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Volumn 7, Issue 1, 2012, Pages

Adaptive efficient compression of genomes

Author keywords

Heuristics; Referential compression; Scalability; Sequence compression

Indexed keywords


EID: 84868670481     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-7-30     Document Type: Article
Times cited : (28)

References (37)
  • 1
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • 10.1038/35057062, 11237011, Consortium IHGS
    • Consortium IHGS Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921. 10.1038/35057062, 11237011, Consortium IHGS.
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
  • 2
    • 78650868150 scopus 로고    scopus 로고
    • A window into third-generation sequencing
    • Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Human Mol Genet 2010, 19(R2):R227-R240. [http://dx.doi.org/10.1093/hmg/ddq416].
    • (2010) Human Mol Genet , vol.19 , Issue.R2
    • Schadt, E.E.1    Turner, S.2    Kasarskis, A.3
  • 3
    • 84855401988 scopus 로고    scopus 로고
    • International Cancer Genome Consortium Data Portal-a one-stop shop for cancer genomics data
    • bar026
    • International Cancer Genome Consortium Data Portal-a one-stop shop for cancer genomics data. Database: the journal of biological databases and curation 2011, 2011(0):bar026. [http://dx.doi.org/10.1093/database/bar026].
    • (2011) Database: the journal of biological databases and curation , vol.2011 , Issue.0
  • 4
    • 79951493627 scopus 로고    scopus 로고
    • On the future of genomic data
    • 10.1126/science.1197891, 21311016
    • Kahn SD. On the future of genomic data. Science 2011, 331(6018):728-729. [http://www.sciencemag.org/content/331/6018/728.abstract], 10.1126/science.1197891, 21311016.
    • (2011) Science , vol.331 , Issue.6018 , pp. 728-729
    • Kahn, S.D.1
  • 5
    • 80052308152 scopus 로고    scopus 로고
    • Biomedical cloud computing with amazon web services
    • Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ. Biomedical cloud computing with amazon web services. PLoS Comput Biol 2011, 7(8):1-6. [https://sremote.pitt.edu:11018/login.aspx?direct=true&db=aph&AN=67016557&site=ehost-live].
    • (2011) PLoS Comput Biol , vol.7 , Issue.8 , pp. 1-6
    • Fusaro, V.A.1    Patil, P.2    Gafni, E.3    Wall, D.P.4    Tonellato, P.J.5
  • 6
    • 77954492012 scopus 로고    scopus 로고
    • Cloud computing and the DNA data race
    • 10.1038/nbt0710-691, 2904649, 20622843
    • Cloud computing and the DNA data race. Nat Biotechnol 2010, 28(7):691-693. [http://dx.doi.org/10.1038/nbt0710-691], 10.1038/nbt0710-691, 2904649, 20622843.
    • (2010) Nat Biotechnol , vol.28 , Issue.7 , pp. 691-693
  • 7
    • 77954526823 scopus 로고    scopus 로고
    • The case for cloud computing in genome informatics
    • 10.1186/gb-2010-11-5-207, 2898083, 20441614
    • The case for cloud computing in genome informatics. Genome Biol 2010, 11(5):207+. [http://dx.doi.org/10.1186/gb-2010-11-5-207], 10.1186/gb-2010-11-5-207, 2898083, 20441614.
    • (2010) Genome Biol , vol.11 , Issue.5
  • 8
    • 79951811877 scopus 로고    scopus 로고
    • Big data, but are we ready?
    • Trelles O, Prins P, Snir M, Jansen RC. Big data, but are we ready?. Nat Rev Genet 2011, 12(3):224. [http://dx.doi.org/10.1038/nrg2857-c1].
    • (2011) Nat Rev Genet , vol.12 , Issue.3 , pp. 224
    • Trelles, O.1    Prins, P.2    Snir, M.3    Jansen, R.C.4
  • 9
    • 79951480044 scopus 로고    scopus 로고
    • Will computers crash genomics?
    • 10.1126/science.331.6018.666, 21310981
    • Pennisim E. Will computers crash genomics?. Science 2011, 331(6018):666-668. [http://dx.doi.org/10.1126/science.331.6018.666], 10.1126/science.331.6018.666, 21310981.
    • (2011) Science , vol.331 , Issue.6018 , pp. 666-668
    • Pennisim, E.1
  • 10
    • 84856608719 scopus 로고    scopus 로고
    • Textual data compression in computational biology: algorithmic techniques
    • Giancarlo R, Scaturro D, Utro F. Textual data compression in computational biology: algorithmic techniques. Comput Sci Rev January 2012, 6(1):1-25.
    • (2012) Comput Sci Rev , vol.6 , Issue.1 , pp. 1-25
    • Giancarlo, R.1    Scaturro, D.2    Utro, F.3
  • 11
    • 77953484795 scopus 로고    scopus 로고
    • Data compression concepts and algorithms and their applications to bioinformatics
    • 2821113, 20157640
    • Nalbantoglu T, Russell DJ, Sayood K. Data compression concepts and algorithms and their applications to bioinformatics. Entropy 2010, 12:34-52. [http://www.mdpi.com/1099-4300/12/1/34/], 2821113, 20157640.
    • (2010) Entropy , vol.12 , pp. 34-52
    • Nalbantoglu, T.1    Russell, D.J.2    Sayood, K.3
  • 13
    • 80052957011 scopus 로고    scopus 로고
    • Compressing the Human Genome Using Exclusively Markov Models
    • Springer, Rocha MP, JMC Rodríguez, Fdez-Riverola F, Valencia A
    • Pratas D, Pinho AJ. Compressing the Human Genome Using Exclusively Markov Models. PACBB, Volume 93 of Advances in Intelligent and Soft Computing 2011, 213-220. Springer, Rocha MP, JMC Rodríguez, Fdez-Riverola F, Valencia A, [http://dblp.uni-trier.de/db/conf/pacbb/pacbb2011.html{set minus}#PratasP11].
    • (2011) PACBB, Volume 93 of Advances in Intelligent and Soft Computing , pp. 213-220
    • Pratas, D.1    Pinho, A.J.2
  • 14
    • 80054918493 scopus 로고    scopus 로고
    • Robust relative compression of genomes with random access
    • 10.1093/bioinformatics/btr505, 21896510
    • Deorowicz S, Grabowski S. Robust relative compression of genomes with random access. Bioinformatics 2011, 27(21):2979-2986. [http://dx.doi.org/10.1093/bioinformatics/btr505], 10.1093/bioinformatics/btr505, 21896510.
    • (2011) Bioinformatics , vol.27 , Issue.21 , pp. 2979-2986
    • Deorowicz, S.1    Grabowski, S.2
  • 17
    • 0001704377 scopus 로고
    • On-line construction of suffix trees
    • [doi:10.1007/BF01206331]
    • Ukkonen E. On-line construction of suffix trees. Algorithmica 1995, 14:249-260. [http://dx.doi.org/10.1007/BF01206331] [doi:10.1007/BF01206331].
    • (1995) Algorithmica , vol.14 , pp. 249-260
    • Ukkonen, E.1
  • 20
    • 34547630480 scopus 로고    scopus 로고
    • A simple statistical algorithm for biological sequence compression
    • IEEE Computer Society, Washington, DC, USA,
    • Duc Cao M, Dix TI, Allison L, Mears C. A simple statistical algorithm for biological sequence compression. Proceedings of the 2007 Data Compression Conference 2007, 43-52. IEEE Computer Society, Washington, DC, USA, [http://dl.acm.org/citation.cfm?id=1251981.1252877].
    • (2007) Proceedings of the 2007 Data Compression Conference , pp. 43-52
    • Duc Cao, M.1    Dix, T.I.2    Allison, L.3    Mears, C.4
  • 21
    • 58349097721 scopus 로고    scopus 로고
    • Human genomes as email attachments
    • 10.1093/bioinformatics/btn582, 18996942
    • Christley S, Lu Y, Li C, Xie X. Human genomes as email attachments. Bioinformatics 2009, 25(2):274-275. [http://dx.doi.org/10.1093/bioinformatics/btn582], 10.1093/bioinformatics/btn582, 18996942.
    • (2009) Bioinformatics , vol.25 , Issue.2 , pp. 274-275
    • Christley, S.1    Lu, Y.2    Li, C.3    Xie, X.4
  • 22
    • 84872262316 scopus 로고    scopus 로고
    • Engineering relative compression of genomes
    • Grabowski S, Deorowicz S. Engineering relative compression of genomes. ArXiv 2011,, [http://arxiv.org/abs/1103.2351].
    • (2011) ArXiv
    • Grabowski, S.1    Deorowicz, S.2
  • 23
    • 77952730117 scopus 로고    scopus 로고
    • LZ77-like compression with fast random access
    • IEEE Computer Society, Washington, DC, USA
    • Kreft S, Navarro G. LZ77-like compression with fast random access. Proceedings of the 2010 Data Compression Conference, DCC '10 2010, 239-248. IEEE Computer Society, Washington, DC, USA, [http://dx.doi.org/10.1109/DCC.2010.29].
    • (2010) Proceedings of the 2010 Data Compression Conference, DCC '10 , pp. 239-248
    • Kreft, S.1    Navarro, G.2
  • 27
  • 28
    • 47049106011 scopus 로고    scopus 로고
    • Grammar-based compression of DNA sequences
    • [Unpublished work]
    • Cherniavsky N, Ladner R. Grammar-based compression of DNA sequences. 2004, [Unpublished work].
    • (2004)
    • Cherniavsky, N.1    Ladner, R.2
  • 31
    • 82555175823 scopus 로고    scopus 로고
    • Improving transmission efficiency of large sequence alignment/map (SAM) files
    • 10.1371/journal.pone.0028251, 3229529, 22164252
    • Sakib MN, Tang J, Zheng WJ, Huang CT. Improving transmission efficiency of large sequence alignment/map (SAM) files. PLoS ONE 2011, 6(12):e28251. [http://dx.doi.org/10.1371], 10.1371/journal.pone.0028251, 3229529, 22164252.
    • (2011) PLoS ONE , vol.6 , Issue.12
    • Sakib, M.N.1    Tang, J.2    Zheng, W.J.3    Huang, C.T.4
  • 32
    • 79955554401 scopus 로고    scopus 로고
    • Efficient storage of high throughput sequencing data using reference-based compression
    • 10.1101/gr.114819.110, 3083090, 21245279
    • Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E. Efficient storage of high throughput sequencing data using reference-based compression. Genome Res 2011, 21(5):734-740. [http://genome.cshlp.org/content/early/2011/01/18/gr.114819.110.abstract], 10.1101/gr.114819.110, 3083090, 21245279.
    • (2011) Genome Res , vol.21 , Issue.5 , pp. 734-740
    • Hsi-Yang Fritz, M.1    Leinonen, R.2    Cochrane, G.3    Birney, E.4
  • 33
    • 42549172448 scopus 로고    scopus 로고
    • BOOST C++ Libraries
    • BOOST C++ Libraries. [http://www.boost.org].
  • 35
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • 10.1038/nature09534, 3042601, 20981092, Consortium GP
    • Consortium GP A map of human genome variation from population-scale sequencing. Nature 2010, 467(7319):1061-1073. [http://dx.doi.org/10.1038/nature09534], 10.1038/nature09534, 3042601, 20981092, Consortium GP.
    • (2010) Nature , vol.467 , Issue.7319 , pp. 1061-1073
  • 37
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • 186604, 12045153
    • Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12045153], 186604, 12045153.
    • (2002) Genome Res , vol.12 , Issue.6 , pp. 996-1006
    • Kent, W.J.1    Sugnet, C.W.2    Furey, T.S.3    Roskin, K.M.4    Pringle, T.H.5    Zahler, A.M.6    Haussler, D.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.