Data integration in microbial genomics ... - Jacobs University

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114 BIBLIOGRAPHY (2006). Microbial diversity in the deep sea and the underexplored ”rare biosphere”. Proc Natl Acad Sci U S A, 103(32):12115–12120. [Stahl et al., 1984] Stahl, D. A., Lane, D. J., Olsen, G. J., and Pace, N. R. (1984). Analysis of hydrothermal vent-associated symbionts by ribosomal rna sequences. Science, 224(4647):409–411. [Stratton et al., 2009] Stratton, M. R., Campbell, P. J., and Futreal, P. A. (2009). The cancer genome. Nature, 458(7239):719–724. [Sullivan et al., 2005] Sullivan, M. B., Coleman, M. L., Weigele, P., Rohwer, F., and Chisholm, S. W. (2005). Three prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol, 3(5):e144. [Taylor et al., 2008] Taylor, C. F., Field, D., Sansone, S.-A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C. A., Binz, P.-A., Bogue, M., Booth, T., Brazma, A., Brinkman, R. R., Clark, A. M., Deutsch, E. W., Fiehn, O., Fostel, J., Ghazal, P., Gibson, F., Gray, T., Grimes, G., Hancock, J. M., Hardy, N. W., Hermjakob, H., Julian, R. K., Kane, M., Kettner, C., Kinsinger, C., Kolker, E., Kuiper, M., Novère, N. L., Leebens-Mack, J., Lewis, S. E., Lord, P., Mallon, A.-M., Marthandan, N., Masuya, H., McNally, R., Mehrle, A., Morrison, N., Orchard, S., Quackenbush, J., Reecy, J. M., Robertson, D. G., Rocca-Serra, P., Rodriguez, H., Rosenfelder, H., Santoyo- Lopez, J., Scheuermann, R. H., Schober, D., Smith, B., Snape, J., Stoeckert, C. J., Tipton, K., Sterk, P., Untergasser, A., Vandesompele, J., and Wiemann, S. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the mibbi project. Nat Biotechnol, 26(8):889–896. [Turnbaugh et al., 2007] Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., and Gordon, J. I. (2007). The human microbiome project. Nature, 449(7164):804–810. [Tyson et al., 2004] Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., and Banfield, J. F. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428(6978):37–43.
BIBLIOGRAPHY 115 [van der Staay et al., 2001] van der Staay, S. Y. M., Wachter, R. D., and Vaulot, D. (2001). Oceanic 18s rdna sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature, 409(6820):607– 610. [Venter et al., 2004] Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.-H., and Smith, H. O. (2004). Environmental genome shotgun sequencing of the sargasso sea. Science, 304(5667):66–74. [Virtanen et al., 2006] Virtanen, R., Oksanen, J., Oksanen, L., and Razzhivin, V. Y. (2006). Broad-scale vegetation-environment relationships in eurasian high-latitude areas. J Veg Sci, 17(4):519–528. [Vogel et al., 2009] Vogel, T. M., Simonet, P., Jansson, J. K., Hirsch, P. R., Tiedje, J. M., van Elsas, J. D., Bailey, M. J., Nalin, R., and Philippot, L. (2009). Terragenome: a consortium for the sequencing of a soil metagenome. Nature Reviews Microbiology, 7(4):252–252. 10.1038/nrmicro2119. [Ward et al., 1990] Ward, D. M., Weller, R., and Bateson, M. M. (1990). 16s rrna sequences reveal numerous uncultured microorganisms in a natural community. Nature, 345(6270):63–65. [Watson and Crick, 1953] Watson, J. D. and Crick, F. H. (1953). Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171(4356):737–738. [Whitman et al., 1998] Whitman, W. B., Coleman, D. C., and Wiebe, W. J. (1998). Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A, 95(12):6578–6583. [Wieczorek et al., 2004] Wieczorek, J., Guo, Q., and Hijmans, R. (2004). The point-radius method for georeferencing locality descriptions and calculating associated uncertainty. International Journal of Geographical Information Science, 18(8):745–767.
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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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4.4. Survey of published parameters
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Page 83 and 84: 5.4. User Access 75 tal context, co
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Page 97 and 98: 7.2. GSC standards development 89 T
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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
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
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Page 127: CHAPTER 9 ACKNOWLEDGEMENTS First, I
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