메뉴 건너뛰기




Volumn 215, Issue , 2017, Pages 2-10

WormBase ParaSite − a comprehensive resource for helminth genomics

Author keywords

Comparative genomics; Ensembl; Functional genomics; Genome browser; Helminths; WormBase

Indexed keywords

ARTICLE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE SEQUENCE; GENE STRUCTURE; HELMINTH; MICROBIAL GENOME; NEMATODE; NONHUMAN; PLATYHELMINTH; PRIORITY JOURNAL; PROTEIN DOMAIN; WEB BROWSER; WORMBASE PARASITE; ANIMAL; BIOLOGY; CLASSIFICATION; GENETIC DATABASE; GENETICS; GENOME; GENOMICS; PROCEDURES;

EID: 85007451784     PISSN: 01666851     EISSN: 18729428     Source Type: Journal    
DOI: 10.1016/j.molbiopara.2016.11.005     Document Type: Article
Times cited : (454)

References (87)
  • 6
    • 67650786530 scopus 로고    scopus 로고
    • Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium, The Schistosoma japonicum genome reveals features of host-parasite interplay. Please see.
    • Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium, The Schistosoma japonicum genome reveals features of host-parasite interplay, Nature, 460, 7253, (2009) 345-51. Please see https://www.ncbi.nlm.nih.gov/pubmed/19606140.
    • (2009) Nature , vol.460 , Issue.7253 , pp. 345-51
  • 30
    • 84925862867 scopus 로고    scopus 로고
    • The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families
    • Schwarz, E.M., Hu, Y., Antoshechkin, I., Miller, M.M., Sternberg, P.W., Aroian, R.V., The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. Nat. Genet. 47:4 (2015), 416–422.
    • (2015) Nat. Genet. , vol.47 , Issue.4 , pp. 416-422
    • Schwarz, E.M.1    Hu, Y.2    Antoshechkin, I.3    Miller, M.M.4    Sternberg, P.W.5    Aroian, R.V.6
  • 31
    • 84937073781 scopus 로고    scopus 로고
    • The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution
    • Cwiklinski, K., Dalton, J.P., Dufresne, P.J., La Course, J., Williams, D.J., Hodgkinson, J., Paterson, S., The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution. Genome Biol., 16, 2015, 71.
    • (2015) Genome Biol. , vol.16 , pp. 71
    • Cwiklinski, K.1    Dalton, J.P.2    Dufresne, P.J.3    La Course, J.4    Williams, D.J.5    Hodgkinson, J.6    Paterson, S.7
  • 38
    • 85020564958 scopus 로고    scopus 로고
    • The 50 Helminth Genomes Initiative
    • Accessed 6 October 2016
    • Wellcome Trust Sanger Institute, The 50 Helminth Genomes Initiative. 2014 http://www.sanger.ac.uk/science/collaboration/50hgp, Accessed 6 October 2016.
    • (2014)
    • Wellcome Trust Sanger Institute1
  • 39
    • 84976870063 scopus 로고    scopus 로고
    • International nucleotide sequence database the international nucleotide sequence database collaboration
    • Cochrane, G., Karsch-Mizrachi, I., Takagi, T., International nucleotide sequence database the international nucleotide sequence database collaboration. Nucleic Acids Res. 44:D1 (2016), D48–D50.
    • (2016) Nucleic Acids Res. , vol.44 , Issue.D1 , pp. D48-D50
    • Cochrane, G.1    Karsch-Mizrachi, I.2    Takagi, T.3
  • 42
    • 84055178433 scopus 로고    scopus 로고
    • MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
    • Holt, C., Yandell, M., MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinf., 12, 2011, 491.
    • (2011) BMC Bioinf. , vol.12 , pp. 491
    • Holt, C.1    Yandell, M.2
  • 44
    • 57149099395 scopus 로고    scopus 로고
    • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    • Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., Borodovsky, M., Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 18:12 (2008), 1979–1990.
    • (2008) Genome Res. , vol.18 , Issue.12 , pp. 1979-1990
    • Ter-Hovhannisyan, V.1    Lomsadze, A.2    Chernoff, Y.O.3    Borodovsky, M.4
  • 45
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf, I., Gene finding in novel genomes. BMC Bioinf., 5, 2004, 59.
    • (2004) BMC Bioinf. , vol.5 , pp. 59
    • Korf, I.1
  • 46
    • 79960403324 scopus 로고    scopus 로고
    • genBlastG: using BLAST searches to build homologous gene models
    • She, R., Chu, J.S., Uyar, B., Wang, J., Wang, K., Chen, N., genBlastG: using BLAST searches to build homologous gene models. Bioinformatics 27:15 (2011), 2141–2143.
    • (2011) Bioinformatics , vol.27 , Issue.15 , pp. 2141-2143
    • She, R.1    Chu, J.S.2    Uyar, B.3    Wang, J.4    Wang, K.5    Chen, N.6
  • 49
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M., Eddy, S.R., tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:5 (1997), 955–964.
    • (1997) Nucleic Acids Res. , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 51
    • 84946069451 scopus 로고    scopus 로고
    • UniProt Consortium,, 43, (Database issue), () D204-12. Please see.
    • UniProt Consortium, UniProt: a hub for protein information, Nucleic Acids Res, 43, (Database issue), (2015) D204-12. Please see https://www.ncbi.nlm.nih.gov/pubmed/25348405.
    • (2015) UniProt: a hub for protein information, Nucleic Acids Res
  • 62
    • 84869078220 scopus 로고    scopus 로고
    • RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways
    • Stoltzfus, J.D., Minot, S., Berriman, M., Nolan, T.J., Lok, J.B., RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways. PLoS Negl. Trop. Dis., 6(10), 2012, e1854.
    • (2012) PLoS Negl. Trop. Dis. , vol.6 , Issue.10 , pp. e1854
    • Stoltzfus, J.D.1    Minot, S.2    Berriman, M.3    Nolan, T.J.4    Lok, J.B.5
  • 64
    • 84874382532 scopus 로고    scopus 로고
    • Adult somatic stem cells in the human parasite Schistosoma mansoni
    • Collins, J.J. 3rd, Wang, B., Lambrus, B.G., Tharp, M.E., Iyer, H., Newmark, P.A., Adult somatic stem cells in the human parasite Schistosoma mansoni. Nature 494:7438 (2013), 476–479.
    • (2013) Nature , vol.494 , Issue.7438 , pp. 476-479
    • Collins, J.J.1    Wang, B.2    Lambrus, B.G.3    Tharp, M.E.4    Iyer, H.5    Newmark, P.A.6
  • 66
    • 84881050928 scopus 로고    scopus 로고
    • Functional genomic characterization of neoblast-like stem cells in larval Schistosoma mansoni
    • Wang, B., Collins, J.J. 3rd, Newmark, P.A., Functional genomic characterization of neoblast-like stem cells in larval Schistosoma mansoni. Elife, 2, 2013, e00768.
    • (2013) Elife , vol.2 , pp. e00768
    • Wang, B.1    Collins, J.J.2    Newmark, P.A.3
  • 68
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates
    • Vilella, A.J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., Birney, E., EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 19:2 (2009), 327–335.
    • (2009) Genome Res. , vol.19 , Issue.2 , pp. 327-335
    • Vilella, A.J.1    Severin, J.2    Ureta-Vidal, A.3    Heng, L.4    Durbin, R.5    Birney, E.6
  • 70
    • 84976875034 scopus 로고    scopus 로고
    • PANTHER version 10: expanded protein families and functions, and analysis tools
    • Mi, H., Poudel, S., Muruganujan, A., Casagrande, J.T., Thomas, P.D., PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 44:D1 (2016), D336–D342.
    • (2016) Nucleic Acids Res. , vol.44 , Issue.D1 , pp. D336-D342
    • Mi, H.1    Poudel, S.2    Muruganujan, A.3    Casagrande, J.T.4    Thomas, P.D.5
  • 71
    • 33645507429 scopus 로고    scopus 로고
    • M-Coffee: combining multiple sequence alignment methods with T-Coffee
    • Wallace, I.M., O'Sullivan, O., Higgins, D.G., Notredame, C., M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34:6 (2006), 1692–1699.
    • (2006) Nucleic Acids Res. , vol.34 , Issue.6 , pp. 1692-1699
    • Wallace, I.M.1    O'Sullivan, O.2    Higgins, D.G.3    Notredame, C.4
  • 72
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    • Katoh, K., Standley, D.M., MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30:4 (2013), 772–780.
    • (2013) Mol. Biol. Evol. , vol.30 , Issue.4 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 77
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
    • Parra, G., Bradnam, K., Korf, I., CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:9 (2007), 1061–1067.
    • (2007) Bioinformatics , vol.23 , Issue.9 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 78
    • 84940907209 scopus 로고    scopus 로고
    • BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
    • Simao, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., Zdobnov, E.M., BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:19 (2015), 3210–3212.
    • (2015) Bioinformatics , vol.31 , Issue.19 , pp. 3210-3212
    • Simao, F.A.1    Waterhouse, R.M.2    Ioannidis, P.3    Kriventseva, E.V.4    Zdobnov, E.M.5
  • 81
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E.L., Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:3 (2001), 567–580.
    • (2001) J. Mol. Biol. , vol.305 , Issue.3 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.