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Volumn 41, Issue D1, 2013, Pages

RhesusBase: A knowledgebase for the monkey research community

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; COMPUTER INTERFACE; COMPUTER SIMULATION; CONTROLLED STUDY; EXON SHUFFLING; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE EXPRESSION PROFILING; GENETIC MODEL; GENETIC RESOURCE; KNOWLEDGE BASE; NONHUMAN; ONLINE SYSTEM; OPEN READING FRAME; PRIORITY JOURNAL; RHESUS MONKEY; RHESUSBASE; RNA SEQUENCE; RNA TRANSCRIPTION; UNTRANSLATED REGION; WEB BROWSER;

EID: 84876540083     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks835     Document Type: Article
Times cited : (27)

References (77)
  • 2
    • 23044501247 scopus 로고    scopus 로고
    • Environmental cardiovascular disease
    • Mastin, J.P. (2005) Environmental cardiovascular disease. Cardiovasc. Toxicol., 5, 91-94.
    • (2005) Cardiovasc. Toxicol. , vol.5 , pp. 91-94
    • Mastin, J.P.1
  • 3
    • 77952574849 scopus 로고    scopus 로고
    • Uncovering the roles of rare variants in common disease through whole-genome sequencing
    • Cirulli, E.T. and Goldstein, D.B. (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet., 11, 415-425.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 415-425
    • Cirulli, E.T.1    Goldstein, D.B.2
  • 4
    • 77955086298 scopus 로고    scopus 로고
    • Evolutionary genetics in wild primates: Combining genetic approaches with field studies of natural populations
    • Tung, J., Alberts, S.C. and Wray, G.A. (2010) Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations. Trends Genet., 26, 353-362.
    • (2010) Trends Genet. , vol.26 , pp. 353-362
    • Tung, J.1    Alberts, S.C.2    Wray, G.A.3
  • 5
    • 75649102520 scopus 로고    scopus 로고
    • Sex-specific and lineage-specific alternative splicing in primates
    • Blekhman, R., Marioni, J.C., Zumbo, P., Stephens, M. and Gilad, Y. (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res., 20, 180-189.
    • (2010) Genome Res. , vol.20 , pp. 180-189
    • Blekhman, R.1    Marioni, J.C.2    Zumbo, P.3    Stephens, M.4    Gilad, Y.5
  • 10
    • 55749086861 scopus 로고    scopus 로고
    • MonkeySNP: A web portal for non-human primate single nucleotide polymorphisms
    • Khouangsathiene, S., Pearson, C., Street, S., Ferguson, B. and Dubay, C. (2008) MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms. Bioinformatics, 24, 2645-2646.
    • (2008) Bioinformatics , vol.24 , pp. 2645-2646
    • Khouangsathiene, S.1    Pearson, C.2    Street, S.3    Ferguson, B.4    Dubay, C.5
  • 11
    • 79959912920 scopus 로고    scopus 로고
    • Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque
    • Fang, X., Zhang, Y., Zhang, R., Yang, L., Li, M., Ye, K., Guo, X., Wang, J. and Su, B. (2011) Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Genome Biol., 12, R63.
    • (2011) Genome Biol. , vol.12
    • Fang, X.1    Zhang, Y.2    Zhang, R.3    Yang, L.4    Li, M.5    Ye, K.6    Guo, X.7    Wang, J.8    Su, B.9
  • 12
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 14
    • 79551495627 scopus 로고    scopus 로고
    • A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
    • Liu, S., Lin, L., Jiang, P., Wang, D. and Xing, Y. (2011) A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res., 39, 578-588.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 578-588
    • Liu, S.1    Lin, L.2    Jiang, P.3    Wang, D.4    Xing, Y.5
  • 15
    • 79952350327 scopus 로고    scopus 로고
    • Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq
    • Liu, Y., Han, D., Han, Y., Yan, Z., Xie, B., Li, J., Qiao, N., Hu, H., Khaitovich, P., Gao, Y. et al. (2011) Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Res., 39, 1408-1418.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 1408-1418
    • Liu, Y.1    Han, D.2    Han, Y.3    Yan, Z.4    Xie, B.5    Li, J.6    Qiao, N.7    Hu, H.8    Khaitovich, P.9    Gao, Y.10
  • 16
    • 77957929225 scopus 로고    scopus 로고
    • Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq
    • Xu, A.G., He, L., Li, Z., Xu, Y., Li, M., Fu, X., Yan, Z., Yuan, Y., Menzel, C., Li, N. et al. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput. Biol., 6, e1000843.
    • (2010) PLoS Comput. Biol. , vol.6
    • Xu, A.G.1    He, L.2    Li, Z.3    Xu, Y.4    Li, M.5    Fu, X.6    Yan, Z.7    Yuan, Y.8    Menzel, C.9    Li, N.10
  • 17
    • 80755189340 scopus 로고    scopus 로고
    • Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques
    • Yan, G., Zhang, G., Fang, X., Zhang, Y., Li, C., Ling, F., Cooper, D.N., Li, Q., Li, Y., van Gool, A.J. et al. (2011) Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat. Biotechnol., 29, 1019-1023.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 1019-1023
    • Yan, G.1    Zhang, G.2    Fang, X.3    Zhang, Y.4    Li, C.5    Ling, F.6    Cooper, D.N.7    Li, Q.8    Li, Y.9    Van Gool, A.J.10
  • 20
    • 78651286166 scopus 로고    scopus 로고
    • The Mouse Genome Database (MGD): Premier model organism resource for mammalian genomics and genetics
    • Blake, J.A., Bult, C.J., Kadin, J.A., Richardson, J.E. and Eppig, J.T. (2011) The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res., 39, D842-D848.
    • (2011) Nucleic Acids Res. , vol.39
    • Blake, J.A.1    Bult, C.J.2    Kadin, J.A.3    Richardson, J.E.4    Eppig, J.T.5
  • 21
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 22
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 23
    • 0034326362 scopus 로고    scopus 로고
    • Analysis of canonical and non-canonical splice sites in mammalian genomes
    • Burset, M., Seledtsov, I.A. and Solovyev, V.V. (2000) Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res., 28, 4364-4375.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4364-4375
    • Burset, M.1    Seledtsov, I.A.2    Solovyev, V.V.3
  • 24
    • 80051941094 scopus 로고    scopus 로고
    • Identification of novel transcripts in annotated genomes using RNA-Seq
    • Roberts, A., Pimentel, H., Trapnell, C. and Pachter, L. (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27, 2325-2329.
    • (2011) Bioinformatics , vol.27 , pp. 2325-2329
    • Roberts, A.1    Pimentel, H.2    Trapnell, C.3    Pachter, L.4
  • 28
    • 84872784072 scopus 로고    scopus 로고
    • ABrowse - A customizable next-generation genome browser framework
    • Kong, L., Wang, J., Zhao, S., Gu, X., Luo, J. and Gao, G. (2012) ABrowse - a customizable next-generation genome browser framework. BMC Bioinformatics, 13, 2.
    • (2012) BMC Bioinformatics , vol.13 , pp. 2
    • Kong, L.1    Wang, J.2    Zhao, S.3    Gu, X.4    Luo, J.5    Gao, G.6
  • 33
    • 0035949674 scopus 로고    scopus 로고
    • A computational analysis of sequence features involved in recognition of short introns
    • Lim, L.P. and Burge, C.B. (2001) A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. USA, 98, 11193-11198.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 11193-11198
    • Lim, L.P.1    Burge, C.B.2
  • 35
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
    • Pruitt, K.D., Tatusova, T., Brown, G.R. and Maglott, D.R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
    • (2012) Nucleic Acids Res. , vol.40
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 36
    • 33645979674 scopus 로고    scopus 로고
    • Using multiple alignments to improve gene prediction
    • Gross, S.S. and Brent, M.R. (2006) Using multiple alignments to improve gene prediction. J. Comput. Biol., 13, 379-393.
    • (2006) J. Comput. Biol. , vol.13 , pp. 379-393
    • Gross, S.S.1    Brent, M.R.2
  • 39
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: Integrating microRNA annotation and deep-sequencing data
    • Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
    • (2011) Nucleic Acids Res. , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 40
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 44
    • 0023216891 scopus 로고
    • CpG Islands in vertebrate genomes
    • Gardiner-Garden, M. and Frommer, M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
    • (1987) J. Mol. Biol. , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 45
    • 66349114167 scopus 로고    scopus 로고
    • Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts
    • Piontkivska, H., Yang, M.Q., Larkin, D.M., Lewin, H.A., Reecy, J. and Elnitski, L. (2009) Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics, 10, 189.
    • (2009) BMC Genomics , vol.10 , pp. 189
    • Piontkivska, H.1    Yang, M.Q.2    Larkin, D.M.3    Lewin, H.A.4    Reecy, J.5    Elnitski, L.6
  • 47
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal microRNA targets
    • Sethupathy, P., Corda, B. and Hatzigeorgiou, A.G. (2006) TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA, 12, 192-197.
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 49
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis, B.P., Burge, C.B. and Bartel, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 51
    • 77955963884 scopus 로고    scopus 로고
    • Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    • Betel, D., Koppal, A., Agius, P., Sander, C. and Leslie, C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol., 11, R90.
    • (2010) Genome Biol. , vol.11
    • Betel, D.1    Koppal, A.2    Agius, P.3    Sander, C.4    Leslie, C.5
  • 52
    • 33746785696 scopus 로고    scopus 로고
    • Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species
    • Zhang, Y., Liu, X.S., Liu, Q.R. and Wei, L. (2006) Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res., 34, 3465-3475.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3465-3475
    • Zhang, Y.1    Liu, X.S.2    Liu, Q.R.3    Wei, L.4
  • 53
    • 50849129426 scopus 로고    scopus 로고
    • Trans-natural antisense transcripts including noncoding RNAs in 10 species: Implications for expression regulation
    • Li, J.T., Zhang, Y., Kong, L., Liu, Q.R. and Wei, L. (2008) Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res., 36, 4833-4844.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 4833-4844
    • Li, J.T.1    Zhang, Y.2    Kong, L.3    Liu, Q.R.4    Wei, L.5
  • 56
    • 33751527925 scopus 로고    scopus 로고
    • Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome
    • Zhang, J., Feuk, L., Duggan, G.E., Khaja, R. and Scherer, S.W. (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenetic Genome Res., 115, 205-214.
    • (2006) Cytogenetic Genome Res. , vol.115 , pp. 205-214
    • Zhang, J.1    Feuk, L.2    Duggan, G.E.3    Khaja, R.4    Scherer, S.W.5
  • 57
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 60
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
    • (2012) Nucleic Acids Res. , vol.40
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 61
    • 79851505266 scopus 로고    scopus 로고
    • Reactome knowledgebase of human biological pathways and processes
    • D'Eustachio, P. (2011) Reactome knowledgebase of human biological pathways and processes. Methods Mol. Biol., 694, 49-61.
    • (2011) Methods Mol. Biol. , vol.694 , pp. 49-61
    • D'Eustachio, P.1
  • 68
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A. and McKusick, V.A. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res., 33, D514-D517.
    • (2005) Nucleic Acids Res. , vol.33
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 70
    • 77149125896 scopus 로고    scopus 로고
    • Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information
    • Zhang, Y., De, S., Garner, J.R., Smith, K., Wang, S.A. and Becker, K.G. (2010) Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. BMC Med. Genomics, 3, 1.
    • (2010) BMC Med. Genomics , vol.3 , pp. 1
    • Zhang, Y.1    De, S.2    Garner, J.R.3    Smith, K.4    Wang, S.A.5    Becker, K.G.6
  • 71
    • 23744479962 scopus 로고    scopus 로고
    • Efficient transposition of the piggyBac (PB) transposon in mammalian cells and mice
    • Ding, S., Wu, X., Li, G., Han, M., Zhuang, Y. and Xu, T. (2005) Efficient transposition of the piggyBac (PB) transposon in mammalian cells and mice. Cell, 122, 473-483.
    • (2005) Cell , vol.122 , pp. 473-483
    • Ding, S.1    Wu, X.2    Li, G.3    Han, M.4    Zhuang, Y.5    Xu, T.6
  • 72
    • 82755166898 scopus 로고    scopus 로고
    • From pharmacogenomic knowledge acquisition to clinical applications: The PharmGKB as a clinical pharmacogenomic biomarker resource
    • McDonagh, E.M., Whirl-Carrillo, M., Garten, Y., Altman, R.B. and Klein, T.E. (2011) From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomarkers Med., 5, 795-806.
    • (2011) Biomarkers Med. , vol.5 , pp. 795-806
    • McDonagh, E.M.1    Whirl-Carrillo, M.2    Garten, Y.3    Altman, R.B.4    Klein, T.E.5
  • 74
    • 79960364957 scopus 로고    scopus 로고
    • Rhesus macaques develop metabolic syndrome with reversible vascular dysfunction responsive to pioglitazone
    • Zhang, X., Zhang, R., Raab, S., Zheng, W., Wang, J., Liu, N., Zhu, T., Xue, L., Song, Z., Mao, J. et al. (2011) Rhesus macaques develop metabolic syndrome with reversible vascular dysfunction responsive to pioglitazone. Circulation, 124, 77-86.
    • (2011) Circulation , vol.124 , pp. 77-86
    • Zhang, X.1    Zhang, R.2    Raab, S.3    Zheng, W.4    Wang, J.5    Liu, N.6    Zhu, T.7    Xue, L.8    Song, Z.9    Mao, J.10
  • 77
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    • Siepel, A. and Haussler, D. (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol., 21, 468-488.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 468-488
    • Siepel, A.1    Haussler, D.2


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