Wei Fan
  • Ning Li
  • Deyin Hou
  • Shancen Zhao
  • Xin Liu
  • Weiming He
  • Yan Zhou
  • Yiran Guo
  • Bo Wang
  • Guangwu Guo
  • Jingxiang Li
  • Tao Jiang
  • Hongmei Zhu
  • Zhaokun Luan
  • Hongkun Zheng
  • Yong Tao
  • Yang Dong
  • Shengkai Pan
  • Fang Chen
  • Zhiming Cai
  • Binghang Liu
  • Hui Xiang
  • Xiaosen Guo
  • Renhua Wu
  • Anders Albrechtsen
  • Haojing Shao
  • Zhonghuai Xiang
  • Quan Chen
  • Bo Li
  • XueDa Hu
  • Xin Jin
  • Hongzhi Cao
  • Jing Zhao
  • Qibin Li
  • Huisong Zheng
  • Jie Chen
  • Lijia Ma
  • Søren Brunak
  • Tao Liu
  • Chi Zhang
  • Søren Vang
  • Aifa Tang
  • Jiumeng Min
  • Xiaojuan Sun
  • Lachlan J M Coin
  • Zesong Li
  • Gengyun Zhang
  • Anders Krogh
  • Ningjia He
  • Jia Ye
  • Yaoting Gui
  • Thorfinn Korneliussen
  • Qingle Cai
  • Zhang Zhang
  • Quanfei Huang
  • Torben Hansen
  • Oluf Pedersen
  • Mingzhi Ye

Detail Information

Publications154 found, 100 shown here

  1. pmc WEGO: a web tool for plotting GO annotations
    Jia Ye
    James D Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310008, China
    Nucleic Acids Res 34:W293-7. 2006
    ..genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at wego@genomics.org.cn...
  2. 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...
  3. 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...
  4. 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...
  5. pmc PigGIS: Pig Genomic Informatics System
    Jue Ruan
    Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
    Nucleic Acids Res 35:D654-7. 2007
    ..We have also recovered 18 700 SNPs and 20 800 unique 60mer oligonucleotide probes for future pig genome analyses. PigGIS can be freely accessed via the web at http://www.piggis.org/ and http://pig.genomics.org.cn/...
  6. pmc The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
    Xun Xu
    BGI Shenzhen, Shenzhen, People s Republic of China
    Nat Biotechnol 29:735-41. 2011
    ..We discuss how the availability of this genome sequence may facilitate genome-scale science for the optimization of biopharmaceutical protein production...
  7. pmc Snap: an integrated SNP annotation platform
    Shengting Li
    The Institute of Human Genetics, University of Aarhus, DK 8000 Aarhus C, Denmark
    Nucleic Acids Res 35:D707-10. 2007
    ..Snap is available at http://snap.humgen.au.dk/ and at http://snap.genomics.org.cn/...
  8. pmc FGF: a web tool for Fishing Gene Family in a whole genome database
    Hongkun Zheng
    Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
    Nucleic Acids Res 35:W121-5. 2007
    ..It is particularly useful to identify pseudogenes and detect changes in gene structure. FGF is freely available on a web server at http://fgf.genomics.org.cn/..
  9. pmc An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis
    Lachlan J M Coin
    BGI Shenzhen, Shenzhen, 518083, China
    Bioinformatics 28:i370-i374. 2012
    ..Exome sequencing is now widely being applied to case-control cohorts and presents an exciting opportunity to look for common CNVs associated with disease...
  10. pmc ChickVD: a sequence variation database for the chicken genome
    Jing Wang
    College of Life Sciences, Peking University, Beijing 100871, China
    Nucleic Acids Res 33:D438-41. 2005
    ..Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn...
  11. pmc Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii
    Inge Seim
    1 Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA 2 Department of Bioinspired Science, Ewha Womans University, Seoul 120 750, South Korea 3
    Nat Commun 4:2212. 2013
    ....
  12. pmc Draft genome sequence of the mulberry tree Morus notabilis
    Ningjia He
    State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
    Nat Commun 4:2445. 2013
    ..The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants...
  13. 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...
  14. 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
    ....
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. 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)...
  21. doi 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. doi 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...
  34. 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...
  35. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  36. ncbi 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
  37. ncbi 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...
  38. 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...
  39. 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...
  40. pmc ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun
    Ruiqiang Li
    James D Watson Institute of Genome Sciences of Zhejiang University, Hangzhou, China
    PLoS Comput Biol 1:e43. 2005
    ..Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences...
  41. pmc SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology
    Jun Duan
    The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, China
    Nucleic Acids Res 38:D453-6. 2010
    ..Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently. SilkDB is publicly available at the new URL of http://www.silkdb.org...
  42. 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
    ....
  43. ncbi Evolution and variation of the SARS-CoV genome
    Jianfei Hu
    College of Life Sciences, Peking University, Beijing 100871, China
    Genomics Proteomics Bioinformatics 1:216-25. 2003
    ..Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us...
  44. 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...
  45. doi Role of melanin-concentrating hormone in the nucleus accumbens shell in rats behaviourally sensitized to methamphetamine
    Li Li Sun
    National Institute on Drug Dependence, Peking University, B38 Xue Yuan Road, Haidian, Beijing, China
    Int J Neuropsychopharmacol 16:1767-80. 2013
    ..Our study suggests that MCH might be a potential target for the treatment of Meth addiction. ..
  46. pmc Rice-Map: a new-generation rice genome browser
    Jun Wang
    Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China
    BMC Genomics 12:165. 2011
    ..Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively...
  47. 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...
  48. ncbi 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...
  49. pmc Nanotoxicity comparison of four amphiphilic polymeric micelles with similar hydrophilic or hydrophobic structure
    Bo Zhao
    State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
    Part Fibre Toxicol 10:47. 2013
    ..Nanocarriers represent an attractive means of drug delivery, but their biosafety must be established before their use in clinical research...
  50. doi 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...
  51. 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...
  52. pmc TreeFam: 2008 Update
    Jue Ruan
    Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
    Nucleic Acids Res 36:D735-40. 2008
    ..The user interface for viewing phylogenetic trees and family information has been improved. Furthermore, a new perl API lets users easily extract data from the TreeFam mysql database...
  53. pmc The Genomes of Oryza sativa: a history of duplications
    Jun Yu
    Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, China
    PLoS Biol 3:e38. 2005
    ..More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family...
  54. 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...
  55. 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...
  56. pmc TreeFam: a curated database of phylogenetic trees of animal gene families
    Heng Li
    Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China
    Nucleic Acids Res 34:D572-80. 2006
    ..TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn...
  57. 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...
  58. ncbi 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...
  59. pmc BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
    Wenming Zhao
    Beijing Genomics Institute BGI, Chinese Academy of Sciences CAS, Beijing Airport Industrial Zone B6, Beijing 101300, China
    Nucleic Acids Res 32:D377-82. 2004
    ..Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/)...
  60. doi Comparative analysis of intermuscular bones in fish of different ploidies
    Ling Li
    Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China
    Sci China Life Sci 56:341-50. 2013
    ..Additionally, IRCC and ITCC had fewer intermuscular bones than WCC. Our observations are significant in both fish bone developmental biology and genetic breeding...
  61. ncbi A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts
    Lan Zhong
    College of Life Sciences, Peking University, Beijing 100871, China
    Genomics Proteomics Bioinformatics 1:43-51. 2003
    ..Thus with optimal length distribution of clone-inserts, a given genome could be assembled better at lower coverage...
  62. 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...
  63. doi 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...
  64. doi 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
    ....
  65. ncbi 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...
  66. pmc A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms
    Gane Ka Shu Wong
    Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China
    Nature 432:717-22. 2004
    ..In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases...
  67. pmc Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)
    Qingyou Xia
    Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
    Science 326:433-6. 2009
    ..These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors...
  68. doi 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...
  69. 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...
  70. ncbi 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...
  71. pmc SilkDB: a knowledgebase for silkworm biology and genomics
    Jing Wang
    College of Life Sciences, Peking University, Beijing 100871, China
    Nucleic Acids Res 33:D399-402. 2005
    ..SilkDB is publicly accessible at http://silkworm.genomics.org.cn...
  72. doi Glycogen synthase kinase 3β in the nucleus accumbens core is critical for methamphetamine-induced behavioral sensitization
    Chun Mei Xu
    National Institute on Drug Dependence, Peking University, Beijing, China
    J Neurochem 118:126-39. 2011
    ....
  73. doi 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...
  74. pmc Clonidine improved laboratory-measured decision-making performance in abstinent heroin addicts
    Xiao Li Zhang
    National Institute on Drug Dependence, Peking University, Beijing, China
    PLoS ONE 7:e29084. 2012
    ..The present study investigated the effects of clonidine, which decreased norepinephrine release through presynaptic alpha-2 receptor activation, on the impaired decision-making performance in abstinent heroin addicts...
  75. doi Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor
    Xun Xu
    BGI Shenzhen, Shenzhen, China
    Cell 148:886-95. 2012
    ....
  76. ncbi 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...
  77. ncbi [Clinical analysis of thoracoscopic lobectomy: a report of 40 cases]
    Yun Li
    Department of Thoracic Surgery, People s Hospital, Peking University, Beijing 100044, China
    Zhonghua Wai Ke Za Zhi 46:405-7. 2008
    ..To review the technology of completely thoracoscopic lobectomy procedures...
  78. 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...
  79. doi 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...
  80. ncbi 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...
  81. doi 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...
  82. 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...
  83. pmc ABrowse--a customizable next-generation genome browser framework
    Lei Kong
    College of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, Peking University, Beijing, 100871, P R China
    BMC Bioinformatics 13:2. 2012
    ..Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects...
  84. 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. ..
  85. ncbi 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...
  86. doi 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...
  87. 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...
  88. ncbi 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...
  89. 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...
  90. 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...
  91. pmc 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...
  92. ncbi 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...
  93. 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
    ....
  94. doi 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...
  95. doi 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...
  96. ncbi 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
    ....
  97. ncbi 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...
  98. ncbi 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)...
  99. doi 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...
  100. doi 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...
  101. ncbi 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...