메뉴 건너뛰기




Volumn 1247, Issue , 2014, Pages 491-511

Metagenomic approaches to disclose disease-associated pathogens: Detection of viral pathogens in honeybees

Author keywords

Diagnosis; Metagenomics; Sequencing; Unknown etiology; Unknown viruses; Virus detection

Indexed keywords

ADULT; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CAPILLARY ELECTROPHORESIS; COST BENEFIT ANALYSIS; DNA EXTRACTION; GEL ELECTROPHORESIS; GENE AMPLIFICATION; HIGH THROUGHPUT SEQUENCING; HONEYBEE; METAGENOMICS; NONHUMAN; QUALITY CONTROL; RNA EXTRACTION; VIRUS CHARACTERIZATION; VIRUS DETECTION; VIRUS PATHOGENESIS;

EID: 84911925058     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2004-4_33     Document Type: Article
Times cited : (3)

References (34)
  • 1
    • 80052221189 scopus 로고    scopus 로고
    • Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples
    • Cheval J, Sauvage V, Frangeul L et al (2011) Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol 49:3268-3275
    • (2011) J Clin Microbiol , vol.49 , pp. 3268-3275
    • Cheval, J.1    Sauvage, V.2    Frangeul, L.3
  • 3
    • 79961183224 scopus 로고    scopus 로고
    • Metagenomic analysis of bacterial infections by means of high-throughput DNA sequencing
    • Nakamura S, Nakaya T, Iida T (2011) Metagenomic analysis of bacterial infections by means of high-throughput DNA sequencing. Exp Biol Med (Maywood) 236:968-971
    • (2011) Exp Biol Med (Maywood) , vol.236 , pp. 968-971
    • Nakamura, S.1    Nakaya, T.2    Iida, T.3
  • 4
    • 77951134860 scopus 로고    scopus 로고
    • Metagenomics for the discovery of novel human viruses
    • Tang P, Chiu C (2010) Metagenomics for the discovery of novel human viruses. Future Microbiol 5:177-189
    • (2010) Future Microbiol , vol.5 , pp. 177-189
    • Tang, P.1    Chiu, C.2
  • 5
    • 83755186199 scopus 로고    scopus 로고
    • A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing
    • Daly GM, Bexfield N, Heaney J et al (2011) A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS One 6:e28879
    • (2011) PLoS One , vol.6
    • Daly, G.M.1    Bexfield, N.2    Heaney, J.3
  • 6
    • 33947607974 scopus 로고    scopus 로고
    • Viral metagenomics
    • Delwart EL (2007) Viral metagenomics. Rev Med Virol 17:115-131
    • (2007) Rev Med Virol , vol.17 , pp. 115-131
    • Delwart, E.L.1
  • 7
    • 24644516529 scopus 로고    scopus 로고
    • Cloning of a human parvovirus by molecular screening of respiratory tract samples
    • Allander T, Tammi MT, Eriksson M et al (2005) Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci U S A 102:12891-12896
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 12891-12896
    • Allander, T.1    Tammi, M.T.2    Eriksson, M.3
  • 8
    • 0035949592 scopus 로고    scopus 로고
    • A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species
    • Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci U S A 98:11609-11614
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 11609-11614
    • Allander, T.1    Emerson, S.U.2    Engle, R.E.3    Purcell, R.H.4    Bukh, J.5
  • 10
    • 39849084772 scopus 로고    scopus 로고
    • Viral genome sequencing by random priming methods
    • Djikeng A, Halpin R, Kuzmickas R et al (2008) Viral genome sequencing by random priming methods. BMC Genomics 9:5
    • (2008) BMC Genomics , vol.9 , pp. 5
    • Djikeng, A.1    Halpin, R.2    Kuzmickas, R.3
  • 11
    • 0026290379 scopus 로고
    • Sequenceindependent, single-primer amplification (SISPA) of complex DNA populations
    • Reyes GR, Kim JP (1991) Sequenceindependent, single-primer amplification (SISPA) of complex DNA populations. Mol Cell Probes 5:473-481
    • (1991) Mol Cell Probes , vol.5 , pp. 473-481
    • Reyes, G.R.1    Kim, J.P.2
  • 12
    • 84864587801 scopus 로고    scopus 로고
    • DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe
    • Rosseel T, Scheuch M, Höper D (2012) DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS One 7:e41967
    • (2012) PLoS One , vol.7
    • Rosseel, T.1    Scheuch, M.2    Höper, D.3
  • 13
    • 33751098497 scopus 로고    scopus 로고
    • Virus discovery by sequence-independent genome amplifi- cation
    • Ambrose HE, Clewley JP (2006) Virus discovery by sequence-independent genome amplifi- cation. Rev Med Virol 16:365-383
    • (2006) Rev Med Virol , vol.16 , pp. 365-383
    • Ambrose, H.E.1    Clewley, J.P.2
  • 14
    • 84883207705 scopus 로고    scopus 로고
    • The effect of preprocessing by sequenceindependent, single-primer amplification (SISPA) on metagenomic detection of viruses
    • Karlsson OE, Belák S, Granberg F (2013) The effect of preprocessing by sequenceindependent, single-primer amplification (SISPA) on metagenomic detection of viruses. Biosecur Bioterror 11(S1):S227-S234
    • (2013) Biosecur Bioterror , vol.11 , Issue.S1 , pp. S227-S234
    • Karlsson, O.E.1    Belák, S.2    Granberg, F.3
  • 15
    • 84884625714 scopus 로고    scopus 로고
    • The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing
    • Rosseel T, Van Borm S, Vandenbussche F et al (2013) The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. PLoS One 8:e76144
    • (2013) PLoS One , vol.8
    • Rosseel, T.1    Van Borm, S.2    Vandenbussche, F.3
  • 16
    • 77952577869 scopus 로고    scopus 로고
    • Recent advances in DNA sequencing methods-general principles of sample preparation
    • Linnarsson S (2010) Recent advances in DNA sequencing methods-general principles of sample preparation. Exp Cell Res 316:1339-1343
    • (2010) Exp Cell Res , vol.316 , pp. 1339-1343
    • Linnarsson, S.1
  • 17
    • 40449115382 scopus 로고    scopus 로고
    • A new arenavirus in a cluster of fatal transplantassociated diseases
    • Palacios G, Druce J, Du L et al (2008) A new arenavirus in a cluster of fatal transplantassociated diseases. N Engl J Med 358:991-998
    • (2008) N Engl J Med , vol.358 , pp. 991-998
    • Palacios, G.1    Druce, J.2    Du, L.3
  • 18
    • 67249156188 scopus 로고    scopus 로고
    • Genetic detection and characterization of Lujo virus, a new hemorrhagic feverassociated arenavirus from southern Africa
    • Briese T, Paweska JT, McMullan LK et al (2009) Genetic detection and characterization of Lujo virus, a new hemorrhagic feverassociated arenavirus from southern Africa. PLoS Pathog 5:e1000455
    • (2009) PLoS Pathog , vol.5
    • Briese, T.1    Paweska, J.T.2    McMullan, L.K.3
  • 19
    • 35348853758 scopus 로고    scopus 로고
    • A metagenomic survey of microbes in honey bee colony collapse disorder
    • Cox-Foster DL, Conlan S, Holmes EC et al (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318:283-287
    • (2007) Science , vol.318 , pp. 283-287
    • Cox-Foster, D.L.1    Conlan, S.2    Holmes, E.C.3
  • 20
    • 84860756398 scopus 로고    scopus 로고
    • Performance comparison of benchtop highthroughput sequencing platforms
    • Loman NJ, Misra RV, Dallman TJ et al (2012) Performance comparison of benchtop highthroughput sequencing platforms. Nat Biotechnol 30:434-439
    • (2012) Nat Biotechnol , vol.30 , pp. 434-439
    • Loman, N.J.1    Misra, R.V.2    Dallman, T.J.3
  • 21
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863-864
    • (2011) Bioinformatics , vol.27 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 22
    • 84875398448 scopus 로고    scopus 로고
    • Statistical guidelines for Apis mellifera research
    • Pirk CWW, Miranda JR, Kramer M, et al. (2013) Statistical guidelines for Apis mellifera research. J Apic Res 52 (doi: 10.3896/ IBRA.1.52.4.13)
    • (2013) J Apic Res , vol.52
    • Pirk, C.W.W.1    Miranda, J.R.2    Kramer, M.3
  • 23
    • 84874547000 scopus 로고    scopus 로고
    • Metagenomic detection of viral pathogens in Spanish honeybees: Co- infection by Aphid lethal paralysis, Israel acute paralysis and Lake Sinai viruses
    • Granberg F, Vicente-Rubiano M, Rubio- Guerri C et al (2013) Metagenomic detection of viral pathogens in Spanish honeybees: co- infection by Aphid lethal paralysis, Israel acute paralysis and Lake Sinai viruses. PLoS One 8:e57459
    • (2013) PLoS One , vol.8
    • Granberg, F.1    Vicente-Rubiano, M.2    Rubio- Guerri, C.3
  • 24
    • 84898431119 scopus 로고    scopus 로고
    • High-throughput sequencing in veterinary infection biology and diagnostics
    • Belák S, Karlsson OE, Leijon M, Granberg F (2013) High-throughput sequencing in veterinary infection biology and diagnostics. Rev Sci Tech 32:893-915
    • (2013) Rev Sci Tech , vol.32 , pp. 893-915
    • Belák, S.1    Karlsson, O.E.2    Leijon, M.3    Granberg, F.4
  • 25
    • 80051688000 scopus 로고    scopus 로고
    • Field guide to nextgeneration DNA sequencers
    • Glenn TC (2011) Field guide to nextgeneration DNA sequencers. Mol Ecol Resour 11:759-769
    • (2011) Mol Ecol Resour , vol.11 , pp. 759-769
    • Glenn, T.C.1
  • 27
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365-386
    • (2000) Methods Mol Biol , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 29
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: Freely available Python tools for computational molecular biology and bioinformatics
    • Cock PJ, Antao T, Chang JT et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422-1423
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.1    Antao, T.2    Chang, J.T.3
  • 30
    • 18644368714 scopus 로고    scopus 로고
    • The Bioperl toolkit: Perl modules for the life sciences
    • Stajich JE, Block D, Boulez K et al (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12:1611-1618
    • (2002) Genome Res , vol.12 , pp. 1611-1618
    • Stajich, J.E.1    Block, D.2    Boulez, K.3
  • 31
    • 84859210032 scopus 로고    scopus 로고
    • Fast gappedread alignment with Bowtie 2
    • Langmead B, Salzberg SL (2012) Fast gappedread alignment with Bowtie 2. Nat Methods 9:357-359
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 32
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, 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
  • 33
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
    • Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178-192
    • (2013) Brief Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 34
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz S, Phillippy A, Delcher AL et al (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12
    • (2004) Genome Biol , vol.5 , pp. R12
    • Kurtz, S.1    Phillippy, A.2    Delcher, A.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.