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Danmarks Tekniske Universitet AFI, Ph.d.-uddannelse September 2005 Ph.d.-studerendes navn: Peter Fischer Hallin Cpr.-nr.: 160877 2053 held at CBS in February 2008: http://www.cbs.dtu.dk/courses/embrace/2008-02- 06/programme.php. Lectures and exercies will be adjusted to cover promoter analysis using the EMBRACE technology. We intend to use graphical as well as statistical approaches to characterize promoter signatures of prokaryotic genomes. These are core topics of the thesis. Poster presentation at Metagenomics 2007, San Diego: “Gene organization of RNA genes and secretion system components of the Sargasso Sea environmental samples” (Her anføres studiets forventede dels formidlings-aktivteter og dels det pålagte pligtarbejde. For hver del angives det skønnede tidsforbrug (f.eks. i uger), der sammenlagt skal svare til 3 måneder). Tidsplan: 1st half year (March 06 –August 06) Publication on rRNA gene predictor (RNAmmer). Comparative Microbial Genomics worksshop in Brasil. Meetings and work for CBS in connection to EMBRACE. 2nd half year (September 06 – Feb 07) Lactococcus microarray project with Chr Hansen. Book chapter on Comparative Genomics, editor Dawn Field. EMBRACE meetings and workshops. 3rd half year (March 07 –August 07) Followup article on RNAmmer – and rRNA/tRNA operons. 4th half year (September 07 – Feb 08) (Oct-Dec) Internship, Craig Benham: Davis, California, Include work from Craig Benhams lab into RNAmmer followup manuscript and prepare SIDDbase application note and article on SIDD measures in prokaryotic promotor sequences. Prepare manuscripts 5th. half year (March 08 –August 08) Course: Globale regulatoriske netværk i mikroorganismer (F2B) Course: Protein structure and computational biology (F5A) Course: 1 week may/june: 27802 Metabolic Engineering and Systems Biology Thesis writing+Prepare manuscripts 6th. half year (September 08 – Feb 09) Course: Introduction to Systems Biology Thesis writing (Tidsplanen bør indeholde tidspunkter/perioder for alle væsentlige aktiviteter her i forbindelse med ph.d.uddannelsen. Det er vigtigt, at tidsplanen er fuldstændig., Den kan vedlægges som appendiks). Kort beskrivelse af vejledningens form: Det kan bl.a. aftales, hvor tit vejledningen sker i form af møder eller ved skriftlig tilbagemelding 4
Danmarks Tekniske Universitet AFI, Ph.d.-uddannelse September 2005 Ph.d.-studerendes navn: Peter Fischer Hallin Cpr.-nr.: 160877 2053 Patenter/innovation: Der er sandsynlighed for, at der under projektet udvikles teknologier eller software, som kan patenteres? Hvis Ja Ja x Nej Kort redegørelse for hvilke metoder, der anvendes til oplæring af den ph.d.-studerende i de innovationsmæssige aspekter Andet: (Her kan anføres andre forhold af betydning for bedømmelsen af studieplanen). 5
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Peter Fischer Hallin | 2009 Peter F
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Preface This Ph.D. thesis is writte
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thesis, the work is just being publ
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ved at blive publiceret i Standards
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Paper VI [Lagesen K, Hallin P] 1 ,
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xii
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3.3.3 Refining E. coli and Shigella
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xvi
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xviii 2.17 Pan- and core-genome plo
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Chapter 1 Introduction Introduction
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Chapter 2 Comparative Genomics 2.1
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Comparative Genomics the publicly a
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Comparative Genomics source CDS tot
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Comparative Genomics 1 mysql -N -B
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Listing 2.8: R code to generate a 2
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1st U C A G U 2nd position C A G 3r
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1st U C A G U 2nd position C A G 3r
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Escherichia coli strain K-12, subst
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Comparative Genomics
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3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
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Streptococcus Escherichia Bacillus
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2.4 Summary Comparative Genomics Th
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Comparative Genomics 2.5 Instant in
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‘ReSourCe is he best online submi
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up to a total of 41 different E. co
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Fig. 2 Genes (or segments) from eac
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Fig. 5 BLASTatlas of Clostridium bo
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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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178
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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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Page 164 and 165: ing platform-‐independent Java
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Page 178 and 179: Chapter 5 Conclusion and perspectiv
Page 180 and 181: Appendix A Appendix: Workshops, tea
Page 182 and 183: Appendix B Appendix: Ph.D. study pl
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Page 188 and 189: Appendix C Appendix: Courses C.1 Gl
Page 190 and 191: D.2 Sample output from queryGenomes
Page 192 and 193: Appendix: Software 13 w a r n " $ o
Page 194 and 195: Appendix: Software 109 m y ( $ m i
Page 196 and 197: Appendix: Software 25 [ ] A l t e r
Page 198 and 199: BIBLIOGRAPHY J. Rogers, P. F. Stadl
Page 200 and 201: BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
Page 202 and 203: BIBLIOGRAPHY Velicer, F.-J. Vorholt
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