Jun Yu

Summary

Country: China

Publications

  1. pmc Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P R China Stem Cell Laboratory, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Nucleic Acids Res 43:D990-5. 2015
  2. pmc MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori
    Jisheng Li
    College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou 310058, P, R, China
    BMC Genomics 15:410. 2014
  3. pmc The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
    Nucleic Acids Res 41:D1199-205. 2013
  4. 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
  5. 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
  6. pmc Functional networking of human divergently paired genes (DPGs)
    Bin Xie
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
    PLoS ONE 8:e78896. 2013
  7. pmc LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
    Evol Bioinform Online 8:39-46. 2012
  8. pmc Both size and GC-content of minimal introns are selected in human populations
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People s Republic of China
    PLoS ONE 6:e17945. 2011
  9. pmc PGAP: pan-genomes analysis pipeline
    Yongbing Zhao
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, People s Republic of China
    Bioinformatics 28:416-8. 2012
  10. pmc A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome
    Yongjun Fang
    Joint Center for Genomics Research JCGR, King Abdulaziz City for Science and Technology KACST and Chinese Academy of Sciences CAS, Riyadh, Kingdom of Saudi Arabia
    PLoS ONE 7:e37164. 2012

Collaborators

  • Songnian Hu
  • Zhang Zhang
  • Peng Cui
  • Jian Wang
  • Qiang Lin
  • Jingfa Xiao
  • Feng Ding
  • Jiayan Wu
  • Dapeng Wang
  • Shuhui Song
  • Jingui Zhu
  • Xiaomeng Ge
  • Jun Li
  • Xiaowei Zhang
  • Gang Wu
  • Yimei Cai
  • Wei Gong
  • Tongwu Zhang
  • Xumin Wang
  • Weiwei Wang
  • Huanming Yang
  • Linlin Pan
  • Lina Ma
  • Yongjun Fang
  • Chengqi Xin
  • Hao Wu
  • Wanfei Liu
  • Guiming Liu
  • Xiaoguang Zhou
  • Qingshu Meng
  • Kaifu Chen
  • Yuanyuan Zhou
  • Yongbing Zhao
  • Qibin Luo
  • Yuxin Yin
  • Xiaomin Yu
  • Xiaoguang Yu
  • Lufeng Ren
  • Hangxiao Zhang
  • Bing Zhang
  • Ibrahim S Al-Mssallem
  • Lei Wang
  • Jiangwei Yan
  • Feng Zhang
  • Chen Chen
  • Yude Yu
  • Yuntao Li
  • Ming Yang
  • Zhenqing Ye
  • Yunchao Ling
  • Jiabin Tang
  • Gaoyuan Sun
  • Weijing Han
  • Kan Liu
  • Yong Biao Zhang
  • Lina Yuan
  • Fei Liu
  • Xiaomei Tong
  • Mengliang Cao
  • Xin Li
  • Hongzhu Qu
  • Lili Hao
  • Yan Li
  • Petrus Tang
  • Yingfeng Luo
  • Hongbin Lin
  • Guoqiang Zhang
  • Fengyu Wang
  • Qing Zhou
  • Gane Ka Shu Wong
  • An Yin
  • Wei Wang
  • Yong Chen
  • Wei Xu
  • Lihuang Zhu
  • Yuli Li
  • Shu Qing Xu
  • Hongxing Lei
  • An Li
  • Junhui Yang
  • Siqi Liu
  • Meili Chen
  • Xiaonuan Li
  • Yong Duan
  • Wei Yan
  • Guangchun Han
  • Bin Xie
  • Dan Yu
  • Ruiqiang Li
  • Mohammed M Ba Abdullah

Detail Information

Publications143 found, 100 shown here

  1. pmc Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P R China Stem Cell Laboratory, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Nucleic Acids Res 43:D990-5. 2015
    ..We hope that Plastid-LCGbase facilitates gene variation (insertion-deletion, translocation and rearrangement) and transcription-level studies of plastid genomes. ..
  2. pmc MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori
    Jisheng Li
    College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou 310058, P, R, China
    BMC Genomics 15:410. 2014
    ..The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production...
  3. pmc The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
    Nucleic Acids Res 41:D1199-205. 2013
    ....
  4. 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...
  5. 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...
  6. pmc Functional networking of human divergently paired genes (DPGs)
    Bin Xie
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
    PLoS ONE 8:e78896. 2013
    ..Based on analyses of disease transcriptome data, we further suggest that this particular module may play crucial roles in HIV infection and its disease mechanism. ..
  7. pmc LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
    Evol Bioinform Online 8:39-46. 2012
    ..LCGbase is freely available at http://lcgbase.big.ac.cn/LCGbase...
  8. pmc Both size and GC-content of minimal introns are selected in human populations
    Dapeng Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People s Republic of China
    PLoS ONE 6:e17945. 2011
    ..Here we analyzed re-sequenced 179 individual genomes (from African, European, and Asian populations) from the data released by the 1000 Genome Project to study the size dynamics of minimal introns...
  9. pmc PGAP: pan-genomes analysis pipeline
    Yongbing Zhao
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, People s Republic of China
    Bioinformatics 28:416-8. 2012
    ..PGAP's performance has been evaluated on 11 Streptococcus pyogenes strains...
  10. pmc A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome
    Yongjun Fang
    Joint Center for Genomics Research JCGR, King Abdulaziz City for Science and Technology KACST and Chinese Academy of Sciences CAS, Riyadh, Kingdom of Saudi Arabia
    PLoS ONE 7:e37164. 2012
    ..In addition, consistent with previous discoveries, there are three co-transcribed gene clusters-18S-5S rRNA, rps3-rpl16 and nad3-rps12-in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms...
  11. pmc On the origin of Tibetans and their genetic basis in adapting high-altitude environments
    Binbin Wang
    National Research Institute for Family Planning, Beijing, People s Republic of China
    PLoS ONE 6:e17002. 2011
    ..Most of these genes were highly correlated with population-specific and beneficial phenotypes, such as high infant survival rate and the absence of chronic mountain sickness...
  12. pmc VCGDB: a dynamic genome database of the Chinese population
    Yunchao Ling
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
    BMC Genomics 15:265. 2014
    ..The currently available human reference genome (GRCh37) is based on sequencing data from 13 anonymous Caucasian volunteers, which might limit the scope of genomics, transcriptomics, epigenetics, and genome wide association studies...
  13. pmc A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor
    An Li
    Institute of Nuclear and New Energy Technology, Tsinghua University, Tsinghua Garden, Haidian District, 100084, Beijing, China
    Biotechnol Biofuels 6:3. 2013
    ..The next-generation high-throughput pyrosequencing platform (Roche/454 GS FLX Titanium) provides a powerful tool for the discovery of novel microbes within the biogas-generating microbial communities...
  14. pmc Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb
    Yuan Yuan
    Beijing Key Laboratory of Functional Genomics for Dao di Herbs, Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
    BMC Genomics 13:195. 2012
    ..Here, we analyzed the transcriptomes and metabolic pathways to evaluate the active medicinal compounds in FLJ and hope that this approach can be used for a variety of medicinal herbs in the future...
  15. pmc Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
    Zhang Zhang
    Computational Bioscience Research Center CBRC, King Abdullah Universitof Science and Technology KAUST, Thuwal 23955 6900, Kingdom of Saudi Arabia
    BMC Bioinformatics 13:43. 2012
    ..However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis...
  16. pmc Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes
    Anding Zhang
    State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
    BMC Genomics 12:523. 2011
    ..Therefore, characterization of genomic features of other serotypes will be required to better understand their virulence potential and phylogenetic relationships among different serotypes...
  17. pmc An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform
    Tongwu Zhang
    Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Plant Methods 7:38. 2011
    ..We also present information and a minimal sequence dataset as a reference for the assembly of other plant organellar genomes...
  18. 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
    ....
  19. pmc Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.)
    Guangyu Zhang
    Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Riyadh, Kingdom of Saudi Arabia
    Plant Mol Biol 79:521-36. 2012
    ..3 % (47,048) of the P. dactylifera gene models are shared with rice, sorghum, Arabidopsis, and grapevine, respectively. We also assigned our gene models into house-keeping and tissue-specific genes based on their tissue specificity...
  20. 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
    ....
  21. 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...
  22. 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...
  23. pmc 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...
  24. 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...
  25. 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...
  26. pmc 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...
  27. 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...
  28. pmc Maternal transmission effect of a PDGF-C SNP on nonsyndromic cleft lip with or without palate from a Chinese population
    Di Wu
    Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People s Republic of China
    PLoS ONE 7:e46477. 2012
    ..Our findings support the involvement of PDGF-C in the development of oral clefts; moreover, the UPD case report contributes to the collective knowledge of rare variants in the human genome...
  29. 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
    ....
  30. doi request reprint Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum
    Qibin Luo
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
    J Genet Genomics 35:349-55. 2008
    ..A hypothetical feedback model has been proposed based on the analysis of the relationship between intronic miRNAs and their host genes in the development of red flour beetle...
  31. 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...
  32. 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...
  33. pmc 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. 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...
  35. 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...
  36. pmc 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...
  37. 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/ ...
  38. pmc PanGP: a tool for quickly analyzing bacterial pan-genome profile
    Yongbing Zhao
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, People s Republic of China and University of Chinese Academy of Sciences, Beijing 100049, People s Republic of China
    Bioinformatics 30:1297-9. 2014
    ..The performance of these two algorithms have been evaluated on four bacteria populations with strain numbers varying from 30 to 200, and the DG algorithm exhibited overwhelming advantage on accuracy and stability than the TR algorithm...
  39. 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...
  40. 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...
  41. 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...
  42. 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...
  43. ncbi request reprint Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs
    Jun Wang
    James D Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310007, China
    Nature 431:1 p following 757; discussion following 757. 2004
  44. 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...
  45. 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
    ....
  46. doi request reprint A pangenomic study of Bacillus thuringiensis
    Yongjun Fang
    James D Watson Institute of Genome Sciences, College of Life Science, Zhejiang University, Hangzhou 310058, China
    J Genet Genomics 38:567-76. 2011
    ..3-2.8Mb and 5.0-5.6Mb. We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed, are very useful for pangenomic studies...
  47. pmc Homeobox D10 gene, a candidate tumor suppressor, is downregulated through promoter hypermethylation and associated with gastric carcinogenesis
    Liangjing Wang
    Laboratory of Digestive Disease, Sir Run Run Shaw Clinical Medicine Institution of Zhejiang University, Hangzhou, China
    Mol Med 18:389-400. 2012
    ..Taken together, our results suggest that HoxD10 functions as a candidate tumor suppressor in gastric cancer, which is inactivated through promoter hypermethylation...
  48. pmc Ribogenomics: the science and knowledge of RNA
    Jiayan Wu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
    Genomics Proteomics Bioinformatics 12:57-63. 2014
    ....
  49. 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...
  50. pmc High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.)
    Yuxin Yin
    Joint Center for Genomics Research JCGR, King Abdulaziz City for Science and Technology KACST and Chinese Academy of Sciences CAS, Riyadh, Kingdom of Saudi Arabia
    Plant Mol Biol 78:617-26. 2012
    ..Most Genes are highly expressed in early stages of development, while late developmental stages are critical for fruit ripening including most of the metabolism associated ones...
  51. 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...
  52. pmc 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
    ....
  53. 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...
  54. 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...
  55. pmc 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...
  56. pmc 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...
  57. 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...
  58. pmc 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
    ....
  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 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...
  61. 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...
  62. 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...
  63. pmc RiceWiki: a wiki-based database for community curation of rice genes
    Zhang Zhang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China, School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
    Nucleic Acids Res 42:D1222-8. 2014
    ....
  64. 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...
  65. pmc 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
    ....
  66. pmc Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630
    Yong Chen
    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST Department of Automation, Tsinghua University, Beijing 100084, China, University of the Chinese Academy of Sciences, Beijing 100049, China, Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Department of Histology and Embryology, University of South China, Hengyang Hunan Province 421001, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, School of Applied Mathematics, Central University of Finance and Economics, Beijing 102206, China, Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Dallas, TX 75083 0688, USA, Institut fur Molekulare Mikrobiologie und Biotechnologie, Westfalische Wilhelms Universitat, Corrensstrasse 3, D 48149 Munster, Germany, Environmental Sciences Department, King Abdulaziz University, Jeddah 21589, Germany
    Nucleic Acids Res 42:1052-64. 2014
    ..Our omics studies provide not only a first integrated omics study of prokaryotic LD organelle, but also a systematic platform for facilitating further prokaryotic LD research and biofuel development. ..
  67. 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...
  68. pmc 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
    ....
  69. 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...
  70. 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...
  71. pmc Transcriptome analysis of skin photoaging in chinese females reveals the involvement of skin homeostasis and metabolic changes
    Wei Yan
    Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
    PLoS ONE 8:e61946. 2013
    ..Photoaging is cumulative damage to skin, caused by chronic, repeated solar radiation exposure. Its molecular mechanisms are poorly understood at the level of global gene expression...
  72. pmc 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...
  73. doi request reprint Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle
    Yuanyuan Zhou
    Beijing Key Laboratory of Genome and Precision Medicine Technologies, CAS Key Laboratory of Genome Sciences and Information, Beijing, China
    Sci China Life Sci 57:340-55. 2014
    ....
  74. pmc 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...
  75. 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...
  76. 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...
  77. pmc On the molecular mechanism of GC content variation among eubacterial genomes
    Hao Wu
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310007, China
    Biol Direct 7:2. 2012
    ..Consequently, an in-depth analysis was conducted to evaluate various potential intrinsic and extrinsic factors in association with GC content variation among eubacterial genomes...
  78. pmc 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...
  79. ncbi request reprint Gene expression profiling in porcine mammary gland during lactation and identification of breed- and developmental-stage-specific genes
    Zhixi Su
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
    Sci China C Life Sci 49:26-36. 2006
    ..The unknown EST sequences and expression profiles at different developmental stages and breeds are very important resources for further research...
  80. pmc SARS-associated coronavirus transmitted from human to pig
    Weijun Chen
    Chinese Academy of Sciences, Beijing, China 101300
    Emerg Infect Dis 11:446-8. 2005
    ..Sequence and epidemiology analyses suggested that the pig was infected by a SARS-CoV of human origin...
  81. 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...
  82. 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...
  83. pmc 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...
  84. doi request reprint Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus
    Guiming Liu
    James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
    Mol Biol Rep 37:3575-81. 2010
    ....
  85. 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
    ....
  86. 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...
  87. pmc 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
    ....
  88. 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...
  89. 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...
  90. doi request reprint Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis
    An Yin
    Joint Center for Genomics Research JCGR, King Abdulaziz City for Science and Technology KACST and Chinese Academy of Sciences CAS, Riyadh, Kingdom of Saudi Arabia CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
    Insect Sci 22:65-82. 2015
    ....
  91. 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...
  92. 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...
  93. pmc 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...
  94. pmc Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development
    Wei Xu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
    Genomics Proteomics Bioinformatics 12:111-9. 2014
    ..Our results from the present study may shed light on the molecular mechanism underlying the postnatal development of the mammalian cerebrum...
  95. pmc 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...
  96. 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
    ....
  97. 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
    ....
  98. 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...
  99. 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...
  100. 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?..
  101. pmc 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...