Computational tools and Interoperability in Comparative ... - CBS
Computational tools and Interoperability in Comparative ... - CBS
Computational tools and Interoperability in Comparative ... - CBS
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Danmarks Tekniske Universitet AFI, Ph.d.-uddannelse<br />
September 2005<br />
Ph.d.-studerendes navn: Peter Fischer Hall<strong>in</strong><br />
Cpr.-nr.: 160877 2053<br />
held at <strong>CBS</strong> <strong>in</strong> February 2008:<br />
http://www.cbs.dtu.dk/courses/embrace/2008-02-<br />
06/programme.php. Lectures <strong>and</strong> exercies will be adjusted to cover<br />
promoter analysis us<strong>in</strong>g the EMBRACE technology. We <strong>in</strong>tend to<br />
use graphical as well as statistical approaches to characterize<br />
promoter signatures of prokaryotic genomes. These are core topics<br />
of the thesis.<br />
Poster presentation at Metagenomics 2007, San Diego: “Gene<br />
organization of RNA genes <strong>and</strong> secretion system components of<br />
the Sargasso Sea environmental samples”<br />
(Her anføres studiets forventede dels formidl<strong>in</strong>gs-aktivteter og dels det pålagte pligtarbejde. For hver del angives<br />
det skønnede tidsforbrug (f.eks. i uger), der sammenlagt skal svare til 3 måneder).<br />
Tidsplan:<br />
1st half year (March 06 –August 06)<br />
Publication on rRNA gene predictor (RNAmmer). <strong>Comparative</strong> Microbial Genomics worksshop <strong>in</strong><br />
Brasil. Meet<strong>in</strong>gs <strong>and</strong> work for <strong>CBS</strong> <strong>in</strong> connection to EMBRACE.<br />
2nd half year (September 06 – Feb 07)<br />
Lactococcus microarray project with Chr Hansen. Book chapter on <strong>Comparative</strong> Genomics, editor<br />
Dawn Field. EMBRACE meet<strong>in</strong>gs <strong>and</strong> workshops.<br />
3rd half year (March 07 –August 07)<br />
Followup article on RNAmmer – <strong>and</strong> rRNA/tRNA operons.<br />
4th half year (September 07 – Feb 08)<br />
(Oct-Dec) Internship, Craig Benham: Davis, California,<br />
Include work from Craig Benhams lab <strong>in</strong>to RNAmmer followup manuscript <strong>and</strong> prepare SIDDbase<br />
application note <strong>and</strong> article on SIDD measures <strong>in</strong> prokaryotic promotor sequences.<br />
Prepare manuscripts<br />
5th. half year (March 08 –August 08)<br />
Course: Globale regulatoriske netværk i mikroorganismer (F2B)<br />
Course: Prote<strong>in</strong> structure <strong>and</strong> computational biology (F5A)<br />
Course: 1 week may/june: 27802 Metabolic Eng<strong>in</strong>eer<strong>in</strong>g <strong>and</strong> Systems Biology<br />
Thesis writ<strong>in</strong>g+Prepare manuscripts<br />
6th. half year (September 08 – Feb 09)<br />
Course: Introduction to Systems Biology<br />
Thesis writ<strong>in</strong>g<br />
(Tidsplanen bør <strong>in</strong>deholde tidspunkter/perioder for alle væsentlige aktiviteter her i forb<strong>in</strong>delse med ph.d.uddannelsen.<br />
Det er vigtigt, at tidsplanen er fuldstændig., Den kan vedlægges som appendiks).<br />
Kort beskrivelse af<br />
vejledn<strong>in</strong>gens form:<br />
Det kan bl.a. aftales, hvor tit vejledn<strong>in</strong>gen sker i form af møder eller ved skriftlig tilbagemeld<strong>in</strong>g<br />
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