Data integration in microbial genomics ... - Jacobs University

More documents

Recommendations

Info

108 BIBLIOGRAPHY [Kitano, 2002] Kitano, H. (2002). Computational systems biology. Nature, 420(6912):206–210. [Kottmann et al., 2008] Kottmann, R., Gray, T., Murphy, S., Kagan, L., Kravitz, S., Lombardot, T., Field, D., Glöckner, F. O., and Consortium, G. S. (2008). A standard migs/mims compliant xml schema: toward the development of the genomic contextual data markup language (gcdml). OMICS, 12(2):115–121. [Kottmann et al., 2010] Kottmann, R., Kostadinov, I., Duhaime, M. B., Buttigieg, P. L., Yilmaz, P., Hankeln, W., Waldmann, J., and Glöckner, F. O. (2010). Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res, 38(Database issue):D391–D395. [Krcmar, 2009] Krcmar, H. (2009). Informationsmanagement. Springer, Berlin, 5 edition. [Lenzerini, 2002] Lenzerini, M. (2002). Data integration: a theoretical perspective. In Proceedings of the twenty-first ACM SIGMOD- SIGACT-SIGART symposium on Principles of database systems, PODS ’02, pages 233–246, New York, NY, USA. ACM. [Liolios et al., 2008] Liolios, K., Mavromatis, K., Tavernarakis, N., and Kyrpides, N. C. (2008). The genomes on line database (gold) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res, 36(Database issue):D475–D479. [Lombardot et al., 2006] Lombardot, T., Kottmann, R., Pfeffer, H., Richter, M., Teeling, H., Quast, C., and Glöckner, F. O. (2006). Megx.net–database resources for marine ecological genomics. Nucleic Acids Res, 34(Database issue):D390–D393. [Ludwig et al., 1994] Ludwig, W., Dorn, S., Springer, N., Kirchhof, G., and Schleifer, K. H. (1994). Pcr-based preparation of 23s rrnatargeted group-specific polynucleotide probes. Appl Environ Microbiol, 60(9):3236–3244. [Ludwig and Schleifer, 1994] Ludwig, W. and Schleifer, K. H. (1994). Bacterial phylogeny based on 16s and 23s rrna sequence analysis. FEMS Microbiol Rev, 15(2-3):155–173.
BIBLIOGRAPHY 109 [Ludwig and Schleifer, 2005] Ludwig, W. and Schleifer, K. H. (2005). Molecular phylogeny of bacteria based on comparative sequence analysis of conserved genes, pages 70–98. Oxford university press, New York, USA. [Ludwig et al., 1998] Ludwig, W., Strunk, O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., Bachleitner, M., and Schleifer, K. H. (1998). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis, 19(4):554–568. Using Smart Source Parsing. [Ludwig et al., 2004] Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I., Gerber, S., Ginhart, A. W., Gross, O., Grumann, S., Hermann, S., Jost, R., König, A., Liss, T., Lüssmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., and Schleifer, K.-H. (2004). Arb: a software environment for sequence data. Nucleic Acids Res, 32(4):1363–1371. [López-García et al., 2001] López-García, P., Rodríguez-Valera, F., Pedrós-Alió, C., and Moreira, D. (2001). Unexpected diversity of small eukaryotes in deep-sea antarctic plankton. Nature, 409(6820):603–607. [Madigan, 2006] Madigan, Michael T & Martinko, J. M. (2006). Brock - Biology of Microorganisms. Pearson / Prentice Hall, 11th edition. [Mardis, 2008] Mardis, E. R. (2008). Next-generation dna sequencing methods. Annu Rev Genomics Hum Genet, 9:387–402. [Markowitz et al., 2008] Markowitz, V. M., Ivanova, N. N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I.-M. A., Grechkin, Y., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K., Hugenholtz, P., and Kyrpides, N. C. (2008). Img/m: a data management and analysis system for metagenomes. Nucleic Acids Res, 36(Database issue):D534–D538. [Martinez et al., 2010] Martinez, A., Tyson, G. W., and Delong, E. F. (2010). Widespread known and novel phosphonate utilization
Page 1:
Max Planck Institute for Marine Mic
Page 4 and 5:
List of abbreviations BLAST Basic L
Page 6 and 7:
Thesis abstract Deoxyribonucleic ac
Page 8 and 9:
4.2 Introduction . . . . . . . . .
Page 10 and 11:
2 1. Introduction syntax: data leve
Page 12 and 13:
4 1. Introduction used to derive ne
Page 14 and 15:
6 1. Introduction croorganisms thri
Page 16 and 17:
8 1. Introduction the middle at the
Page 18 and 19:
10 1. Introduction marker genes hel
Page 20 and 21:
12 1. Introduction what kind and wh
Page 22 and 23:
14 1. Introduction possibilities li
Page 24 and 25:
16 1. Introduction tual data acquis
Page 26 and 27:
18 1. Introduction Doug Wendel, Owe
Page 29 and 30:
CHAPTER 2 METABAR A tool for consis
Page 31 and 32:
2.2. Background 23 molecular sequen
Page 33 and 34:
2.2. Background 25 printing of data
Page 35 and 36:
2.4. Results 27 KML export function
Page 37 and 38:
2.4. Results 29 Figure 2.3: Screens
Page 39 and 40:
2.5. Discussion 31 taking samples i
Page 41 and 42:
2.5. Discussion 33 Handlebar MetaBa
Page 43 and 44:
2.6. Conclusion 35 rine Microbiolog
Page 45:
2.6. Conclusion 37 RK advised progr
Page 48 and 49:
40 3. CDinFusion Genomic Standards
Page 50 and 51:
42 3. CDinFusion sortium (GSC), an
Page 52 and 53:
44 3. CDinFusion tiFASTA file with
Page 54 and 55:
46 3. CDinFusion offered the option
Page 56 and 57:
48 3. CDinFusion AMD Opteron TM pro
Page 58 and 59:
50 3. CDinFusion able separately an
Page 60 and 61:
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 114 and 115: 106 BIBLIOGRAPHY [Giovannoni et al.
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
show all

Data integration in microbial genomics ... - Jacobs University

Create successful ePaper yourself

Delete template?

Save as template?