메뉴 건너뛰기




Volumn 26, Issue 4, 2014, Pages 917-928

Answering the demands of digital genomics

Author keywords

cloud computing; computational genomics; DNA sequence analysis

Indexed keywords

CLOUD COMPUTING; DNA SEQUENCES; GENE ENCODING; LARGE DATASET; PROGRAM PROCESSORS;

EID: 84894252156     PISSN: 15320626     EISSN: 15320634     Source Type: Journal    
DOI: 10.1002/cpe.2925     Document Type: Article
Times cited : (2)

References (60)
  • 1
    • 78751654336 scopus 로고    scopus 로고
    • 3rd ed. Garland Science: New York, NY, USA
    • Brown TA,. Genomes 3. 3rd ed. Garland Science: New York, NY, USA, 2006.
    • (2006) Genomes 3
    • Brown, T.A.1
  • 4
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
    • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al,. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995; 269 (5223): 496-512.
    • (1995) Science , vol.269 , Issue.5223 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3    Clayton, R.A.4    Kirkness, E.F.5
  • 5
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000; 408 (6814): 796-815.
    • (2000) Nature , vol.408 , Issue.6814 , pp. 796-815
  • 6
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • The International Human Genome Sequencing Consortium
    • The International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001; 409 (6822): 860-921.
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
  • 7
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al,. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437 (7057): 376-380.
    • (2005) Nature , vol.437 , Issue.7057 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 8
    • 79953167500 scopus 로고    scopus 로고
    • The next-generation sequencing technology and application
    • Zhou X, Ren L, Meng Q, Li Y, Yu Y, et al,. The next-generation sequencing technology and application. Protein & Cell 2010; 1 (6): 520-536.
    • (2010) Protein & Cell , vol.1 , Issue.6 , pp. 520-536
    • Zhou, X.1    Ren, L.2    Meng, Q.3    Li, Y.4    Yu, Y.5
  • 9
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, et al,. A map of human genome variation from population-scale sequencing. Nature 2010; 467 (7319): 1061-1073.
    • (2010) Nature , vol.467 , Issue.7319 , pp. 1061-1073
    • Durbin, R.M.1    Abecasis, G.R.2    Altshuler, D.L.3    Auton, A.4    Brooks, L.D.5
  • 11
    • 77956279237 scopus 로고    scopus 로고
    • Assembly of large genomes using second-generation sequencing
    • Schatz MC, Delcher AL, Salzberg SL,. Assembly of large genomes using second-generation sequencing. Genome Research 2010; 20: 1165-1173.
    • (2010) Genome Research , vol.20 , pp. 1165-1173
    • Schatz, M.C.1    Delcher, A.L.2    Salzberg, S.L.3
  • 12
    • 66149192669 scopus 로고    scopus 로고
    • How to map billions of short reads onto genomes
    • Trapnell C, Salzberg SL,. How to map billions of short reads onto genomes. Nature Biotechnology 2009; 27 (5): 455-457.
    • (2009) Nature Biotechnology , vol.27 , Issue.5 , pp. 455-457
    • Trapnell, C.1    Salzberg, S.L.2
  • 13
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al,. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010; 28 (5): 511-515.
    • (2010) Nature Biotechnology , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5
  • 14
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al,. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462 (7271): 315-322.
    • (2009) Nature , vol.462 , Issue.7271 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3    Hawkins, R.D.4    Hon, G.5
  • 15
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson DS, Mortazavi A, Myers RM, Wold B,. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007; 316 (5830): 1497-1502.
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 16
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al,. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009; 326 (5950): 289-293.
    • (2009) Science , vol.326 , Issue.5950 , pp. 289-293
    • Lieberman-Aiden, E.1    Van Berkum, N.L.2    Williams, L.3    Imakaev, M.4    Ragoczy, T.5
  • 17
    • 77951134860 scopus 로고    scopus 로고
    • Metagenomics for the discovery of novel human viruses
    • Tang P, Chiu C,. Metagenomics for the discovery of novel human viruses. Future Microbiology 2010; 5 (2): 177-189.
    • (2010) Future Microbiology , vol.5 , Issue.2 , pp. 177-189
    • Tang, P.1    Chiu, C.2
  • 18
    • 79956051868 scopus 로고    scopus 로고
    • Adaptation in the age of ecological genomics: Insights from parallelism and convergence
    • Elmer KR, Meyer A,. Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends in Ecology & Evolution 2011; 26 (6): 298-306.
    • (2011) Trends in Ecology & Evolution , vol.26 , Issue.6 , pp. 298-306
    • Elmer, K.R.1    Meyer, A.2
  • 20
    • 79960036578 scopus 로고    scopus 로고
    • Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
    • Puente XS, Pinyol M, Quesada V, Conde L, Ordonez GR, et al,. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011; 475 (7354): 101-105.
    • (2011) Nature , vol.475 , Issue.7354 , pp. 101-105
    • Puente, X.S.1    Pinyol, M.2    Quesada, V.3    Conde, L.4    Ordonez, G.R.5
  • 21
    • 79953766940 scopus 로고    scopus 로고
    • Tumour evolution inferred by single-cell sequencing
    • Navin N, Kendall J, Troge J, Andrews P, Rodgers L, et al,. Tumour evolution inferred by single-cell sequencing. Nature 2011; 472 (7341): 90-94.
    • (2011) Nature , vol.472 , Issue.7341 , pp. 90-94
    • Navin, N.1    Kendall, J.2    Troge, J.3    Andrews, P.4    Rodgers, L.5
  • 23
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al,. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011; 473 (7345): 43-49.
    • (2011) Nature , vol.473 , Issue.7345 , pp. 43-49
    • Ernst, J.1    Kheradpour, P.2    Mikkelsen, T.S.3    Shoresh, N.4    Ward, L.D.5
  • 24
    • 3142654211 scopus 로고    scopus 로고
    • The challenge of emerging and re-emerging infectious diseases
    • Morens DM, Folkers GK, Fauci AS,. The challenge of emerging and re-emerging infectious diseases. Nature 2004; 430 (6996): 242-249.
    • (2004) Nature , vol.430 , Issue.6996 , pp. 242-249
    • Morens, D.M.1    Folkers, G.K.2    Fauci, A.S.3
  • 26
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks J, Nekrutenko A, Taylor J,. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 2010; 11 (8): R86.
    • (2010) Genome Biology , vol.11 , Issue.8
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 27
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD,. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 1970; 48 (3): 443-453.
    • (1970) Journal of Molecular Biology , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 28
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS,. Identification of common molecular subsequences. Journal of Molecular Biology 1981; 147 (1): 195-197.
    • (1981) Journal of Molecular Biology , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 32
    • 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,. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009; 10 (3): R25.
    • (2009) Genome Biology , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 36
    • 37549003336 scopus 로고    scopus 로고
    • MapReduce: Simplified data processing on large clusters
    • Dean J, Ghemawat S,. MapReduce: simplified data processing on large clusters. Communications of the ACM 2008; 51 (1): 107-113.
    • (2008) Communications of the ACM , vol.51 , Issue.1 , pp. 107-113
    • Dean, J.1    Ghemawat, S.2
  • 38
    • 84894281007 scopus 로고    scopus 로고
    • Hadoop. Available from
    • Hadoop. Available from: http://hadoop.apache.org/
  • 40
    • 65649120715 scopus 로고    scopus 로고
    • CloudBurst: Highly sensitive read mapping with MapReduce
    • Schatz MC,. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 2009; 25 (11): 1363-1369.
    • (2009) Bioinformatics , vol.25 , Issue.11 , pp. 1363-1369
    • Schatz, M.C.1
  • 42
    • 66449114324 scopus 로고    scopus 로고
    • SNP detection for massively parallel whole-genome resequencing
    • Li R, Li Y, Fang X, Yang H, Wang J, et al,. SNP detection for massively parallel whole-genome resequencing. Genome Research 2009; 19 (6): 1124-1132.
    • (2009) Genome Research , vol.19 , Issue.6 , pp. 1124-1132
    • Li, R.1    Li, Y.2    Fang, X.3    Yang, H.4    Wang, J.5
  • 44
    • 77955343193 scopus 로고    scopus 로고
    • Cloud-scale RNA-sequencing differential expression analysis with Myrna
    • Langmead B, Hansen KD, Leek JT,. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology 2010; 11 (8): R83.
    • (2010) Genome Biology , vol.11 , Issue.8
    • Langmead, B.1    Hansen, K.D.2    Leek, J.T.3
  • 45
    • 79955676390 scopus 로고    scopus 로고
    • PeakRanger: A cloud-enabled peak caller for ChIP-seq data
    • Feng X, Grossman R, Stein L,. PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics 2011; 12: 139.
    • (2011) BMC Bioinformatics , vol.12 , pp. 139
    • Feng, X.1    Grossman, R.2    Stein, L.3
  • 46
    • 78650811522 scopus 로고    scopus 로고
    • An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
    • Taylor RC,. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics 2010; 11 (Suppl 12): S1.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 12
    • Taylor, R.C.1
  • 47
    • 84894233844 scopus 로고    scopus 로고
    • Available from
    • AWS solutions. Available from: http://aws.amazon.com/solutions/aws- solutions/
    • AWS Solutions
  • 48
    • 84879633298 scopus 로고    scopus 로고
    • Available from
    • Top500 supercomputers. Available from: http://www.top500.org/
    • Top500 Supercomputers
  • 49
    • 84894249462 scopus 로고    scopus 로고
    • Available from
    • BGI Cloud. Available from: https://cloud.genomics.cn/
    • BGI Cloud
  • 50
    • 84894255043 scopus 로고    scopus 로고
    • Available from
    • Jnomics Website. Available from: http://jnomics.sourceforge.net
    • Jnomics Website
  • 51
    • 0025048105 scopus 로고
    • Molecular dynamics simulations in biology
    • Karplus M, Petsko GA,. Molecular dynamics simulations in biology. Nature 1990; 347 (6294): 631-639.
    • (1990) Nature , vol.347 , Issue.6294 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 52
    • 79955473704 scopus 로고    scopus 로고
    • Performance enhancements for GROMACS nonbonded interactions on BlueGene
    • Abraham MJ,. Performance enhancements for GROMACS nonbonded interactions on BlueGene. Journal of Computational Chemistry 2011; 32 (9): 2041-2046.
    • (2011) Journal of Computational Chemistry , vol.32 , Issue.9 , pp. 2041-2046
    • Abraham, M.J.1
  • 53
    • 84894253762 scopus 로고    scopus 로고
    • GPU-based acceleration of the genetic algorithm
    • in. Faculty of Information Technology BUT: Brno, CZ
    • Pospíchal P,. GPU-based acceleration of the genetic algorithm. in Počítačové architektury a diagnostika 2010, PAD 2010. Faculty of Information Technology BUT: Brno, CZ, 2010.
    • (2010) Počítačové Architektury A Diagnostika 2010, PAD 2010
    • Pospíchal, P.1
  • 54
    • 67349120241 scopus 로고    scopus 로고
    • Implementation of a Lattice-Boltzmann method for numerical fluid mechanics using the nVIDIA CUDA technology
    • Riegel E, Indinger T, Adams N,. Implementation of a Lattice-Boltzmann method for numerical fluid mechanics using the nVIDIA CUDA technology. Computer Science-Research and Development 2009; 23 (3): 241-247.
    • (2009) Computer Science - Research and Development , vol.23 , Issue.3 , pp. 241-247
    • Riegel, E.1    Indinger, T.2    Adams, N.3
  • 55
    • 43349092363 scopus 로고    scopus 로고
    • CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
    • Manavski SA, Valle G,. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics 2008; 9 (Suppl 2): S10.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 2
    • Manavski, S.A.1    Valle, G.2
  • 57
    • 65649118549 scopus 로고    scopus 로고
    • Many-core algorithms for statistical phylogenetics
    • Suchard MA, Rambaut A,. Many-core algorithms for statistical phylogenetics. Bioinformatics 2009; 25 (11): 1370-1376.
    • (2009) Bioinformatics , vol.25 , Issue.11 , pp. 1370-1376
    • Suchard, M.A.1    Rambaut, A.2
  • 58
    • 69949100622 scopus 로고    scopus 로고
    • Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment
    • Trapnell C, Schatz MC,. Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment. Parallel Computing 2009; 35 (8-9): 429-440.
    • (2009) Parallel Computing , vol.35 , Issue.89 , pp. 429-440
    • Trapnell, C.1    Schatz, M.C.2
  • 59
    • 84894237691 scopus 로고    scopus 로고
    • Available from
    • Ion torrent products. Available from: http://www.iontorrent.com/homepage- sequence-and-map-data/
    • Ion Torrent Products
  • 60
    • 77953808473 scopus 로고    scopus 로고
    • Next-generation genomics: An integrative approach
    • Hawkins RD, Hon GC, Ren B,. Next-generation genomics: an integrative approach. Nature Reviews. Genetics 2010; 11 (7): 476-486
    • (2010) Nature Reviews. Genetics , vol.11 , Issue.7 , pp. 476-486
    • Hawkins, R.D.1    Hon, G.C.2    Ren, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.