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Volumn 719, Issue , 2011, Pages 3-30

Omics Technologies, Data and Bioinformatics Principles

Author keywords

Bioinformatics; Data integration; Genomics; High throughput; Interactomics; Omics; Omics databases; Omics tools; Proteomics; Transcriptomics

Indexed keywords

BIOINFORMATICS; DATA INTEGRATION; GENOMICS; INTERACTOMICS; PROTEOMICS; TRANSCRIPTOMICS; ANIMAL; BIOLOGY; GENE EXPRESSION PROFILING; HUMAN; INFORMATION RETRIEVAL; MASS SPECTROMETRY; METHODOLOGY; REVIEW;

EID: 79958247861     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-027-0_1     Document Type: Chapter
Times cited : (96)

References (47)
  • 1
    • 52949109838 scopus 로고    scopus 로고
    • Use of conventional and-omics based methods for health claims of dietary antioxidants: A critical overview
    • Knasmüller, S. et al. (2008) Use of conventional and-omics based methods for health claims of dietary antioxidants: A critical overview. Br J Nutr 99, ES3–52.
    • (2008) Br J Nutr , vol.99 , pp. ES3-52
    • Knasmüller, S.1
  • 2
    • 38749149152 scopus 로고    scopus 로고
    • Whole-genome sequencing and variant discovery in C. elegans
    • Hillieret, L.W. et al. (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5, 183–88.
    • (2008) Nat Methods , vol.5 , pp. 183-188
    • Hillieret, L.W.1
  • 3
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein–DNA interactions
    • Johnson, D.S. et al. (2007) Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1441–42.
    • (2007) Science , vol.316 , pp. 1441-1442
    • Johnson, D.S.1
  • 4
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • Mortazavi, A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621–8.
    • (2008) Nat Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1
  • 5
    • 58749115963 scopus 로고    scopus 로고
    • Data storage and analysis in ArrayExpress and Expression Profiler
    • Rustici, G. et al. (2008) Data storage and analysis in ArrayExpress and Expression Profiler. Curr Protoc Bioinformatics 7, 7–13.
    • (2008) Curr Protoc Bioinformatics , vol.7 , pp. 7-13
    • Rustici, G.1
  • 6
    • 33645277092 scopus 로고    scopus 로고
    • The MGED Ontology: A resource for semantics-based description of microarray experiments
    • Whetzel, P.L. et al. (2006) The MGED Ontology: A resource for semantics-based description of microarray experiments. Bioinformatics 22, 866–73.
    • (2006) Bioinformatics , vol.22 , pp. 866-873
    • Whetzel, P.L.1
  • 7
    • 84862486195 scopus 로고    scopus 로고
    • Top 10 future challenges for bioinformatics
    • Burge, C., Birney, E., and Fickett, J. (2002) Top 10 future challenges for bioinformatics. Genome Technol 17, 1–3.
    • (2002) Genome Technol , vol.17 , pp. 1-3
    • Burge, C.1    Birney, E.2    Fickett, J.3
  • 8
    • 1842717960 scopus 로고    scopus 로고
    • The Atlas genome assembly system
    • Havlak, P. et al. (2004) The Atlas genome assembly system. Genome Res 14, 721–32.
    • (2004) Genome Res , vol.14 , pp. 721-732
    • Havlak, P.1
  • 9
    • 0036144823 scopus 로고    scopus 로고
    • ARACHNE: A whole genome shotgun assembler
    • Batzoglou, S. et al. (2002) ARACHNE: A whole genome shotgun assembler. Genome Res 12, 177–89.
    • (2002) Genome Res , vol.12 , pp. 177-189
    • Batzoglou, S.1
  • 10
    • 0034708758 scopus 로고    scopus 로고
    • A whole-genome assembly of Drosophila
    • Myers, E.W. et al. (2000) A whole-genome assembly of Drosophila. Science 287, 2196–204.
    • (2000) Science , vol.287 , pp. 2196-2204
    • Myers, E.W.1
  • 11
    • 0141853948 scopus 로고    scopus 로고
    • PCAP: A whole-genome assembly program
    • Huang, X. et al. (2003) PCAP: A whole-genome assembly program. Genome Res 13, 2164–70.
    • (2003) Genome Res , vol.13 , pp. 2164-2170
    • Huang, X.1
  • 12
    • 0037263854 scopus 로고    scopus 로고
    • The Phusion assembler
    • Mullikin, J.C., and Ning, Z. (2003) The Phusion assembler. Genome Res 13, 81–90.
    • (2003) Genome Res , vol.13 , pp. 81-90
    • Mullikin, J.C.1    Ning, Z.2
  • 13
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • Pevzner, P.A., Tang, H., and Waterman, M.S. (2001) An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 14, 9748–53.
    • (2001) Proc Natl Acad Sci USA , vol.14 , pp. 9748-9753
    • Pevzner, P.A.1    Tang, H.2    Waterman, M.S.3
  • 15
    • 0029312687 scopus 로고
    • A new algorithm for DNA sequence assembly
    • Idury, R., and Waterman, M. (1995) A new algorithm for DNA sequence assembly. J Comput Biol 2, 291–306.
    • (1995) J Comput Biol , vol.2 , pp. 291-306
    • Idury, R.1    Waterman, M.2
  • 16
    • 0035232164 scopus 로고    scopus 로고
    • Fragment assembly with double-barrelled data
    • Pevzner, P., and Tang, H. (2001) Fragment assembly with double-barrelled data. Bioinformatics 17, S225–33.
    • (2001) Bioinformatics , vol.17 , pp. S225-S233
    • Pevzner, P.1    Tang, H.2
  • 17
    • 39049156065 scopus 로고    scopus 로고
    • Short read fragment assembly of bacterial genomes
    • Chaisson, M.J., and Pevzner, P.A. (2008) Short read fragment assembly of bacterial genomes. Genome Res 18, 324–30.
    • (2008) Genome Res , vol.18 , pp. 324-330
    • Chaisson, M.J.1    Pevzner, P.A.2
  • 18
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D.R., and Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821–9.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 19
    • 57149099394 scopus 로고    scopus 로고
    • Sequencing of natural strains of Arabidopsis thaliana with short reads
    • Ossowski, S. et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18, 2024–33.
    • (2008) Genome Res , vol.18 , pp. 2024-2033
    • Ossowski, S.1
  • 20
    • 58149291658 scopus 로고    scopus 로고
    • De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads
    • Farrer, R.A. et al. (2009) De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett 1, 103–11.
    • (2009) FEMS Microbiol Lett , Issue.1 , pp. 103-111
    • Farrer, R.A.1
  • 21
    • 38549094621 scopus 로고    scopus 로고
    • DBTSS: Database of transcription start sites, progress report
    • Wakaguri, H. et al. (2008) DBTSS: Database of transcription start sites, progress report. Nucleic Acids Res 36, D97–101.
    • (2008) Nucleic Acids Res , vol.36 , pp. D97-101
    • Wakaguri, H.1
  • 22
    • 78650480483 scopus 로고    scopus 로고
    • High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis
    • Chen, X. et al. (2009) High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biol Evol 1, 165–75.
    • (2009) Genome Biol Evol , vol.1 , pp. 165-175
    • Chen, X.1
  • 23
    • 43149086380 scopus 로고    scopus 로고
    • ALLPATHS: De novo assembly of whole-genome shotgun micro-reads
    • Butler, J. et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun micro-reads. Genome Res 18, 810–20.
    • (2008) Genome Res , vol.18 , pp. 810-820
    • Butler, J.1
  • 24
    • 47249091503 scopus 로고    scopus 로고
    • Assembly for double-ended short-read sequencing technologies
    • edited by E. Mardis, S. Kim, and H. Tang. Artech House Publishers, Boston
    • Chen, J., and Skiena, S. (2007) Assembly for double-ended short-read sequencing technologies. In ‘Advances in Genome Sequencing Technology and Algorithms’, edited by E. Mardis, S. Kim, and H. Tang. Artech House Publishers, Boston.
    • (2007) Advances in Genome Sequencing Technology and Algorithms
    • Chen, J.1    Skiena, S.2
  • 25
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J.T. et al. (2009) ABySS: A parallel assembler for short read sequence data. Genome Res 9, 1117–23.
    • (2009) Genome Res , vol.9 , pp. 1117-1123
    • Simpson, J.T.1
  • 26
    • 60849111957 scopus 로고    scopus 로고
    • Parallel short sequence assembly of transcriptomes
    • Jackson, B.G., Schnable, P.S., and Aluru, S. (2009) Parallel short sequence assembly of transcriptomes. BMC Bioinformatics 10, S1–14.
    • (2009) BMC Bioinformatics , vol.10 , pp. S1-14
    • Jackson, B.G.1    Schnable, P.S.2    Aluru, S.3
  • 28
    • 70349091863 scopus 로고    scopus 로고
    • A guide to the Proteomics Identifications Database proteomics data repository
    • Vizcaíno, J.A. et al. (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9, 4276–83.
    • (2009) Proteomics , vol.9 , pp. 4276-4283
    • Vizcaíno, J.A.1
  • 29
    • 58149203231 scopus 로고    scopus 로고
    • InterPro: The integrative protein signature database
    • Hunter, S. et al. (2009) InterPro: The integrative protein signature database. Nucleic Acids Res 37, 211–15.
    • (2009) Nucleic Acids Res , vol.37 , pp. 211-215
    • Hunter, S.1
  • 30
    • 14844282107 scopus 로고    scopus 로고
    • Comparative inter-atcomics
    • Cesareni, G. et al. (2005) Comparative inter-atcomics. FEBS Lett 579, 1828–33.
    • (2005) FEBS Lett , vol.579 , pp. 1828-1833
    • Cesareni, G.1
  • 31
    • 18344396568 scopus 로고    scopus 로고
    • Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
    • Brazma, A. et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29, 365–71.
    • (2001) Nat Genet , vol.29 , pp. 365-371
    • Brazma, A.1
  • 32
    • 35648976118 scopus 로고    scopus 로고
    • The diploid genome sequence of an individual human
    • Levy, S. et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5, 2113–44.
    • (2007) Plos Biol , vol.5 , pp. 2113-2144
    • Levy, S.1
  • 33
    • 42249087308 scopus 로고    scopus 로고
    • The complete genome of an individual by massively parallel DNA sequencing
    • Wheeler, D.A. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–76.
    • (2008) Nature , vol.452 , pp. 872-876
    • Wheeler, D.A.1
  • 34
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter, J.C. et al. (2001) The sequence of the human genome. Science 291, 1304–51.
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, J.C.1
  • 35
    • 33749416027 scopus 로고    scopus 로고
    • The influence of recombination on human genetic diversity
    • Spencer, C.C. et al. (2006) The influence of recombination on human genetic diversity. PLoS Genet 2, e148.
    • (2006) Plos Genet , vol.2 , pp. e148
    • Spencer, C.C.1
  • 36
    • 0037246058 scopus 로고    scopus 로고
    • ArrayExpress – A public repository for microarray gene expression data at the EBI
    • Brazma, A. et al. (2003) ArrayExpress – A public repository for microarray gene expression data at the EBI. Nucleic Acids Res 31, 68–71.
    • (2003) Nucleic Acids Res , vol.31 , pp. 68-71
    • Brazma, A.1
  • 37
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar, R., Domrachev, M., and Lash, A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30, 207–10.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 38
    • 0347122079 scopus 로고    scopus 로고
    • CIBEX: Center for information biology gene expression database
    • Ikeo, K. et al. (2003) CIBEX: Center for information biology gene expression database. C R Biol 326, 1079–82.
    • (2003) C R Biol , vol.326 , pp. 1079-1082
    • Ikeo, K.1
  • 39
    • 58149204055 scopus 로고    scopus 로고
    • ArrayExpress update – From an archive of functional genomics experiments to the atlas of gene expression
    • Parkinson, H. et al. (2009) ArrayExpress update – From an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37, 868–72.
    • (2009) Nucleic Acids Res , vol.37 , pp. 868-872
    • Parkinson, H.1
  • 40
    • 75549087047 scopus 로고    scopus 로고
    • The IntAct molecular interaction database
    • Aranda, B. et al. (2009) The IntAct molecular interaction database. Nucleic Acid Res. 1–7 doi:10.1093/nar/gkp878.
    • (2009) Nucleic Acid Res , pp. 1-7
    • Aranda, B.1
  • 41
    • 34249107988 scopus 로고    scopus 로고
    • The minimum information required for reporting a molecular interaction experiment (MIMIx)
    • Orchard, O. et al. (2007) The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 25, 894–8.
    • (2007) Nat Biotechnol , vol.25 , pp. 894-898
    • Orchard, O.1
  • 42
    • 34548863332 scopus 로고    scopus 로고
    • Comparative interactomics: Comparing apples and pears?
    • Kiemer, L., and Cesareni, G. (2007) Comparative interactomics: Comparing apples and pears? Trends Biotechnol 25, 448–54.
    • (2007) Trends Biotechnol , vol.25 , pp. 448-454
    • Kiemer, L.1    Cesareni, G.2
  • 43
    • 33947712535 scopus 로고    scopus 로고
    • WI-PHI: A weighted yeast interactome enriched for direct physical interactions
    • Kiemer, L. et al. (2007) WI-PHI: A weighted yeast interactome enriched for direct physical interactions. Proteomics 7, 932–43.
    • (2007) Proteomics , vol.7 , pp. 932-943
    • Kiemer, L.1
  • 44
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating ‘omics’ data sets
    • Joyce, A.R., and Palsson, B.Ø. (2006) The model organism as a system: Integrating ‘omics’ data sets. Nat Rev Mol Cell Biol 7, 198–210.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.Ø.2
  • 45
    • 80052938745 scopus 로고    scopus 로고
    • Techniques for integrating-omics Data
    • Akula, S.P. et al. (2009) Techniques for integrating-omics Data. Bioinformation 3, 284–6.
    • (2009) Bioinformation , vol.3 , pp. 284-286
    • Akula, S.P.1
  • 46
    • 67849095416 scopus 로고    scopus 로고
    • BioMart Central Portal – Unified access to biological data
    • Haider, S. et al. (2009) BioMart Central Portal – Unified access to biological data. Nucleic Acids Res 1, W23–27.
    • (2009) Nucleic Acids Res , vol.1 , pp. W23-W27
    • Haider, S.1
  • 47
    • 51249104057 scopus 로고    scopus 로고
    • Performing statistical analyses on quantitative data in Taverna work-flows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data
    • Li, P. et al. (2008) Performing statistical analyses on quantitative data in Taverna work-flows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data. BMC Bioinformatics 9, 334.
    • (2008) BMC Bioinformatics , vol.9
    • Li, P.1


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