Research Topics
Genomes and Genes | Jun YuSummaryAffiliation: Chinese Academy of Sciences Country: China Publications
| Collaborators
|
Detail Information
Publications
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tagsJan 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...- Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE dataShuhui 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.... - Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencingRasmus 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... - The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradationQi 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... - A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidaePeng 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.... - Transcriptome analysis of Deinagkistrodon acutus venomous gland focusing on cellular structure and functional aspects using expressed sequence tagsBing 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?.. - 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... - Computing Ka and Ks with a consideration of unequal transitional substitutionsZhang Zhang
Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
BMC Evol Biol 6:44. 2006.... - A content-centric organization of the genetic codeJun 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... - Genome biology: the second modern synthesisJun Yu
Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
Genomics Proteomics Bioinformatics 3:3-4. 2005 - The Genomes of Oryza sativa: a history of duplicationsJun 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... - A comprehensive crop genome research project: the Superhybrid Rice Genome Project in ChinaJun 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... - Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental linesXiaomeng 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.... - Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental linesWeiwei Wang
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Proteomics 8:4808-21. 2008.... - 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... - Evolutionary transients in the rice transcriptomeJun 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... - Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functionsJiabin 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... - HRGD: a database for mining potential heterosis-related genes in plantsShuhui 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/ ... - Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer lineHuitao 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... - A discovery of novel microRNAs in the silkworm (Bombyx mori) genomeXiaomin Yu
Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
Genomics 94:438-44. 2009.... - Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineageJun 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... - Diverse LEA (late embryogenesis abundant) and LEA-like genes and their responses to hypersaline stress in post-diapause embryonic development of Artemia franciscanaGang 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... - BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomicsWenming 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/)... - [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... - Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivarsJingyue 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... - A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plantsPeng 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.... - The most redundant sequences in human CpG island library are derived from mitochondrial genomeXimiao 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... - A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencingPeng 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... - A comparison of rice chloroplast genomesJiabin 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... - KaKs_Calculator: calculating Ka and Ks through model selection and model averagingZhang 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... - Discovery, identification and comparative analysis of non-specific lipid transfer protein (nsLtp) family in SolanaceaeWanfei 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.... - 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... - The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expressionPeng 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... - Phylogenetic analysis of brine shrimp (Artemia) in China using DNA barcodingWeiwei 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.... - Genome organization of the SARS-CoVJing 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... - A transcriptomic analysis of superhybrid rice LYP9 and its parentsGang 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... - Comparing the whole-genome-shotgun and map-based sequences of the rice genomeJun 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... - Allele frequencies of mitochondrial D-loop (CA)n repeat polymorphism in six Chinese ethnic groupsJiangwei 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... - Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genesDapeng 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... - Hydroxyurea-induced global transcriptional suppression in mouse ES cellsPeng 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... - Origin and evolution of new exons in rodentsWen 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... - 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... - 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... - A novel role for minimal introns: routing mRNAs to the cytosolJiang 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... - Sequence signatures of nucleosome positioning in Caenorhabditis elegansKaifu 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.... - A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscanaWie 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... - Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomesHongzhu 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... - A systematic survey of mini-proteins in bacteria and archaeaFengyu 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... - Screening and assessing 11 Mycobacterium tuberculosis proteins as potential serodiagnostical markers for discriminating TB patients from BCG vaccineesGuoqiang 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... - The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowering plants: a genome-wide investigation of indica riceXiangjun 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... - Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus researchSuhua 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... - The study of neighboring nucleotide composition and transition/transversion biasHui 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... - Evaluation of six methods for estimating synonymous and nonsynonymous substitution ratesZhang 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... - The next-generation sequencing technology and applicationXiaoguang 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... - Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoformsJingui 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... - A genetic variation map for chicken with 2.8 million single-nucleotide polymorphismsGane 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... - Genetic analysis of 15 STR loci on Chinese Tibetan in Qinghai ProvinceJiangwei 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... - A novel DNA sequence periodicity decodes nucleosome positioningKaifu 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... - 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.... - A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposasesQingshu 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... - A scenario on the stepwise evolution of the genetic codeJing 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... - An evolutionary analysis of trypanosomatid GP63 proteasesLina 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... - Neighboring-nucleotide effects on the mutation patterns of the rice genomeHui 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... - A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolatesChen Chen
Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China
PLoS ONE 2:e315. 2007..However, the molecular mechanisms underlying STSS are poorly understood... - A novel mechanism of epigenetic regulation: nucleosome-space occupancyPeng 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... - On the nature of human housekeeping genesJiang 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... - Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution ratesDa 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.... - Human functional genetic studies are biased against the medically most relevant primate-specific genesLili 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... - Inactivated SARS-CoV vaccine prepared from whole virus induces a high level of neutralizing antibodies in BALB/c miceLin Tang
Beijing Genomics Institute, Chinese Academy of Sciences, People s Republic of China
DNA Cell Biol 23:391-4. 2004.... - A brief review on the mechanisms of miRNA regulationYimei 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.... - The analysis of large-scale gene expression correlated to the phase changes of the migratory locustLe 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... - GC content variability of eubacteria is governed by the pol III alpha subunitXiaoqian 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... - Modeling transcriptome based on transcript-sampling dataJiang 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?.. - Genomic organization, transcript variants and comparative analysis of the human nucleoporin 155 (NUP155) geneXiuqing 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... - Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genomeYan 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... - Mutations at 17 STR loci in Chinese populationJiangwei 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... - RePS: a sequence assembler that masks exact repeats identified from the shotgun dataJun 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... - The next-generation sequencing technology: a technology review and future perspectiveXiaoguang 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... - The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stagesXiaomin 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... - Detection of HPV-2 and identification of novel mutations by whole genome sequencing from biopsies of two patients with multiple cutaneous hornsWei 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... - KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategiesDapeng 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/... - Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparisonChengdao 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... - A genome-wide microsatellite polymorphism database for the indica and japonica riceZhonghua Zhang
James D Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
DNA Res 14:37-45. 2007..Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR... - DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptationDongsheng Zhou
Laboratory of Analytical Microbiology, National Centre for Biomedical Analysis, Army Center for Microbial Detection and Research, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
J Bacteriol 186:5138-46. 2004..Our data strongly support that the modern plague originated from Yunnan Province in China, due to the arising of biovar orientalis from biovar antiqua rather than mediaevalis... - A population threshold for functional polymorphismsGane Ka Shu Wong
University of Washington Genome Center, Department of Medicine, Seattle, Washington 98195, USA
Genome Res 13:1873-9. 2003..population-specific functional polymorphisms, and (4). adaptive variants that are accumulating in the population as a response to the dramatic environmental changes of the last 7000 approximately 17000 years... - Compositional gradients in Gramineae genesGane 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... - Identification and characterization of simple sequence repeats in the genomes of Shigella speciesJian Yang
Laboratory of Bioinformatics, Institute of Biophysics, CAS, Datun Road 15, Chaoyang District, 100101 Beijing, China
Gene 322:85-92. 2003..Hence, SSRs may serve as genotyping markers for epidemiological investigations, and may offer insights into evolutionary adaptation of the pathogens... - The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeastsPatrick 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... - A complete sequence of the T. tengcongensis genomeQiyu 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... - A draft sequence for the genome of the domesticated silkworm (Bombyx mori)Qingyou Xia
Southwest Agricultural University, Chongqing Beibei, 400716, China
Science 306:1937-40. 2004..Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content... - The DNA sequence, annotation and analysis of human chromosome 3Donna M Muzny
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
Nature 440:1194-8. 2006.... - Preliminary DNA identification for the tsunami victims in ThailandYa Jun Deng
The Key Laboratory of the Ministry of Health for Forensic Sciences, Xi'an Jiaotong University, Xi'an 710061, China
Genomics Proteomics Bioinformatics 3:143-57. 2005..Our results provide valuable evidence and protocols for the future forensic practice... - A comparative gene expression profile of the whole eye from human, mouse, and guinea pigXiangtian Zhou
School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical College, Wenzhou, Zhejiang, China
Mol Vis 13:2214-21. 2007..To characterize and compare gene expression patterns of the whole eyeball among human, mouse, and guinea pig based on expressed sequence tags (ESTs)... - Revisiting the molecular evolutionary history of Shigella sppJian Yang
State Key Laboratory for Molecular Virology and Genetic Engineering, 6 Rongjing East Street, BDA Beijing 100176, PR China
J Mol Evol 64:71-9. 2007..coli multiple times during a prolonged period of time, resulting in Shigella species with diverse genomes but similar pathogenic properties... - Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3Fengping 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... - Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: implications for uroplakin structure and functionAntonio Garcia-Espana
Unitat de Recerca, University Hospital Joan XXIII, Universitat Rovira i Virgili, 46007 Tarragona, Spain
Mol Phylogenet Evol 41:355-67. 2006..The structure and function of uroplakins, which are also expressed in Xenopus kidney, oocytes and fat body, are much more versatile than hitherto appreciated... - Bioinformatics in China: a personal perspectiveLiping Wei
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, People's Republic of China
PLoS Comput Biol 4:e1000020. 2008 - The rice mitochondrial genomes and their variationsXiangjun Tian
James D. Watson Institute of Genome Sciences, Zhejiang University and Hangzhou Genomics Institute, Zhejiang Provincial Key Laboratory of Genomic Bioinformatics, Hangzhou 310008, China
Plant Physiol 140:401-10. 2006..09% for indels, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago... - ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgunRuiqiang 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... - What are you going to conquer with the spear?Jun Yu
Genomics Proteomics Bioinformatics 3:1-2. 2005 - Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysisYujun Han
College of Life Sciences, Peking University, Beijing 100871, China
Sci China C Life Sci 48:300-6. 2005..With the increasing number of organisms being sequenced, we believe that DB data will play an important role both in other assembly procedures and in future genomic studies...