Jun Yu

Summary

Affiliation: Chinese Academy of Sciences
Country: China

Publications

  1. 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
  2. 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
  3. pmc The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation
    Qi Long Qin
    State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
    BMC Genomics 11:247. 2010
  4. pmc A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidae
    Peng Cui
    Key Laboratory of Dairy Biotechnology and Engineering Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
    BMC Genomics 8:241. 2007
  5. pmc Transcriptome analysis of Deinagkistrodon acutus venomous gland focusing on cellular structure and functional aspects using expressed sequence tags
    Bing Zhang
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
    BMC Genomics 7:152. 2006
  6. pmc A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China
    Jun Yu
    Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, People s Republic of China
    Philos Trans R Soc Lond B Biol Sci 362:1023-34. 2007
  7. ncbi request reprint Genome biology: the second modern synthesis
    Jun Yu
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 3:3-4. 2005
  8. 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
  9. ncbi request reprint A content-centric organization of the genetic code
    Jun Yu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 5:1-6. 2007
  10. pmc Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines
    Xiaomeng Ge
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, PR China
    BMC Plant Biol 8:114. 2008

Collaborators

  • Songnian Hu
  • Jingui Zhu
  • Jian Wang
  • Peng Cui
  • Zhang Zhang
  • Feng Ding
  • Gane Ka Shu Wong
  • Shuhui Song
  • Jun Li
  • Xiaomeng Ge
  • Huanming Yang
  • Weiwei Wang
  • Xiaomin Yu
  • Yimei Cai
  • Bing Zhang
  • Gang Wu
  • Lina Ma
  • Dapeng Wang
  • Kaifu Chen
  • Jiangwei Yan
  • Xiuqing Zhang
  • Fei Liu
  • Tongwu Zhang
  • Qingshu Meng
  • Chen Chen
  • Wei Dong
  • Jianfei Hu
  • Hangxiao Zhang
  • Songgang Li
  • Wanfei Liu
  • Linlin Pan
  • Xiaoguang Zhou
  • Qing Zhou
  • Qibin Luo
  • Ruiqiang Li
  • Bin Liu
  • Jian Yang
  • Jiabin Tang
  • Yujun Han
  • Jia Ye
  • Xiaoqian Zhao
  • Xiangjun Tian
  • Jing Sun
  • Qiang Lin
  • Hao Wu
  • Chengqi Xin
  • Mengliang Cao
  • Xiaomei Tong
  • Hui Zhao
  • Hongzhu Qu
  • Lili Hao
  • Yingfeng Luo
  • Wei Li
  • Peixiang Ni
  • Guoqiang Zhang
  • Jingyue Bao
  • Fengyu Wang
  • Ximiao He
  • Yan Zhou
  • Haibo Sun
  • Jing Liu
  • Wei Wang
  • Liping Wei
  • Jan Gorodkin
  • Lihuang Zhu
  • Rasmus Wernersson
  • Xiaowei Zhang
  • Siqi Liu
  • Wei Gong
  • Shu Qing Xu
  • Heng Li
  • Huan Ming Yang
  • Le Kang
  • Lars Bolund
  • Wen Wang
  • Jianguo Zhang
  • Jin Yang
  • Yong Zhang
  • Huitao Liu
  • Caixia Yu
  • Wei Hua Chen
  • Fuhong He
  • Runsheng Chen
  • Lei Wang
  • Kan Liu
  • Jiucheng Liu
  • Qi Long Qin
  • Lufeng Ren
  • Xiaoguang Zheng
  • Yuntao Li

Detail Information

Publications124 found, 100 shown here

  1. 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...
  2. 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...
  3. pmc The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation
    Qi Long Qin
    State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
    BMC Genomics 11:247. 2010
    ..This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes...
  4. pmc A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidae
    Peng Cui
    Key Laboratory of Dairy Biotechnology and Engineering Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
    BMC Genomics 8:241. 2007
    ....
  5. pmc Transcriptome analysis of Deinagkistrodon acutus venomous gland focusing on cellular structure and functional aspects using expressed sequence tags
    Bing Zhang
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
    BMC Genomics 7:152. 2006
    ..As far as the molecular mechanism of toxin secretion and metabolism is concerned, we still knew a little. Therefore, a fundamental question being arisen is what genes are expressed in the snake venom glands besides many toxin components?..
  6. pmc A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China
    Jun Yu
    Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, People s Republic of China
    Philos Trans R Soc Lond B Biol Sci 362:1023-34. 2007
    ..In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops...
  7. ncbi request reprint Genome biology: the second modern synthesis
    Jun Yu
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 3:3-4. 2005
  8. 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...
  9. ncbi request reprint A content-centric organization of the genetic code
    Jun Yu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    Genomics Proteomics Bioinformatics 5:1-6. 2007
    ..The renovated codon table is useful in predicting abundant amino acids and positioning the amino acids with related or distinct physico-chemical properties...
  10. pmc Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines
    Xiaomeng Ge
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, PR China
    BMC Plant Biol 8:114. 2008
    ....
  11. doi request reprint Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines
    Weiwei Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Proteomics 8:4808-21. 2008
    ....
  12. doi request reprint Novel microRNAs in silkworm (Bombyx mori)
    Yimei Cai
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
    Funct Integr Genomics 10:405-15. 2010
    ..Target prediction uncovers that considerable silkworm miRNAs may aim at modulating more than one hormone signaling pathway components and/or hormone biosynthesis-related proteins implying their important roles in silkworm development...
  13. doi request reprint Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis
    Peng Cui
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 10:82-93. 2012
    ..In conclusion, we present two very important findings. One is that H3K4me3 and H3K27me3 rarely occur in silent genes. The other is that bivalent domains may adopt a "winner-takes-all" principle to regulate gene expression...
  14. 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...
  15. doi request reprint The most redundant sequences in human CpG island library are derived from mitochondrial genome
    Ximiao He
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Genomics Proteomics Bioinformatics 8:81-91. 2010
    ..These results may further our understanding of how the mtDNA regulates DNA methylation in the nucleus...
  16. ncbi request reprint Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions
    Jiabin Tang
    Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
    Mol Genet Genomics 274:467-76. 2005
    ..The expression of these genes clearly reflected the unique functional characteristics of YPO. Furthermore, we estimated that there are about 10,000 mRNAs specifically expressed in rice YPO...
  17. pmc Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars
    Jingyue Bao
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Plant Physiol 138:1216-31. 2005
    ..Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice...
  18. doi request reprint Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing
    Wei Gong
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
    Sci China Life Sci 56:1-12. 2013
    ..These findings further our understanding of the molecular mechanisms that regulate testis development. Our study also demonstrates significant advantages of RNA-seq technology for studying transcriptome during development...
  19. doi request reprint A discovery of novel microRNAs in the silkworm (Bombyx mori) genome
    Xiaomin Yu
    Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
    Genomics 94:438-44. 2009
    ....
  20. doi request reprint HRGD: a database for mining potential heterosis-related genes in plants
    Shuhui Song
    Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101300, China
    Plant Mol Biol 69:255-60. 2009
    ..The HRGD data resource is publicly available at http://hrgd.genomics.org.cn/ ...
  21. 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...
  22. pmc Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line
    Huitao Liu
    The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    BMC Genomics 12:163. 2011
    ..In the present work, we describe the mitochondrial genome of a wheat K-type CMS line and compare it with its maintainer line...
  23. doi request reprint The association between H3K4me3 and antisense transcription
    Peng Cui
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 10:74-81. 2012
    ..Our results provide a novel insight into the epigenetic roles of H3K4me3 and the regulatory mechanism of antisense transcription...
  24. pmc Gene and genome parameters of mammalian liver circadian genes (LCGs)
    Gang Wu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 7:e46961. 2012
    ..Taken together, we suggest that the circadian system selects gene parameters in a cost effective way to improve tissue-specific functions by adapting temporal variations from the environment over evolutionary time scales...
  25. pmc Transposable-element associated small RNAs in Bombyx mori genome
    Yimei Cai
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 7:e36599. 2012
    ..Taken together, these discoveries expand the small RNA pool in B. mori genome and lead to new knowledge on the diversity and functional significance of TE-associated small RNAs...
  26. pmc Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data
    Shuhui Song
    Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    BMC Plant Biol 7:49. 2007
    ....
  27. doi request reprint An evolutionary analysis of trypanosomatid GP63 proteases
    Lina Ma
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No 7 Beitucheng West Road, Chaoyang District, Beijing 100029, People s Republic of China
    Parasitol Res 109:1075-84. 2011
    ..These sites may contribute to the functional variations of the GP63 proteases and provide clues for vaccine development...
  28. ncbi request reprint [Complete sequence and gene organization of the Tibetan chicken mitochondrial genome]
    Xiao Mei Tong
    Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    Yi Chuan 28:769-77. 2006
    ..A possible explanation is that the ancestor of Tibetan chicken lived in a relatively isolated environment after entering into the high altitude area and developed unique genetic characters...
  29. ncbi request reprint A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plants
    Peng Cui
    The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, People s Republic of China
    J Genet 88:299-307. 2009
    ....
  30. doi request reprint Diverse LEA (late embryogenesis abundant) and LEA-like genes and their responses to hypersaline stress in post-diapause embryonic development of Artemia franciscana
    Gang Wu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Comp Biochem Physiol B Biochem Mol Biol 160:32-9. 2011
    ..This result suggested that the LEA and LEA-like genes may play different roles in resistance to hypersaline stress...
  31. 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/)...
  32. 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...
  33. doi request reprint Expression profiling of abundant genes in pulmonary and cardiac muscle tissues of Tibetan Antelope (Pantholops hodgsonii)
    Xiaomei Tong
    Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    Gene 523:187-91. 2013
    ..These data provide useful information for studying on molecular adaptation to high-altitude in humans as well as other mammals...
  34. doi request reprint The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids
    Zhang Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Genomics Proteomics Bioinformatics 10:175-80. 2012
    ....
  35. doi request reprint A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing
    Peng Cui
    The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China
    Genomics 96:259-65. 2010
    ..Finally, through comparative analyses of gene expression profiles among multiple datasets, we demonstrated that different RNA sample preparations may result in significant variations in gene expression profiles...
  36. pmc A transcriptomic analysis of superhybrid rice LYP9 and its parents
    Gang Wei
    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Proc Natl Acad Sci U S A 106:7695-701. 2009
    ..In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosis-related genes...
  37. pmc The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression
    Peng Cui
    The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 6:e23219. 2011
    ..This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types...
  38. 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...
  39. doi request reprint Phylogenetic analysis of brine shrimp (Artemia) in China using DNA barcoding
    Weiwei Wang
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 6:155-62. 2008
    ....
  40. 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...
  41. doi request reprint Discovery, identification and comparative analysis of non-specific lipid transfer protein (nsLtp) family in Solanaceae
    Wanfei Liu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 8:229-37. 2010
    ....
  42. pmc How many human genes can be defined as housekeeping with current expression data?
    Jiang Zhu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    BMC Genomics 9:172. 2008
    ..Although many studies have aimed at large-scale and thorough categorization of human HK genes, a meaningful consensus has yet to be reached...
  43. doi request reprint Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation
    Hangxiao Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    Sci China Life Sci 56:440-52. 2013
    ..We propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes...
  44. 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...
  45. ncbi request reprint The study of neighboring nucleotide composition and transition/transversion bias
    Hui Zhao
    Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100030, China
    Sci China C Life Sci 49:395-402. 2006
    ..For SNPs in O. sativa, the neighboring effect of A and T nucleotides is limited to 2 nucleotides on both sides; for SNPs in Arabidopsis, the effect extends no more than 4 nucleotides on both sides...
  46. doi request reprint An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells
    Lina Ma
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 10:326-35. 2012
    ..Differential expression of 20 manually-selected genes was further validated using qRT-PCR. Our observations may help to further our understanding of cellular mechanism(s) in the transition from immortalization to tumorigenesis...
  47. doi request reprint Does the genetic code have a eukaryotic origin?
    Zhang Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
    Genomics Proteomics Bioinformatics 11:41-55. 2013
    ..The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes...
  48. doi request reprint Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition
    Hao Wu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Genomics Proteomics Bioinformatics 10:186-96. 2012
    ....
  49. doi request reprint Distinct contributions of replication and transcription to mutation rate variation of human genomes
    Peng Cui
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 10:4-10. 2012
    ..In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes...
  50. pmc Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
    Biol Direct 6:13. 2011
    ..We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what their particular functions and evolutionary dynamics are, through comparative genomics...
  51. ncbi request reprint Comparing the whole-genome-shotgun and map-based sequences of the rice genome
    Jun Yu
    Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing 101300, China
    Trends Plant Sci 11:387-91. 2006
    ..Differences in published gene counts and polymorphism rates are similarly resolved by considering how transposable elements affect the sequence analysis...
  52. doi request reprint How do variable substitution rates influence Ka and Ks calculations?
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 7:116-27. 2009
    ..We believe that the sensitivity of our new methods has been improved than that of their original methods under diverse conditions and it is advantageous to introduce novel parameters for Ka/Ks computation...
  53. doi request reprint Hydroxyurea-induced global transcriptional suppression in mouse ES cells
    Peng Cui
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No 7 Beitucheng West Road, Chaoyang, 100029 Beijing, China
    Carcinogenesis 31:1661-8. 2010
    ..Our result provides novel clues for the understanding of how cells respond to HU and further suggests that high-throughput sequencing technology provides a powerful tool to study mechanisms of clinical drugs at the cellular level...
  54. ncbi request reprint Allele frequencies of mitochondrial D-loop (CA)n repeat polymorphism in six Chinese ethnic groups
    Jiangwei Yan
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing Airport Industrial Zone B 6, PR China
    Leg Med (Tokyo) 9:330-1. 2007
    ..A total of 542 individuals were typed. Comparative analyses between our population data and other populations gathered from the literature were performed...
  55. ncbi request reprint Genetic analysis of 15 STR loci on Chinese Tibetan in Qinghai Province
    Jiangwei Yan
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, PR China
    Forensic Sci Int 169:e3-6. 2007
    ..The forensic parameters from the data showed high values. In conclusion, the 15 STR loci are useful for forensic analysis, paternity tests for Tibetans in the region, and population genetic studies...
  56. 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...
  57. pmc BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler
    Tongwu Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    BMC Res Notes 5:567. 2012
    ..There is one commercial tool box (Newbler) developed for re-sequencing projects based on the Roche 454 sequencing platform. However, the genome with large repeat regions cannot be well assembled in Newbler...
  58. pmc LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria)
    Zongyuan Ma
    National Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
    BMC Genomics 7:11. 2006
    ..We developed the first transcriptomic database of the locust (LocustDB), building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future...
  59. doi request reprint Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes
    Hongzhu Qu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Res Microbiol 161:838-46. 2010
    ..Furthermore, strand-biased gene distribution enhances the purine-richness of LeS for DnaE3-PolC genomes and T-richness of LeS for DnaE1-DnaE1 and DnaE2-dnaE1 genomes...
  60. doi request reprint Sequence signatures of nucleosome positioning in Caenorhabditis elegans
    Kaifu Chen
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Genomics Proteomics Bioinformatics 8:92-102. 2010
    ....
  61. pmc A systematic survey of mini-proteins in bacteria and archaea
    Fengyu Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 3:e4027. 2008
    ..However, the functions of the majority of mini-proteins are still largely unknown due to the constraints of experimental methods and bioinformatic analysis...
  62. pmc A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscana
    Wie Hua Chen
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
    BMC Genomics 10:52. 2009
    ..Although previous work has accumulated ample data, the molecular mechanism underlying diapause and reactivation from it remain elusive...
  63. pmc A novel role for minimal introns: routing mRNAs to the cytosol
    Jiang Zhu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 5:e10144. 2010
    ..A remarkable fraction of vertebrate introns have a minimal size of about 100 bp, while majority of introns expand to several kilobases even megabases in length...
  64. doi request reprint Screening and assessing 11 Mycobacterium tuberculosis proteins as potential serodiagnostical markers for discriminating TB patients from BCG vaccinees
    Guoqiang Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 7:107-15. 2009
    ..Thus the approach combining comparative genomics, bioinformatics and ELISA techniques can be employed to identify new seroantigens distinguishing M. tuberculosis infection from BCG vaccination...
  65. ncbi request reprint The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowering plants: a genome-wide investigation of indica rice
    Xiangjun Tian
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    J Mol Evol 64:299-307. 2007
    ..Phylogenetic analyses of the migrated tRNA genes and their original copies suggest that intergenomic tRNA gene transfer is an ongoing process with noticeable discriminatory routes among genomes in flowering plants...
  66. pmc Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research
    Suhua Chang
    Beijing Institute of Genomics, Chinese Academy of Sciences, B 6 Airport Industrial Zone, Beijing 101300, China
    Nucleic Acids Res 35:D376-80. 2007
    ..IVDB is publicly available at http://influenza.genomics.org.cn...
  67. ncbi request reprint Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates
    Zhang Zhang
    Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
    Genomics Proteomics Bioinformatics 4:173-81. 2006
    ..We recommend that conclusions related to or derived from Ka and Ks analyses should not be readily drawn only according to results from one method...
  68. doi request reprint BIGpre: a quality assessment package for next-generation sequencing data
    Tongwu Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 9:238-44. 2011
    ..Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http://bigpre.sourceforge.net...
  69. pmc Sequence Variation and Expression Analysis of Seed Dormancy- and Germination-Associated ABA- and GA-Related Genes in Rice Cultivars
    Fei Liu
    CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
    Front Plant Sci 2:17. 2011
    ..Third, we surveyed and compared differentially expressed genes in dry seeds between 9311 and PA64s to show that these differentially expressed genes may play roles in seed dormancy and germination...
  70. pmc Computing Ka and Ks with a consideration of unequal transitional substitutions
    Zhang Zhang
    Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
    BMC Evol Biol 6:44. 2006
    ....
  71. pmc Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing
    Wanfei Liu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
    Front Genet 2:93. 2011
    ..These results define a collection of novel transcripts in the mouse genome and indicate their potential functions in the mouse tissues and cells...
  72. pmc Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoforms
    Jingui Zhu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
    BMC Genomics 10:117. 2009
    ..Tarantula has been used as a model system for studying skeletal muscle structure and function, yet data on the genes expressed in tarantula muscle are lacking...
  73. 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
    ....
  74. pmc A novel DNA sequence periodicity decodes nucleosome positioning
    Kaifu Chen
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Graduate University of Chinese Academy of Sciences, Beijing, China
    Nucleic Acids Res 36:6228-36. 2008
    ..We conclude that this novel DNA sequence periodicity is a signature of nucleosome organization suggesting that nucleosomes are well-positioned with regularity, especially near the 5'-end of transcripts...
  75. doi request reprint The next-generation sequencing technology and application
    Xiaoguang Zhou
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Protein Cell 1:520-36. 2010
    ..In this article, we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications...
  76. 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...
  77. doi request reprint A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases
    Qingshu Meng
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    J Genet Genomics 38:63-70. 2011
    ..Our results provide basic information for the understanding of the function and evolution of tvBac transposons in particular and other related transposon families in general...
  78. doi request reprint A scenario on the stepwise evolution of the genetic code
    Jing Fa Xiao
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 5:143-51. 2007
    ..This model predicts gradual replacements of RNA-made molecular mechanisms, cellular processes by proteins, and informational exploitation by DNA...
  79. doi request reprint A novel mechanism of epigenetic regulation: nucleosome-space occupancy
    Peng Cui
    The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China
    Biochem Biophys Res Commun 391:884-9. 2010
    ..We therefore proposed that nucleosome-space occupancy as a novel mechanism of epigenetic gene regulation, creating a vital environment for transcriptional activation...
  80. ncbi request reprint Neighboring-nucleotide effects on the mutation patterns of the rice genome
    Hui Zhao
    Beijing Genomics Institute, Chinese Academy of Sciences CAS, Beijing 101300, China
    Genomics Proteomics Bioinformatics 3:158-68. 2005
    ..These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications...
  81. doi request reprint On the nature of human housekeeping genes
    Jiang Zhu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Trends Genet 24:481-4. 2008
    ..Housekeeping genes primarily use CpG-dependent core promoters, whereas the majority of tissue-specific genes possess neither CpG-islands nor TATA-boxes in their core promoters...
  82. pmc A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates
    Chen Chen
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 2:e315. 2007
    ..However, the molecular mechanisms underlying STSS are poorly understood...
  83. pmc Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
    Da Peng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
    Biol Direct 4:20. 2009
    ....
  84. doi request reprint A brief review on the mechanisms of miRNA regulation
    Yimei Cai
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 7:147-54. 2009
    ....
  85. 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...
  86. pmc Human functional genetic studies are biased against the medically most relevant primate-specific genes
    Lili Hao
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China
    BMC Evol Biol 10:316. 2010
    ..Many functional, structural and evolutionary features of human genes have been observed to correlate with expression breadth and/or gene age. Here, we systematically explore these correlations...
  87. ncbi request reprint Inactivated SARS-CoV vaccine prepared from whole virus induces a high level of neutralizing antibodies in BALB/c mice
    Lin Tang
    Beijing Genomics Institute, Chinese Academy of Sciences, People s Republic of China
    DNA Cell Biol 23:391-4. 2004
    ....
  88. ncbi request reprint GC content variability of eubacteria is governed by the pol III alpha subunit
    Xiaoqian Zhao
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
    Biochem Biophys Res Commun 356:20-5. 2007
    ..Since horizontal gene transfer is very frequent among bacterial genomes, exceptions of the grouping scheme, a few percents of the total, are readily identifiable and should be excluded from in-depth analyses on nucleotide compositions...
  89. pmc Modeling transcriptome based on transcript-sampling data
    Jiang Zhu
    Chinese Academy of Sciences CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 3:e1659. 2008
    ..for different cell types (transcriptome diversity) and the distribution of their copy numbers (transcriptome dynamics)? What is the probability that a transcript with a given expression level to be detected at a certain sampling depth?..
  90. 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...
  91. 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...
  92. 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...
  93. ncbi request reprint Mutations at 17 STR loci in Chinese population
    Jiangwei Yan
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing Airport Industrial Zone B 6, Beijing, PR China
    Forensic Sci Int 162:53-4. 2006
    ..In order to enrich the reference data of STRs mutations which are valuable for forensic application, we suggest the establishment of such database and ask the whole forensic community for data contribution including China...
  94. pmc The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages
    Xiaomin Yu
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 3:e2997. 2008
    ..The Bombyx mori genome sequence provides opportunities for a thorough survey for miRNAs as well as comparative analyses with other sequenced insect species...
  95. doi request reprint The next-generation sequencing technology: a technology review and future perspective
    Xiaoguang Zhou
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Sci China Life Sci 53:44-57. 2010
    ..We also suggest that scientists from China should play an active role in this campaign that will have profound impact on both scientific research and societal healthcare systems...
  96. ncbi request reprint Detection of HPV-2 and identification of novel mutations by whole genome sequencing from biopsies of two patients with multiple cutaneous horns
    Wei Wang
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    J Clin Virol 39:34-42. 2007
    ..Human papillomavirus-2 (HPV-2) is generally associated with common warts. The association of cutaneous horns with HPV-2 infection has never been reported...
  97. doi request reprint KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Genomics Proteomics Bioinformatics 8:77-80. 2010
    ..net/projects/kakscalculator2/...
  98. ncbi request reprint Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison
    Chengdao Li
    Department of Agriculture, 3 Baron Hay Court, WA 6151, South Perth, Australia
    Funct Integr Genomics 4:84-93. 2004
    ..The wheat chromosome 4AL QTL region for seed dormancy was syntenic to both rice chromosome 3 and 11. In both cases, corresponding QTLs for seed dormancy have been mapped in rice...
  99. pmc Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3
    Fengping Wang
    Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, Xiamen, People s Republic of China
    PLoS ONE 3:e1937. 2008
    ..The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature...
  100. ncbi request reprint The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, PR China
    FEBS Lett 555:469-77. 2003
    ..Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts...
  101. pmc A complete sequence of the T. tengcongensis genome
    Qiyu Bao
    Beijing Genomics Institute Genomics and Bioinformatics Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences CAS, Beijing 100101, China
    Genome Res 12:689-700. 2002
    ..It is concluded that thermophiles are a biologically and phylogenetically divergent group of prokaryotes that have converged to sustain extreme environmental conditions over evolutionary timescale...