Data integration in microbial genomics ... - Jacobs University

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102 BIBLIOGRAPHY [Beynon-Davies, 2002] Beynon-Davies, P. (2002). Information Systems: an Introduction to Informatics in Organizations. Palgrave Macmillan. ISBN 0333963903. [Bialas et al., 2007] Bialas, J., Greinert, J., Linke, P., and Pfannkuche, O. (2007). Rv sonne fahrtbericht / cruise report so 191 - new vents ”puaretanga hou” : Wellington - napier - auckland, 11.01. - 23.03.2007. Cruise Report 10.3289/ifm-geomar_rep_9_2007, Kiel, Germany. [Binnewies et al., 2006] Binnewies, T., Motro, Y., Hallin, P., Lund, O., Dunn, D., La, T., Hampson, D., Bellgard, M., Wassenaar, T., and Ussery, D. (2006). Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics. [Booth et al., 2007] Booth, T., Gilbert, J., Neufeld, J. D., Ball, J., Thurston, M., Chipman, K., Joint, I., and Field, D. (2007). Handlebar: a flexible, web-based inventory manager for handling barcoded samples. Biotechniques, 42(3):300, 302. [Breitling et al., 2008] Breitling, R., Gilbert, D., Heiner, M., and Orton, R. (2008). A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Brief Bioinform, 9(5):404–421. [Brussaard et al., 2008] Brussaard, C. P. D., Wilhelm, S. W., Thingstad, F., Weinbauer, M. G., Bratbak, G., Heldal, M., Kimmance, S. A., Middelboe, M., Nagasaki, K., Paul, J. H., Schroeder, D. C., Suttle, C. A., Vaqué, D., and Wommack, K. E. (2008). Globalscale processes with a nanoscale drive: the role of marine viruses. ISME J, 2(6):575–578. [Caporaso et al., 2010] Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R. (2010). Qiime allows analysis of high-
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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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Page 63 and 64: CHAPTER 4 MIMARKS The Minimum infor
Page 65 and 66: 4.2. Introduction 57 edge generatio
Page 67 and 68: 4.3. Development of MIMARKS 59 in t
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Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
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Page 81 and 82: 5.4. User Access 73 5.4 User Access
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 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
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Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
Page 120 and 121: 112 BIBLIOGRAPHY [Ramette, 2007] Ra
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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