Data integration in microbial genomics ... - Jacobs University

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106 BIBLIOGRAPHY [Giovannoni et al., 1990] Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., and Field, K. G. (1990). Genetic diversity in sargasso sea bacterioplankton. Nature, 345(6270):60–63. [Glöckner and Joint, 2010] Glöckner, F. O. and Joint, I. (2010). Marine microbial genomics in europe: current status and perspectives. Microb Biotechnol, 3(5):523–530. [Goonesekere et al., 2010] Goonesekere, N. C. W., Shipely, K., and O’Connor, K. (2010). The challenge of annotating protein sequences: The tale of eight domains of unknown function in pfam. Comput Biol Chem, 34(3):210–214. [Green et al., 2008] Green, J. L., Bohannan, B. J. M., and Whitaker, R. J. (2008). Microbial biogeography: from taxonomy to traits. Science, 320(5879):1039–1043. [Gruber, 1993] Gruber, T. R. (1993). A translation approach to portable ontology specifications. Knowl. Acquis., 5:199–220. [Hall, 2007] Hall, N. (2007). Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol, 210(Pt 9):1518– 1525. [Handelsman, 2004] Handelsman, J. (2004). Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev, 68(4):669–685. [Hankeln et al., 2010] Hankeln, W., Buttigieg, P. L., Fink, D., Kottmann, R., Yilmaz, P., and Glöckner, F. O. (2010). Metabar - a tool for consistent contextual data acquisition and standards compliant submission. BMC Bioinformatics, 11:358. [Hanner, 2009] Hanner, R. (2009). Data standards for barcode records in insdc (bris). [Henry et al., 2010] Henry, C., Overbeek, R., and Stevens, R. L. (2010). Building the blueprint of life. Biotechnol J, 5(7):695–704. [Henry et al., 2007] Henry, C. S., Broadbelt, L. J., and Hatzimanikatis, V. (2007). Thermodynamics-based metabolic flux analysis. Biophys J, 92(5):1792–1805.
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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
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
Page 69 and 70: 4.4. Survey of published parameters
Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
Page 73 and 74: 4.6. Conclusions and call for actio
Page 75 and 76: CHAPTER 5 MEGX.NET Integrated datab
Page 77 and 78: 5.3. New database structure and con
Page 79 and 80: 5.3. New database structure and con
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
Page 85: 5.5. Summary 77 access charge: Max
Page 88 and 89: 80 6. Domains of unknown function 6
Page 90 and 91: 82 6. Domains of unknown function F
Page 92 and 93: 84 6. Domains of unknown function p
Page 95 and 96: CHAPTER 7 SUMMARY AND DISCUSSION Th
Page 97 and 98: 7.2. GSC standards development 89 T
Page 99 and 100: 7.2. GSC standards development 91 o
Page 101 and 102: 7.4. In silico Hypothesis Generatio
Page 103: 7.5. Getting the most out of the da
Page 106 and 107: 98 8. Conclusion and outlook nities
Page 108 and 109: 100 8. Conclusion and outlook plina
Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
Page 116 and 117: 108 BIBLIOGRAPHY [Kitano, 2002] Kit
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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