Data integration in microbial genomics ... - Jacobs University

More documents

Recommendations

Info

104 BIBLIOGRAPHY oceanic regions by small-subunit rrna gene cloning and sequencing. Appl Environ Microbiol, 67(7):2932–2941. [Etchemendy, 1999] Etchemendy, J. B. . J. (1999). Language, Proof and Logic. Seven Bridges Press,U.S. [Falkowski et al., 1998] Falkowski, Barber, and Smetacek (1998). Biogeochemical controls and feedbacks on ocean primary production. Science, 281(5374):200–207. [Field et al., 1998] Field, Behrenfeld, Randerson, and Falkowski (1998). Primary production of the biosphere: integrating terrestrial and oceanic components. Science, 281(5374):237–240. [Field, 2008] Field, D. (2008). Working together to put molecules on the map. Nature, 453(7198):978. [Field et al., 2008] Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M. J., Angiuoli, S. V., Ashburner, M., Axelrod, N., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., Dawyndt, P., Vos, P. D., DePamphilis, C., Edwards, R., Faruque, N., Feldman, R., Gilbert, J., Gilna, P., Glöckner, F. O., Goldstein, P., Guralnick, R., Haft, D., Hancock, D., Hermjakob, H., Hertz-Fowler, C., Hugenholtz, P., Joint, I., Kagan, L., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann, R., Kolker, E., Kravitz, S., Kyrpides, N., Leebens-Mack, J., Lewis, S. E., Li, K., Lister, A. L., Lord, P., Maltsev, N., Markowitz, V., Martiny, J., Methe, B., Mizrachi, I., Moxon, R., Nelson, K., Parkhill, J., Proctor, L., White, O., Sansone, S.-A., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward, N., Whetzel, T., Gil, I. S., Wilson, G., and Wipat, A. (2008). The minimum information about a genome sequence (migs) specification. Nat Biotechnol, 26(5):541–547. [Finn et al., 2008] Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H.-R., Ceric, G., Forslund, K., Eddy, S. R., Sonnhammer, E. L. L., and Bateman, A. (2008). The pfam protein families database. Nucleic Acids Res, 36(Database issue):D281– D288.
BIBLIOGRAPHY 105 [Floridi, 2003] Floridi, L. (2003). Two approaches to the philosophy of information. Minds Mach., 13:459–469. [Francis et al., 2007] Francis, C. A., Beman, J. M., and Kuypers, M. M. M. (2007). New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J, 1(1):19–27. [Fruchterman and Reingold, 1991] Fruchterman, T. M. J. and Reingold, E. M. (1991). Graph drawing by force-directed placement. Software Pract Ex, 21(11):1129–1164. [Fuhrman, 2009] Fuhrman, J. A. (2009). Microbial community structure and its functional implications. Nature, 459(7244):193–199. [Fuhrman et al., 2006] Fuhrman, J. A., Hewson, I., Schwalbach, M. S., Steele, J. A., Brown, M. V., and Naeem, S. (2006). Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci U S A, 103(35):13104–13109. [Fuhrman et al., 1992] Fuhrman, J. A., McCallum, K., and Davis, A. A. (1992). Novel major archaebacterial group from marine plankton. Nature, 356(6365):148–149. [Fuhrman et al., 2008] Fuhrman, J. A., Steele, J. A., Hewson, I., Schwalbach, M. S., Brown, M. V., Green, J. L., and Brown, J. H. (2008). A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci U S A, 105(22):7774–7778. [Galperin and Koonin, 2010] Galperin, M. Y. and Koonin, E. V. (20032010). From complete genome sequence to ’complete’ understanding? Trends Biotechnol, 28(8):398–406. [Gilbert et al., 2009] Gilbert, J. A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., Somerfield, P. J., Huse, S., and Joint, I. (2009). The seasonal structure of microbial communities in the western english channel. Environ Microbiol, 11(12):3132–3139. [Gilbert and Maxam, 1973] Gilbert, W. and Maxam, A. (1973). The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A, 70(12):3581–3584.
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 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 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?