Data integration in microbial genomics ... - Jacobs University

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112 BIBLIOGRAPHY [Ramette, 2007] Ramette, A. (2007). Multivariate analyses in microbial ecology. FEMS Microbiol Ecol, 62(2):142–160. [Rappé and Giovannoni, 2003] Rappé, M. S. and Giovannoni, S. J. (2003). The uncultured microbial majority. Annu Rev Microbiol, 57:369–394. [Ratnasingham and Hebert, 2007] Ratnasingham, S. and Hebert, P. D. N. (2007). bold: The barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes, 7(3):355–364. [Richter, 2003] Richter, S. (2003). Feature-based Programming - Planung, Programmierung, Projekt-Management: Über die Kunst systematisch zu planen und mit Agilität umzusetzen. ADDISON- WESLEY. [Roberts, 2004] Roberts, R. J. (2004). Identifying protein function–a call for community action. PLoS Biol, 2(3):E42. [Roberts et al., 2011] Roberts, R. J., Chang, Y.-C., Hu, Z., Rachlin, J. N., Anton, B. P., Pokrzywa, R. M., Choi, H.-P., Faller, L. L., Guleria, J., Housman, G., Klitgord, N., Mazumdar, V., McGettrick, M. G., Osmani, L., Swaminathan, R., Tao, K. R., Letovsky, S., Vitkup, D., Segrè, D., Salzberg, S. L., Delisi, C., Steffen, M., and Kasif, S. (2011). Combrex: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res, 39(Database issue):D11–D14. [Rocca-Serra et al., 2010] Rocca-Serra, P., Brandizi, M., Maguire, E., Sklyar, N., Taylor, C., Begley, K., Field, D., Harris, S., Hide, W., Hofmann, O., Neumann, S., Sterk, P., Tong, W., and Sansone, S.-A. (2010). Isa software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics, 26(18):2354–2356. [Rowley, 2007] Rowley, J. (2007). The wisdom hierarchy: representations of the dikw hierarchy. 33(2):163–180. Journal of Information Science, [Rusch et al., 2007] Rusch, D. B., Halpern, A. L., Sutton, G., Heidelberg, K. B., Williamson, S., Yooseph, S., Wu, D., Eisen, J. A.,
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Max Planck Institute for Marine Mic
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List of abbreviations BLAST Basic L
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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2 1. Introduction syntax: data leve
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4 1. Introduction used to derive ne
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6 1. Introduction croorganisms thri
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8 1. Introduction the middle at the
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10 1. Introduction marker genes hel
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12 1. Introduction what kind and wh
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14 1. Introduction possibilities li
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16 1. Introduction tual data acquis
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18 1. Introduction Doug Wendel, Owe
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CHAPTER 2 METABAR A tool for consis
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2.2. Background 23 molecular sequen
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2.2. Background 25 printing of data
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2.4. Results 27 KML export function
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2.4. Results 29 Figure 2.3: Screens
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2.5. Discussion 31 taking samples i
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2.5. Discussion 33 Handlebar MetaBa
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2.6. Conclusion 35 rine Microbiolog
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2.6. Conclusion 37 RK advised progr
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40 3. CDinFusion Genomic Standards
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42 3. CDinFusion sortium (GSC), an
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44 3. CDinFusion tiFASTA file with
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46 3. CDinFusion offered the option
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48 3. CDinFusion AMD Opteron TM pro
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50 3. CDinFusion able separately an
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52 3. CDinFusion and upload it with
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CHAPTER 4 MIMARKS The Minimum infor
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4.2. Introduction 57 edge generatio
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4.3. Development of MIMARKS 59 in t
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Page 83 and 84: 5.4. User Access 75 tal context, co
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Page 88 and 89: 80 6. Domains of unknown function 6
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Page 97 and 98: 7.2. GSC standards development 89 T
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Page 106 and 107: 98 8. Conclusion and outlook nities
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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
Page 114 and 115: 106 BIBLIOGRAPHY [Giovannoni et al.
Page 116 and 117: 108 BIBLIOGRAPHY [Kitano, 2002] Kit
Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
Page 122 and 123: 114 BIBLIOGRAPHY (2006). Microbial
Page 124 and 125: 116 BIBLIOGRAPHY [Williamson et al.
Page 127: CHAPTER 9 ACKNOWLEDGEMENTS First, I
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