Computational tools and Interoperability in Comparative ... - CBS

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Acknowledgments I would like to express a deep gratitude to my supervisor Prof. David Ussery for his support during my Ph.D. project. It has been a great pleasure to work with him during my time at CBS and I will miss the time of organizing workshops and preparing for conferences. A thanks to Prof. and center director Søren Brunak for creating a unique and inspiring environment at CBS which enabled this project. I would like to extend my heartfelt gratitude to Craig and Marcia Benham for the incribile hospitality and openness towards our family during my research visit at University of California, Davis in 2007. I would like to thank a great collegue and friend of mine, Tim T. Binnewies, for support during conferences, manuscript preperations and our daily colaborations - it has been a pleasure to work with Tim. A thanks to Karin Lagesen for great research collaboration during the development of RNAmmer and Hanni Willenbrock for great collaboration and for driving numerous publications. I would also like thank all the people I worked with during the development of the ENCODE pipeline, Ramneek Gupta, Thomas Blicher, Haakan Svensson, Henrik Nielsen, Rasmus Wernersson, Morten Bo Johansen and Eleonora Kulberkyte. A special thanks to Hans-Henrik Stærfeldt for valuable feedback and all the inspiring and productive sessions of finalizing GeneWiz Browser and composing web services software. A special thanks to Kristoffer Rapacki for being a great travel companion, for always finding solutions, and for the many fruitfull discussions we have had - I hope there will be more. I would like to thank the numerous people with whom I have had the pleasure of working with, during research projects and courses. Former center administrators Johanne Keiding and Anne Christensen, current center administrator Dorthe Kjærsgaard, Lone Boesen and Malene Beck for your extrodinary efforts of making the CBS engine running efficient. Lone Boesen deserves special praise for smoothly arranging and handling travel details for my many trips abroad, including five continents. vii
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Page 1 and 2: Peter Fischer Hallin | 2009 Peter F
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different applications, such as ide
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1 Comparative Genomics 2.7 Paper II
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166 literally millions of bacterial
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168
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170 resistance genes on mobile gene
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172 involved in generating diversit
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174 recipient DNA. A feature observ
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176 Fig. 5 Genome length distributi
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180 reasons why organisms remain un
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182 A final problem has to do with
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184 Middendorf B, Hochhut B, Leipol
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1 Comparative Genomics 2.8 Paper II
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2 O. N. Reva et al. Fig. 1. Genome
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4 O. N. Reva et al. decrease of the
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6 O. N. Reva et al. of which are kn
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8 O. N. Reva et al. compiled into a
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10 O. N. Reva et al. encoded by a c
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12 O. N. Reva et al. systems and ef
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1 2.9 Paper IV: The origins of Vibr
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phylogenies based on alternative ho
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Figure 1 Phylogenetic tree of the 1
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25000 20000 15000 10000 5000 0 Pan
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Gap F 2M 2.5M Gap E 875k 750k 625k
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Table 2 A selection of genes locate
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Open Access This article is distrib
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1 Comparative Genomics 2.10 Paper V
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4314 74 Tools Abstract: Of the plet
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4316 74 Tools Size distribution of
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4318 74 Tools Genome atlas Intrinsi
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4320 74 Tools Genome atlas Intrinsi
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4322 74 Tools for Comparison of Bac
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4324 74 Tools for Comparison of Bac
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4326 74 Tools information, as genet
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Chapter 3 rRNA operons and promoter
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tuB murI Fis III Fis II Fis I UP -3
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Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
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RNA operons and promoter analysis O
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Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
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Code Meaning Example C Coding CCCCC
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RNA operons and promoter analysis 3
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P2 -10 -35 UP P1 -10 -35 UP FIS FIS
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1 rRNA operons and promoter analysi
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Using HMMs also simplifies the use
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Information content Information con
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of the annotation. Some of the majo
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where match states stop around 10 c
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1 rRNA operons and promoter analysi
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synthesis in flow cells to simultan
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Read absence. A boolean where ‘on
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Hallin, et al. Figure 4 | The dataf
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Genome homology: Comparing multiple
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ing platform-‐independent Java
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34. Wang H, Noordewier M, Benham CJ
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Chapter 4 Web Services and Interope
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Web Services and Interoperability i
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Chapter 5 Conclusion and perspectiv
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Appendix A Appendix: Workshops, tea
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Appendix B Appendix: Ph.D. study pl
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Danmarks Tekniske Universitet AFI,
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Danmarks Tekniske Universitet AFI,
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Appendix C Appendix: Courses C.1 Gl
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D.2 Sample output from queryGenomes
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Appendix: Software 13 w a r n " $ o
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Appendix: Software 109 m y ( $ m i
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Appendix: Software 25 [ ] A l t e r
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BIBLIOGRAPHY J. Rogers, P. F. Stadl
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BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
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BIBLIOGRAPHY Velicer, F.-J. Vorholt
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