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...
- 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
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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...
- 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
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- 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...
- 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...
- 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...
- 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
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- Analysis of CYP3A4 genetic polymorphisms in Han Chinese
Qing Zhou
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
J Hum Genet 56:415-22. 2011
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- 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...
- 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...
- 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
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- 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
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- 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...
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
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- Systematic analysis of alternative first exons in plant genomes
Wei Hua Chen
Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
BMC Plant Biol 7:55. 2007
..Our current understanding of AFEs in plants is still limited, including important issues such as their regulation, contribution to protein diversity, and evolutionary conservation...
- [Sequence and evolutionary analysis of VP1 gene of ovine rotavirus NT]
Yanjun Chen
Key Lab of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
Wei Sheng Wu Xue Bao 49:1055-62. 2009
..Based on the VP1 gene was one of the important structural proteins of rotavirus, we studied on the evolutional characteristics of VP1...
- 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...
- EST-based identification of genes expressed in skeletal muscle of the mandarin fish (Siniperca chuatsi)
Feng Ding
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Genomics Proteomics Bioinformatics 9:30-6. 2011
..86% of the total EST sequences. Our work provides a transcript profile expressed in the white muscle of the mandarin fish, laying down a foundation in better understanding of fish genomics...
- 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
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- 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...
- 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...
- Involvement of the GP63 protease in infection of Trichomonas vaginalis
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 109:71-9. 2011
..vaginalis cells to HeLa cells. The results presented in here suggest that GP63 protease plays a vital role in T. vaginalis infection process, but may not be related to the adherence of parasitic cells to their hosts...
- 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...
- 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...
- Identification and analysis of muscle-related protein isoforms expressed in the white muscle of the mandarin fish (Siniperca chuatsi)
Guoqiang Zhang
Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, People s Republic of China
Mar Biotechnol (NY) 13:151-62. 2011
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- 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/ ...
- 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
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- 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...
- 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...
- 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...
- 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
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- 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...
- 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...
- A modified enrichment method to construct microsatellite library from plateau pika genome (Ochotona curzoniae)
Jianing Geng
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
Genomics Proteomics Bioinformatics 8:72-6. 2010
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- 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...
- Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data
Yong Tao
Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, People s Republic of China
Proc Natl Acad Sci U S A 108:12042-7. 2011
..These distinct functions of mutations at different stages may reflect the genetic interactions underlying tumor growth...
- 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...
- wapRNA: a web-based application for the processing of RNA sequences
Wenming Zhao
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
Bioinformatics 27:3076-7. 2011
..Moreover, we provide the executable packages for installation on user's local server...
- 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...
- 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...
- 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...
- [Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea]
Fan Zhang
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
Wei Sheng Wu Xue Bao 49:1445-53. 2009
..Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time...
- Genetic relationships of ethnic minorities in Southwest China revealed by microsatellite markers
Hongbin Lin
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
PLoS ONE 5:e9895. 2010
..Aggregation patterns of these populations accord well with their linguistic affiliations, suggesting that deciphering of genetic relationships does in fact offer clues for study of ethnic differentiation...
- Characterization of evolutionarily conserved microRNAs in amphioxus
Lei Wang
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
Genomics Proteomics Bioinformatics 8:10-21. 2010
..Compared with ciona, amphioxus had an apparent miRNA gene expansion, but phylogenetic analysis showed that the duplicated miRNAs or clusters of amphioxus had a higher homology level than those duplicated ones in vertebrates...
- Single nucleotide polymorphisms and haplotype of four genes encoding cardiac ion channels in Chinese and their association with arrhythmia
Yu Zhang
Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Ann Noninvasive Electrocardiol 13:180-90. 2008
..We hypothesized that specific single nucleotide polymorphisms in cardiac ion channels were associated with cardiac rhythm disturbance in the Chinese population...
- Complete genome sequence of the pathogenic bacterium Riemerella anatipestifer strain RA-GD
Jianfeng Yuan
Beijing Institute of Genomics, Chinese Academy of Sciences, No 7 Beitucheng West Road, Chaoyang District, Beijing 100029, People s Republic of China
J Bacteriol 193:2896-7. 2011
..Here we obtained the complete genome sequence of R. anatipestifer strain RA-GD, which was isolated from an infected duck in Guangzhou, China, and was cultivated in our laboratory...
- 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...
- Whole genome sequencing of lamb rotavirus and comparative analysis with other mammalian rotaviruses
Yanjun Chen
Key Lab of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No 7 Beitucheng West Road, Chaoyang District, Beijing, 100029, China
Virus Genes 38:302-10. 2009
..Besides, this study also makes a significant foundation for the study of genetic classification, epidemiology, and antigenic diversity of rotaviruses on the molecular level...
- Complete genome sequence of Alicyclobacillus acidocaldarius strain Tc-4-1
Yaping Chen
Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No 7 Beitucheng West Road, Chaoyang District, Beijing 100029, China
J Bacteriol 193:5602-3. 2011
..This organism is both thermophilic and acidophilic. It can produce heat- and acid-stable enzymes, such as amylase and esterase, which may be important in industry. Here we report the whole genome sequence of the strain...
- Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14
Feng Ding
The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
BMC Genomics 10:158. 2009
..Multiple serotype 14 clinical isolates were also genotyped by multilocus sequence typing (MLST)...
- 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...
- Complete genome sequence of the ureolytic Streptococcus salivarius strain 57.I
Jianing Geng
The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, People s Republic of China
J Bacteriol 193:5596-7. 2011
..It can utilize urea as the sole nitrogen source via the activity of urease. Complete genome sequencing of S. salivarius 57.I revealed a chromosome and a phage which are absent in strain SK126...
