메뉴 건너뛰기




Volumn 8, Issue 9, 2013, Pages

Mining RNA-Seq Data for Infections and Contaminations

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL PROLIFERATION; COLORECTAL CARCINOMA; COMPUTER PROGRAM; DATA MINING; FUSOBACTERIUM; GENE EXPRESSION; HELA CELL; HUMAN PAPILLOMAVIRUS TYPE 18; INFECTION; METAGENOMICS; MICROBIAL CONTAMINATION; RNA SEQUENCE; SEQUENCE ALIGNMENT; SPECIES IDENTIFICATION; STRAIN IDENTIFICATION; TRANSCRIPTOMICS; VIRUS GENOME;

EID: 84883372948     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073071     Document Type: Article
Times cited : (11)

References (40)
  • 1
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL, (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
  • 2
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36.
    • (2013) Genome Biol , vol.14
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5
  • 3
    • 78649345104 scopus 로고    scopus 로고
    • MapSplice: accurate mapping of RNA-seq reads for splice junction discovery
    • Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, et al. (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38: e178.
    • (2010) Nucleic Acids Res , vol.38
    • Wang, K.1    Singh, D.2    Zeng, Z.3    Coleman, S.J.4    Huang, Y.5
  • 4
    • 80052745094 scopus 로고    scopus 로고
    • Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
    • Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, et al. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics 27: 2518-2528.
    • (2011) Bioinformatics , vol.27 , pp. 2518-2528
    • Grant, G.R.1    Farkas, M.H.2    Pizarro, A.D.3    Lahens, N.F.4    Schug, J.5
  • 6
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 7
    • 84867882225 scopus 로고    scopus 로고
    • A context-based approach to identify the most likely mapping for RNA-seq experiments
    • Bonfert T, Csaba G, Zimmer R, Friedel CC (2012) A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics (Suppl 6): S9.
    • (2012) BMC Bioinformatics , Issue.SUPPL. 6
    • Bonfert, T.1    Csaba, G.2    Zimmer, R.3    Friedel, C.C.4
  • 9
    • 84866919768 scopus 로고    scopus 로고
    • Real-time tran-scriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection
    • Marcinowski L, Lidschreiber M, Windhager L, Rieder M, Bosse JB, et al. (2012) Real-time tran-scriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog 8: e1002908.
    • (2012) PLoS Pathog , vol.8
    • Marcinowski, L.1    Lidschreiber, M.2    Windhager, L.3    Rieder, M.4    Bosse, J.B.5
  • 10
    • 0032840918 scopus 로고    scopus 로고
    • Human papillo-mavirus is a necessary cause of invasive cervical cancer worldwide
    • Walboomers JM, Jacobs MV, Manos MM, Bosch FX, Kummer JA, et al. (1999) Human papillo-mavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol 189: 12-19.
    • (1999) J Pathol , vol.189 , pp. 12-19
    • Walboomers, J.M.1    Jacobs, M.V.2    Manos, M.M.3    Bosch, F.X.4    Kummer, J.A.5
  • 11
    • 0036559896 scopus 로고    scopus 로고
    • Papillomaviruses and cancer: from basic studies to clinical application
    • zur Hausen H, (2002) Papillomaviruses and cancer: from basic studies to clinical application. Nat Rev Cancer 2: 342-350.
    • (2002) Nat Rev Cancer , vol.2 , pp. 342-350
    • zur Hausen, H.1
  • 12
    • 0023945720 scopus 로고
    • Nucleotide sequences of cDNAs for human papillomavirus type 18 transcripts in HeLa cells
    • Inagaki Y, Tsunokawa Y, Takebe N, Nawa H, Nakanishi S, et al. (1988) Nucleotide sequences of cDNAs for human papillomavirus type 18 transcripts in HeLa cells. J Virol 62: 1640-1646.
    • (1988) J Virol , vol.62 , pp. 1640-1646
    • Inagaki, Y.1    Tsunokawa, Y.2    Takebe, N.3    Nawa, H.4    Nakanishi, S.5
  • 13
  • 14
    • 79955930966 scopus 로고    scopus 로고
    • The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue
    • Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chnard C, et al. (2011) The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS One 6: e19838.
    • (2011) PLoS One , vol.6
    • Moore, R.A.1    Warren, R.L.2    Freeman, J.D.3    Gustavsen, J.A.4    Chnard, C.5
  • 15
    • 84883349233 scopus 로고    scopus 로고
    • Metagenomics and meta-transcriptomics: Windows on CF-associated viral and microbial communities
    • Lim YW, Schmieder R, Haynes M, Willner D, Furlan M, et al. (2012) Metagenomics and meta-transcriptomics: Windows on CF-associated viral and microbial communities. J Cyst Fibros.
    • (2012) J Cyst Fibros
    • Lim, Y.W.1    Schmieder, R.2    Haynes, M.3    Willner, D.4    Furlan, M.5
  • 16
    • 84857580551 scopus 로고    scopus 로고
    • Metatranscriptomics and pyrosequencing facilitate discovery of potential viral natural enemies of the invasive Caribbean crazy ant, Nylanderia pubens
    • Valles SM, Oi DH, Yu F, Tan XX, Buss EA, (2012) Metatranscriptomics and pyrosequencing facilitate discovery of potential viral natural enemies of the invasive Caribbean crazy ant, Nylanderia pubens. PLoS One 7: e31828.
    • (2012) PLoS One , vol.7
    • Valles, S.M.1    Oi, D.H.2    Yu, F.3    Tan, X.X.4    Buss, E.A.5
  • 17
    • 84860477454 scopus 로고    scopus 로고
    • Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing
    • Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, et al. (2012) Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One 7: e36009.
    • (2012) PLoS One , vol.7
    • Xiong, X.1    Frank, D.N.2    Robertson, C.E.3    Hung, S.S.4    Markle, J.5
  • 18
    • 84861633828 scopus 로고    scopus 로고
    • Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge
    • Yu K, Zhang T, (2012) Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge. PLoS One 7: e38183.
    • (2012) PLoS One , vol.7
    • Yu, K.1    Zhang, T.2
  • 20
    • 82755170566 scopus 로고    scopus 로고
    • Accurate genome relative abundance estimation based on shotgun metagenomic reads
    • Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F, (2011) Accurate genome relative abundance estimation based on shotgun metagenomic reads. PLoS One 6: e27992.
    • (2011) PLoS One , vol.6
    • Xia, L.C.1    Cram, J.A.2    Chen, T.3    Fuhrman, J.A.4    Sun, F.5
  • 21
    • 84871725334 scopus 로고    scopus 로고
    • Metagenomic abundance estimation and diagnostic testing on species level
    • Lindner MS, Renard BY, (2013) Metagenomic abundance estimation and diagnostic testing on species level. Nucleic Acids Res 41: e10.
    • (2013) Nucleic Acids Res , vol.41
    • Lindner, M.S.1    Renard, B.Y.2
  • 23
    • 0025952277 scopus 로고
    • Divergence measures based on the Shannon entropy
    • Lin J, (1991) Divergence measures based on the Shannon entropy. IEEE Transactions on Information theory 37: 145-151.
    • (1991) IEEE Transactions on Information Theory , vol.37 , pp. 145-151
    • Lin, J.1
  • 25
    • 77955644289 scopus 로고    scopus 로고
    • Mammalian microRNAs predominantly act to decrease target mRNA levels
    • Guo H, Ingolia NT, Weissman JS, Bartel DP, (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840.
    • (2010) Nature , vol.466 , pp. 835-840
    • Guo, H.1    Ingolia, N.T.2    Weissman, J.S.3    Bartel, D.P.4
  • 26
    • 77956095453 scopus 로고    scopus 로고
    • Metagenomic sequencing of an in vitro-simulated microbial community
    • Morgan JL, Darling AE, Eisen JA, (2010) Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One 5: e10209.
    • (2010) PLoS One , vol.5
    • Morgan, J.L.1    Darling, A.E.2    Eisen, J.A.3
  • 27
    • 70449713952 scopus 로고    scopus 로고
    • The NIH Human Microbiome Project
    • NIH HMP Working Group
    • NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, et al (2009) The NIH Human Microbiome Project. Genome Res 19: 2317-2323.
    • (2009) Genome Res , vol.19 , pp. 2317-2323
    • Peterson, J.1    Garges, S.2    Giovanni, M.3    McInnes, P.4
  • 28
    • 82355175140 scopus 로고    scopus 로고
    • Primary human cervical carcinoma cells require human papillomavirus E6 and E7 expression for ongoing proliferation
    • Magaldi TG, Almstead LL, Bellone S, Prevatt EG, Santin AD, et al. (2012) Primary human cervical carcinoma cells require human papillomavirus E6 and E7 expression for ongoing proliferation. Virology 422: 114-124.
    • (2012) Virology , vol.422 , pp. 114-124
    • Magaldi, T.G.1    Almstead, L.L.2    Bellone, S.3    Prevatt, E.G.4    Santin, A.D.5
  • 29
    • 35348814352 scopus 로고    scopus 로고
    • Brd4-independent transcriptional repression function of the papillomavirus e2 proteins
    • Schweiger MR, Ottinger M, You J, Howley PM, (2007) Brd4-independent transcriptional repression function of the papillomavirus e2 proteins. J Virol 81: 9612-9622.
    • (2007) J Virol , vol.81 , pp. 9612-9622
    • Schweiger, M.R.1    Ottinger, M.2    You, J.3    Howley, P.M.4
  • 30
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R, (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 31
    • 40449120475 scopus 로고    scopus 로고
    • Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1
    • Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P, et al. (2008) Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics 91: 335-346.
    • (2008) Genomics , vol.91 , pp. 335-346
    • Pfeiffer, F.1    Schuster, S.C.2    Broicher, A.3    Falb, M.4    Palm, P.5
  • 32
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5
  • 33
    • 79960713932 scopus 로고    scopus 로고
    • Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
    • Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M, (2011) Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 12Suppl 2: S4.
    • (2011) BMC Genomics , vol.12
    • Liu, B.1    Gibbons, T.2    Ghodsi, M.3    Treangen, T.4    Pop, M.5
  • 34
    • 67649887316 scopus 로고    scopus 로고
    • SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
    • Monzoorul Haque M, Ghosh TS, Komanduri D, Mande SS, (2009) SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics 25: 1722-1730.
    • (2009) Bioinformatics , vol.25 , pp. 1722-1730
    • Monzoorul Haque, M.1    Ghosh, T.S.2    Komanduri, D.3    Mande, S.S.4
  • 35
    • 77949511566 scopus 로고    scopus 로고
    • MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences
    • Horton M, Bodenhausen N, Bergelson J, (2010) MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences. Bioinformatics 26: 568-569.
    • (2010) Bioinformatics , vol.26 , pp. 568-569
    • Horton, M.1    Bodenhausen, N.2    Bergelson, J.3
  • 36
    • 77955179934 scopus 로고    scopus 로고
    • Mltreemap-accurate maximum likelihood placement of environmental dna sequences into taxonomic and functional reference phylogenies
    • Stark M, Berger SA, Stamatakis A, von Mering C, (2010) Mltreemap-accurate maximum likelihood placement of environmental dna sequences into taxonomic and functional reference phylogenies. BMC Genomics 11: 461.
    • (2010) BMC Genomics , vol.11 , pp. 461
    • Stark, M.1    Berger, S.A.2    Stamatakis, A.3    von Mering, C.4
  • 39
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A, Salzberg SL, (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 6: 673-676.
    • (2009) Nat Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 40
    • 79955778143 scopus 로고    scopus 로고
    • PathSeq: software to identify or discover microbes by deep sequencing of human tissue
    • Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RGW, et al. (2011) PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol 29: 393-396.
    • (2011) Nat Biotechnol , vol.29 , pp. 393-396
    • Kostic, A.D.1    Ojesina, A.I.2    Pedamallu, C.S.3    Jung, J.4    Verhaak, R.G.W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.