Computational tools and Interoperability in Comparative ... - CBS

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Publications and manuscripts Publications included in this thesis are listed in the order they appear. All other articles are sorted by publication date, descending. For papers with five and more citations this number is indicated. Paper I Hallin PF, Binnewies TT, Ussery DW. The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst 4:363-71 (2008). Paper II Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D. La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW. Ten years of bacterial genome sequencing: comparative– genomics–based discoveries. Funct Integr Genomics 6:165-85 (2006) - 56 citations. Paper III Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW Global features of the Alcanivorax borkumensis SK2 genome. Environ Microbiol 10:614- 25 (2008). Paper IV Vesth T, Hallin PF, Snipen L, Lagesen K, Wassenaar TM, Ussery DW. The origins of Vibrio species. Microbial Ecology (2009) doi:10.1007/s00248-009-9596-7 Paper V Wassenaar TM, Binnewies TT, Hallin PF, and Ussery DW Tools for comparison of bacterial genomes. Book chapter, Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds, Springer-Verlag, Heidelberg, Germany, 2009. ix
Paper VI [Lagesen K, Hallin P] 1 , Rodland EA, Stærfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100-8 (2007) - 8 citations 2 Paper VII Hallin PF, Stærfeldt H, Rotenberg E, Binnewies TT, Benham CJ, and Ussery DW. GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes. Standards in Genomic Sciences 1:204-215 (2009) doi:10.4056/sigs.28177. Papers not included Contributions have been made to the following papers during my PhD project. • Miller WG, Parker CT, Rubenfield M, Mendz GL, Wosten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE. The complete genome sequence and analysis of the human pathogen Arcobacter butzleri. PLoS ONE 2:e1358 (2007) • Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol 8:R267 (2007) Earlier papers, 2004–2006 • Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW Origin of replication in circular prokaryotic chromosomes. Environ Microbiol 8:353-61 (2006) - 28 citations • Kill K, Binnewies TT, Sicheritz-Ponten T, Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW Genome update: sigma factors in 240 bacterial genomes. Microbiology 151:3147-50 (2005) • Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW Genome update: prediction of membrane proteins in prokaryotic genomes. Microbiology 151:2119-21 (2005) • Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Ponten T, Ussery DW Genome update: prediction of secreted proteins in 225 bacterial proteomes. Microbiology 151:1725-7 (2005) • Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW Genome Update: Protein secretion systems in 225 bacterial genomes. Microbiology 151:1013-6 (2005) • Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW Genome update: base skews in 200+ bacterial chromosomes. Microbiology 151:633-7 (2005) 1 Both authors contributed equally 2 Additionally 8 citations for the first 8 GEBA genomes published in SIGS journal; being part of a standard pipeline, RNAmmer will be cited for future GEBA articles. x
Page 1 and 2: Peter Fischer Hallin | 2009 Peter F
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1 Comparative Genomics 2.7 Paper II
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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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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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