Difference between revisions of "DNA Microarray Analysis (academic course)"

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(→‎Course Programme: major format changes)
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=== 2-Jan-2006 (Monday): <I>Introduction to microarray technology and R software</I> ===
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=== 2-Jan-2006 (Monday): ''Introduction to microarray technology and R software'' ===
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<DL>
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<DT>9.00-9.30 
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<DD>Introduction to course ([http://www.cbs.dtu.dk/~hbjorn/Teaching/course.intro.web.pdf Lecture slides])
+
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<BR>H. Bj&oslash;rn Nielsen
+
  
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<DT>9.30-9.45 
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: 09.00-09.30
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<DD>Pre-test
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:: Introduction to course ([http://www.cbs.dtu.dk/~hbjorn/Teaching/course.intro.web.pdf Lecture slides])
−
<BR>H. Bj&oslash;rn Nielsen  
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:: H. Bj&oslash;rn Nielsen  
  
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<DT>9.45-10.30
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: 09.30-09.45
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<dd>Overview over gene expression and DNA microarray technology (Chapter 1)
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:: Pre-test
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([http://www.cbs.dtu.dk/chipcourse/Lectures/OverviewJan06.ppt Lecture slides])</dd>
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:: H. Bj&oslash;rn Nielsen
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<DD>Jeppe S. Spicker
+
  
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<DT>10.30-10.45
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: 9.45-10.30
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<DD><I>Break</I>
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:: Overview over gene expression and DNA microarray technology (Chapter 1)([http://www.cbs.dtu.dk/chipcourse/Lectures/OverviewJan06.ppt Lecture slides])
 +
:: Jeppe S. Spicker
  
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<DT>10.45-11.45
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: 10.30-10.45
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<DD><b>Case story:</b> Analysis of the cell cycle
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:: ''Break''
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(<A href="cell.cycle.lecture.pdf" target=_blank>Lecture slides</A>,
+
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<A href="deLichtenberg.Bioformatics.2004.pdf" target=_blank>de Lichtenberg <i>et al</i>. 2004</A>)
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<BR>Ulrik de Lichtenberg
+
  
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<DT>11.45-12.15 
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: 10.45-11.45
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<DD>Demonstration of microarray equipment at CBS (in groups)
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:: '''Case story''': Analysis of the cell cycle ([http://www.cbs.dtu.dk/chipcourse/cell.cycle.lecture.pdf Lecture slides],[http://www.cbs.dtu.dk/chipcourse/deLichtenberg.Bioformatics.2004.pdf de Lichtenberg <i>et al</i>. 2004])
 +
:: Ulrik de Lichtenberg
  
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<BR>Tim Binnewies and Thomas Jensen
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: 11.45-12.15
 +
:: Demonstration of microarray equipment at CBS (in groups)
 +
:: Tim Binnewies and Thomas Jensen
  
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<DT>12.15-13.00  
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: 12.15-13.00
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<DD><I>Lunch Break</I>
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:: ''Lunch Break''
  
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<DT>13.00-13.30  
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: 13.00-13.30
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<DD>Introduction to UNIX and R ( <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/BasicR.pdf" target=_blank >Lecture slides</A> )
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:: Introduction to UNIX and [[R programming language|R]] ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/BasicR.pdf Lecture slides])
−
<DD>Carsten Friis <BR>
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:: Carsten Friis
  
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<DT>13.30-15.15
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: 13.30-15.15
−
<DD>Exercise: Introduction to UNIX and R  
+
:: Exercise: Introduction to UNIX and R ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/ Exercise],[http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/Ex_BasicR_Hard.php Extra exercise])
−
(<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/" target=_blank >Exercise</A>, <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/Ex_BasicR_Hard.php" target=_blank >Extra exercise </A> )
+
:: Carsten Friis, Jeppe S. Spicker, Agnieszka Juncker and H. Bj&oslash;rn Nielsen
−
<DD>Carsten Friis, Jeppe S. Spicker, Agnieszka Juncker and H. Bj&oslash;rn Nielsen<BR>
+
  
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<DT>15.15-15.30
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: 15.15-15.30
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<DD>Test of the day
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:: Test of the day
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<DD>Jeppe S. Spicker
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:: Jeppe S. Spicker
  
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</DD>
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=== 3-Jan-2006 (Tuesday): ''Preprocessing and Bioconductor'' ===
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<BR>
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</DL>
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<HR>
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<B>Tuesday, January 3</B>
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<HR>
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<I> Preprocessing and Bioconductor</I><DL>
+
  
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<dt>9.00-9.45</dt>
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: 09.00-09.45
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<DD>Hybridization, scanning and image analysis  
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:: Hybridization, scanning and image analysis ([http://www.cbs.dtu.dk/chipcourse/scanning_and_imageanalysis.ppt Lecture slides])
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(<A href="http://www.cbs.dtu.dk/chipcourse/scanning_and_imageanalysis.ppt" target=_blank>Lecture slides</A> )
+
:: H. Bj&oslash;rn Nielsen
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<BR>H. Bj&oslash;rn Nielsen  
+
  
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<dt>9.45-10.45</dt>
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: 09.45-10.45
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<DD><font color="#003000">Project introduction - group formation </font>
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:: '''Project introduction - group formation'''
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<BR>H. Bj&oslash;rn Nielsen  
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:: H. Bj&oslash;rn Nielsen
  
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<dt>10.45-11.00</dt>
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: 10.45-11.00
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<dd><I>Break</I></dd>
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:: ''Break''
  
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<dt>11.00-12.00</dt>
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: 11.00-12.00
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<DD><b>Case story:</b> Disease Gene Finding, (poster)<BR>
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:: '''Case story''': Disease Gene Finding, (poster)
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Kasper Lage Hansen
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:: Kasper Lage Hansen
  
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<DT>12.00-13.00  
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: 12.00-13.00
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<DD><I>Lunch Break</I>
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:: ''Lunch Break''
  
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<DT>13.00-13.30
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: 13.00-13.30
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<DD>Introduction to Bioconductor  
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:: Introduction to Bioconductor ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Bioconductor.pdf Lecture slides])
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(<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Bioconductor.pdf" target=_blank>Lecture slides</A>)
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:: Carsten Friis
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<DD>Carsten Friis
+
  
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<DT>13.30-14.30
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: 13.30-14.30
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<DD>Exercise: Introduction to Bioconductor
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:: Exercise: Introduction to Bioconductor ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Bioconductor/ Exercise])
−
(<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Bioconductor/" target=_blank>Exercise</A>)
+
:: Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
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<DD>Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
+
  
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<dt>14.30-14.45</dt>
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: 14.30-14.45
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<dd><I>Break</I></dd>
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:: ''Break''
  
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<DT>14.45-16.15
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: 14.45-16.15
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<dd><font color="#003000">Public data - available for project (1) </font>
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:: '''Public data - available for project (1)'''
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<dd>Agnieszks Junker
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:: Agnieszks Junker
  
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<DT>16.15-16.30
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: 16.15-16.30
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<DD>Test of the day
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:: Test of the day
−
<DD>H. Bj&oslash;rn Nielsen
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:: H. Bj&oslash;rn Nielsen
  
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</DL>
+
=== 4-Jan-2006 (Wednesday): ''Data Normalization'' ===
−
<HR>
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<B>Wednesday, January 4</B>
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<HR>
+
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<I>Data Normalization </I>
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<DL>
+
  
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<DT>9.00-10.00  
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: 09.00-10.00  
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<DD>Normalization and expression index calculation (Section 3.1-3.4) (
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:: Normalization and expression index calculation (Section 3.1-3.4) ([http://www.cbs.dtu.dk/chipcourse/Normalization.pdf Lecture slides])
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<A href="Normalization.pdf" target=_blank>Lecture slides</A>)
+
:: H. Bj&oslash;rn Nielsen  
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<BR>H. Bj&oslash;rn Nielsen  
+
  
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<DT>10.00-10.15
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: 10.00-10.15
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<DD><I>Break</I>
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:: ''Break''
  
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<DT>10.15-12.00
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: 10.15-12.00
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<dd>Exercise: Normalization methods and expression index calculation,
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:: Exercise: Normalization methods and expression index calculation ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Normalization/ Exercise])
−
(<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Normalization/" target=_blank>Exercise</A>)
+
:: Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
−
</font>
+
−
<DD>Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
+
  
−
<DT>12.00-13.00  
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: 12.00-13.00
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<DD><I>Lunch Break</I>
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:: ''Lunch Break''
  
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<DT>13.00-14.00  
+
: 13.00-14.00  
−
<DD><b>Case story:</b> A key regulator of pathogen defense responses in <i>Arabidopsis</i>
+
:: '''Case story''': A key regulator of pathogen defense responses in ''Arabidopsis'' ([http://www.cbs.dtu.dk/chipcourse/Petersen_et_al.00.pdf Petersen et al. 2000])
−
(<a href="Petersen_et_al.00.pdf">Petersen et al. 2000</a>)
+
:: H. Bj&oslash;rn Nielsen
−
<DD>H. Bj&oslash;rn Nielsen
+
  
−
<DT>14.00-14.15
+
: 14.00-14.15
−
<DD><I>Break</I>
+
:: ''Break''
  
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<DT>14.15-15:00
+
: 14.15-15:00
−
<DD><font color="#003000">Project work - problem formulation</font>
+
:: '''Project work''' - problem formulation
  
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<DT>15.00-15.30
+
: 15.00-15.30
−
<DD><b>Case story:</b> Epistasis by microarray
+
:: '''Case story''': Epistasis by microarray
−
<DD>H. Bjørn Nielsen
+
:: H. Bjørn Nielsen
  
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<DT>15.30-15.45
+
: 15.30-15.45
−
<DD>Test of the day
+
:: Test of the day
−
<DD>H. Bj&oslash;rn Nielsen
+
:: H. Bj&oslash;rn Nielsen
  
−
</DL>
+
=== 5-Jan-2006 (Thursday): ''Statistical analysis'' ===
−
<HR>
+
−
<B>Thursday, January 5</B>
+
−
<HR>
+
−
<i>Statistical analysis</i><DL>
+
  
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<dt>9.00-10.00
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: 09.00-10.00
−
<dd>Statistical analysis (Section 3.5-3.6) (<A href="StatisticalAnalysis.ppt" target=_blank>Lecture slides</A>)
+
:: Statistical analysis (Section 3.5-3.6) ([http://www.cbs.dtu.dk/chipcourse/StatisticalAnalysis.ppt Lecture slides])
−
<BR>H. Bj&oslash;rn Nielsen</dd>
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:: H. Bj&oslash;rn Nielsen
  
−
<DT>10.00-10.15
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: 10.00-10.15
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<DD><I>Coffee Break</I>
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:: ''Coffee Break''
  
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<DT>10.15-12.00
+
: 10.15-12.00
−
<DD>Exercise: Statistical analysis including multiple testing correction (
+
:: Exercise: Statistical analysis including multiple testing correction ([http://www.cbs.dtu.dk/chipcourse/statistics.html Exercise],[http://www.cbs.dtu.dk/chipcourse/data.tab data.tab], [http://www.cbs.dtu.dk/chipcourse/annotation.tab annotation.tab], [http://www.cbs.dtu.dk/chipcourse/Listeria.pdf Lecture])
−
<A href="http://www.cbs.dtu.dk/chipcourse/statistics.html" target=_blank>Exercise</A>,  
+
:: Jeppe S. Spicker, Hanni Willenbrock and Carsten Friis
−
<A href="data.tab" target=_blank>data.tab</A>,  
+
−
<A href="annotation.tab" target=_blank>annotation.tab</A>
+
−
)(<A href="Listeria.pdf" target=_blank>Lecture</A>)
+
−
<dd>Jeppe S. Spicker, Hanni Willenbrock and Carsten Friis
+
  
−
<DT>12.00-13.00  
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: 12.00-13.00
−
<DD><i>Lunch Break </i>
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:: ''Lunch Break''
  
−
<DT>13.00-13.45
+
: 13.00-13.45
−
<dd><b>Case story:</b> Regulation of the storage protein hordein C production in barley - How to reduce N-waste
+
:: '''Case story''': Regulation of the storage protein hordein C production in barley - How to reduce N-waste
−
<DD>Michael Hansen</DD>
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:: Michael Hansen
  
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<DT>13.45-14.00
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: 13.45-14.00
−
<DD><I>Break</I>
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:: ''Break''
  
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<DT>14.00-16.00
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: 14.00-16.00
−
<dd><font color="#003000">Public data - available for project (Human tissue, Spike-in, Cell cycle) </font>
+
:: '''Public data''' - available for project (Human tissue, Spike-in, Cell cycle)
−
<dd>Carsten Friis
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:: Carsten Friis
  
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<DT>16.00-16.15
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: 16.00-16.15
−
<DD>Test of the day
+
:: Test of the day
−
<DD>H. Bj&oslash;rn Nielsen
+
:: H. Bj&oslash;rn Nielsen
  
−
</DL>
+
=== 6-Jan-2006 (Friday): ''Data visualization and class prediction'' ===
−
<HR>
+
−
<B>Friday, January 6</B>
+
−
<HR>
+
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<i>Data visualization and class prediction</i><DL>
+
  
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<DT>9.00-9.45
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: 09.00-09.45
−
<dd>Dimension reduction: PCA and Clustering (Chapter 4 and 5)  
+
:: Dimension reduction: PCA and Clustering (Chapter 4 and 5) ([http://www.cbs.dtu.dk/chipcourse/Cluster.lecture.v1.0.ppt Lecture slides])
−
(<a href="Cluster.lecture.v1.0.ppt">Lecture slides</a>)
+
:: Agnieszka Juncker
−
<dd>Agnieszka Juncker</dd>
+
  
−
<DT>9.45-10.00
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: 09.45-10.00
−
<DD><I>Break</I>
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:: ''Break''
  
−
<DT>10.00-11.15
+
: 10.00-11.15
−
<dd>Exercise: Dimension reduction: PCA and Clustering  
+
:: Exercise: Dimension reduction: PCA and Clustering ([http://www.cbs.dtu.dk/chipcourse/DimentionalReduction.htm Exercise])
−
(<a href="DimentionalReduction.htm">Exercise</a>)
+
:: Jeppe S. Spicker and Agnieszka Juncker
−
<dd>Jeppe S. Spicker and Agnieszka Juncker</dd>
+
  
−
<DT>11.15-12.00
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: 11.15-12.00
−
<DD>Classification (Chapter 8)
+
:: Classification (Chapter 8) ([http://www.cbs.dtu.dk/chipcourse/Class.lecture.v1.1.ppt Lecture slides])
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(<a href="Class.lecture.v1.1.ppt">Lecture slides</a>)</DD>
+
:: Agnieszka Juncker
−
<DD>Agnieszka Juncker</DD>
+
  
−
<DT>12.00-13.00  
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: 12.00-13.00
−
<DD><i>Lunch Break </i>
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:: ''Lunch Break''
  
−
<DT>13.00-14.00  
+
: 13.00-14.00  
−
<DD><b>Case story:</b> Predicting Toxicity - An Unfinished Case Story<BR>
+
:: '''Case story''': Predicting Toxicity - An Unfinished Case Story
−
Jeppe S. Spicker
+
:: Jeppe S. Spicker
  
−
<DT>14.00-14.15  
+
: 14.00-14.15
−
<DD><I>Break</I>
+
:: ''Break''
  
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<DT>14.15-15.00
+
: 14.15-15.00
−
<DD>Exercise: Classification, (
+
:: Exercise: Classification, ([http://www.cbs.dtu.dk/chipcourse/Classification_Exercise.htm Exercise])
−
<a href="Classification_Exercise.htm">Exercise</a>)
+
:: Jeppe S. Spicker and Agnieszka Juncker
−
<DD>Jeppe S. Spicker and Agnieszka Juncker
+
  
−
<DT>15.00-15.15
+
: 15.00-15.15
−
<DD>Test of the day
+
:: Test of the day
−
<DD>Agnieszka Juncker
+
:: Agnieszka Juncker
  
−
</DL>
+
=== 9-Jan-2006 (Monday): ''Gene annotation analysis'' ===
−
<HR>
+
−
<B>Monday, January 9</B>
+
−
<HR>
+
−
<i>Gene annotation analysis</i><DL>
+
−
<DT>9.00-11.00
+
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<DD>Gene Onthology (GO), KEGG and ChIp-chip
+
−
(<A href="GO.annotation.introduction.v1.2.ppt" target=_blank>Lecture slides</A>,
+
−
<A href="GO_exercise_2005.htm" target=_blank>Exercise</A>,
+
−
<A href="GO.solutions" target=_blank>Solutions</A>)
+
−
<DD>Agnieszka Juncker and  Hanni Willenbrock
+
  
−
<DT>11.00-11.15
+
: 09.00-11.00
−
<DD><I>Break</I>
+
:: Gene Onthology (GO), KEGG and ChIp-chip ([http://www.cbs.dtu.dk/chipcourse/GO.annotation.introduction.v1.2.ppt Lecture slides], [http://www.cbs.dtu.dk/chipcourse/GO_exercise_2005.htm Exercise], [http://www.cbs.dtu.dk/chipcourse/GO.solutions Solutions])
 +
:: Agnieszka Juncker and  Hanni Willenbrock
  
−
<DT>11.15-12.00
+
: 11.00-11.15
−
<DD><b>Case story:</b> F.A.R.O.
+
:: ''Break''
  
−
<DT>12.00-13.00  
+
: 11.15-12.00
−
<DD><i>Lunch Break </i>
+
:: '''Case story''': F.A.R.O.
  
−
<DT>13.00-13.45
+
: 12.00-13.00
−
<DD><b>Case story:</b> DNA Chip prognosis of breast cancer - a meta analysis
+
:: ''Lunch Break''
−
<DD>Steen Knudsen
+
  
−
<DT>13.45-14.00
+
: 13.00-13.45
−
<DD><I>Break</I>
+
:: '''Case story''': DNA Chip prognosis of breast cancer - a meta analysis
 +
:: Steen Knudsen
  
−
<DT>14.00-16.00
+
: 13.45-14.00
−
<dd><font color="#003000">Public data - available for project (Leukemia, Plant mutants,  Rosetta compendium) </font>
+
:: ''Break''
−
<dd>H. Bjørn Nielsen
+
  
−
<DT>15.15-15.30
+
: 14.00-16.00
−
<DD>Test of the day
+
:: '''Public data''' - available for project (Leukemia, Plant mutants, Rosetta compendium)
−
</font>
+
:: H. Bjørn Nielsen
−
<DD>Agnieszka Juncker
+
−
</DL>
+
  
−
<HR>
+
: 15.15-15.30
−
<B>Tuesday, January 10</B>
+
:: Test of the day
−
<HR>
+
:: Agnieszka Juncker
−
<i>Integrative Biology</i><DL>
+
  
−
<Dt>9:00-11:00
+
=== 10-Jan-2006 (Tuesday): ''Integrative Biology'' ===
−
<DD>Integrative Biology (with <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_IntBiol/" target=_blank>exercise</A>)
+
−
<DD>Carsten Friis
+
  
−
<Dt>11:00-12:00
+
: 09:00-11:00
−
<DD><font color="#003000">Project work - (project outline)</font>
+
:: Integrative Biology (with [http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_IntBiol/ exercise])
 +
:: Carsten Friis
  
−
<DT>12.00-13.00  
+
: 11:00-12:00
−
<DD><i>Lunch Break </i>
+
:: '''Project work''' - (project outline)
  
−
<DT>13.00-13.45
+
: 12.00-13.00
−
<DD>Comparative Genomic Hybridization (CGH)
+
:: ''Lunch Break''
−
<DD>Hanni Willenbrock
+
  
−
<DT>13.45-14.00
+
: 13.00-13.45
−
<DD>Test of the day
+
:: Comparative Genomic Hybridization (CGH)
−
<DD>Hanni Willenbrock
+
:: Hanni Willenbrock
−
</DD>
+
−
</DL>
+
  
−
<HR>
+
: 13.45-14.00
−
<B>Wednesday, January 11</B>
+
:: Test of the day
−
<HR>
+
:: Hanni Willenbrock
−
<i>Project Problem Formulation</i><DL>
+
  
−
<dt> 9.00-11.00
+
=== 11-Jan-2006 (Wednesday): ''Project Problem Formulation'' ===
−
<dd>Probe design using OligoWiz 2.0 ([http://www.cbs.dtu.dk/phdcourse/cookbooks/OligoWizLectureApril2005.ppt lecture notes]<br>
+
−
<a href="../dtucourse/cookbooks/raz/27803/probedesign.php" target=_blank>Exercise guide</a> &nbsp;
+
−
<a href="http://www.cbs.dtu.dk/services/OligoWiz2/" target=_blank>OligoWiz 2.0 server</a>
+
−
<dd>Rasmus Wernersson
+
  
−
<dt>11.00-11.15</dt>
+
: 09.00-11.00
−
<dd><I>Break</I></dd>
+
:: Probe design using OligoWiz 2.0 ([http://www.cbs.dtu.dk/phdcourse/cookbooks/OligoWizLectureApril2005.ppt lecture notes], [http://www.cbs.dtu.dk/dtucourse/cookbooks/raz/27803/probedesign.php Exercise guide], [http://www.cbs.dtu.dk/services/OligoWiz2/ OligoWiz 2.0 server]
 +
:: Rasmus Wernersson
  
−
<Dt>11.15-12.00
+
: 11.00-11.15
−
<DD><b>Case story:</b> From genome sequence to gene expression data in Campylobacter jejuni
+
:: ''Break''
−
<DD>Peter F. Hallin
+
  
−
<DT>12.00-13.00  
+
: 11.15-12.00
−
<DD><i>Lunch Break </i>
+
:: '''Case story''': From genome sequence to gene expression data in ''Campylobacter jejuni''
 +
:: Peter F. Hallin
  
−
<Dt>13:00-14:00
+
: 12.00-13.00  
−
<DD><font color="#003000">Project work - (Deadline for Problem formulation - hand in written P.F.)</font>
+
:: ''Lunch Break''
  
−
<dt>14.00-14.15</dt>
+
: 13:00-14:00
−
<dd><I>Break</I></dd>
+
:: '''Project work''' - (Deadline for Problem formulation - hand in written P.F.)
  
−
<Dt>14:15-15:15
+
: 14.00-14.15
−
<DD>Exercise: Reading Data into R (<a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_DataIntoR/">Exercise</a>)
+
:: ''Break''
  
−
<DD>Carsten Friis
+
: 14:15-15:15
 +
:: Exercise: Reading Data into R ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_DataIntoR/ Exercise])
 +
:: Carsten Friis
  
−
<DT>15.15-15.30
+
: 15.15-15.30
−
<DD>Test of the day
+
:: Test of the day
−
<DD>Rasmus Wernersson
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:: Rasmus Wernersson
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</DD>
+
−
</DL>
+
  
−
<HR>
+
=== 12-Jan-2006 (Thursday): ''Problem Presentations'' ===
−
<B>Thursday, January 12</B>
+
−
<HR>
+
−
<i>Problem Presentations</i><DL>
+
  
−
<DT>9.00-10.30
+
: 09.00-10.30
−
<DD>Promoter analysis  
+
:: Promoter analysis ([http://www.cbs.dtu.dk/chipcourse/cis-analysis.lecture.ppt Lecture slides], [http://www.cbs.dtu.dk/courses/thaiworkshop/exercises/cis-analysis/cis-exercise.php Exercise])
−
(<A href="cis-analysis.lecture.ppt" target=_blank>Lecture slides</A>)
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:: H. Bj&oslash;rn Nielsen and Agnieszka Juncker
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(<A href="http://www.cbs.dtu.dk/courses/thaiworkshop/exercises/cis-analysis/cis-exercise.php" target=_blank>Exercise</A>)
+
−
<DD>H. Bj&oslash;rn Nielsen and Agnieszka Juncker
+
  
−
<dt>10.30-10.45</dt>
+
: 10.30-10.45
−
<dd><I>Break</I></dd>
+
:: ''Break''
  
−
<DT>10.45-12.00
+
: 10.45-12.00
−
<DD><font color="#003000">Problem presentations (5min pr. group, one slide)</font>
+
:: '''Problem presentations''' (5min pr. group, one slide)
−
<DD>Project groups
+
:: Project groups
  
−
<DT>12.00-13.00  
+
: 12.00-13.00  
−
<DD><i>Lunch Break </i>
+
:: ''Lunch Break''
  
−
<DT>13.00-13.30
+
: 13.00-13.30
−
<DD>course summary  
+
:: course summary  
−
<DD>H. Bj&oslash;rn Nielsen
+
:: H. Bj&oslash;rn Nielsen
  
−
<DT>13.30-
+
: 13.30-
−
<DD><font color="#003000">Project work </font>
+
:: '''Project work'''
  
−
</DD></DL>
+
=== 13-Jan-2006 (Friday) &mdash; 19-Jan-2006 (Thursday): ''Project Work'' ===
  
−
<HR>
+
: 10.00-12.00
−
<B>Friday, January 13 - Thursday, January 19</B>
+
:: '''Office Hours''' - one or more Teacher(s) can be found in auditorium 51
−
<HR>
+
−
<i>Project Work</i><DL>
+
−
<DT>10.00-12.00
+
−
<DD><font color="#003000">Office Hours - one or more Teacher(s) can be found in auditorium 51 </font>
+
−
</DD></DL>
+
  
−
<HR>
+
=== 20-Jan-2006 (Friday): ''Poster Session'' ===
−
<B>Friday, January 20</B>
+
−
<HR>
+
−
<i>Poster Session</i><DL>
+
−
<DT>10.00-15.00
+
−
<DD><font color="#003000">Poster Session (<B>exam</B>) - In the hall infront of CBS (building 208)</font>
+
  
−
</DD></DL>
+
: 10.00-15.00
 +
:: '''Poster Session (exam)''' - In the hall infront of CBS (building 208)
  
−
<HR>
+
=== 18-Jan-2006 (Wednesday) &mdash; 21-Jan-2006 (Saturday) ===
−
<B>Wednesday, January 18 - Saturday, January 21</B>
+
 
−
<HR>
+
:: Course evaluation on [http://www.campusnet.dtu.dk/ CampusNet]
−
<DD>Course evaluation on <a href="http://www.campusnet.dtu.dk/">CampusNet</a><br>
+
:: Please, use your student number and password to login
−
<DD>Please, use your student number and password to login
+
−
<DD>
+
  
 
[[Category:Academic Courses]]
 
[[Category:Academic Courses]]

Revision as of 15:48, 2 January 2006

Overview

Aim/objectives

The DNA microarray technology plays a significant role in molecular biology, systems biology and pharmaceutical research. The aim of this course is to give students a general knowledge of methods for microarray analysis as well as the ability to apply computerized analyses on gene expression data. Furthermore, it is a goal that the students learn to formulate interesting problems/questions that can be addressed by gene expressions analysis

Content

The technology behind GeneChips and cDNA arrays; normalization of data before comparison between experiments; statistical significance of changes in expression; reduction and visualization of large data matrices: PCA and clustering; reverse engineering of regulatory networks; promoter analysis and functional analysis; integration of data; case stories. Finally a poster presentation based on a problem formulated in cooperation with the teachers.

Remarks

The evaluated exercises/projects will be done in groups and the work done by each student must be identified, so that each student can receive and individual grade.

Contact

  • Professor: Henrik Bjørn Nielsen, build. 208, room 018, (+45) 4525 2489, hbjorn@cbs.dtu.dk
  • Department: 27 BioCentrum-DTU
  • Home Page: http://www.cbs.dtu.dk/chipcourse/
  • Course code: 27612

Key words

DNA Microarrays, Expression Analysis, GeneChip, Regulatory networks, classification, systems biology

Course Programme

The course will be held from January 2 - 20, 2006 (incl.)


Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, auditorium 51, in Lyngby.


2-Jan-2006 (Monday): Introduction to microarray technology and R software

09.00-09.30
Introduction to course (Lecture slides)
H. Bjørn Nielsen
09.30-09.45
Pre-test
H. Bjørn Nielsen
9.45-10.30
Overview over gene expression and DNA microarray technology (Chapter 1)(Lecture slides)
Jeppe S. Spicker
10.30-10.45
Break
10.45-11.45
Case story: Analysis of the cell cycle (Lecture slides,de Lichtenberg et al. 2004)
Ulrik de Lichtenberg
11.45-12.15
Demonstration of microarray equipment at CBS (in groups)
Tim Binnewies and Thomas Jensen
12.15-13.00
Lunch Break
13.00-13.30
Introduction to UNIX and R (Lecture slides)
Carsten Friis
13.30-15.15
Exercise: Introduction to UNIX and R (Exercise,Extra exercise)
Carsten Friis, Jeppe S. Spicker, Agnieszka Juncker and H. Bjørn Nielsen
15.15-15.30
Test of the day
Jeppe S. Spicker

3-Jan-2006 (Tuesday): Preprocessing and Bioconductor

09.00-09.45
Hybridization, scanning and image analysis (Lecture slides)
H. Bjørn Nielsen
09.45-10.45
Project introduction - group formation
H. Bjørn Nielsen
10.45-11.00
Break
11.00-12.00
Case story: Disease Gene Finding, (poster)
Kasper Lage Hansen
12.00-13.00
Lunch Break
13.00-13.30
Introduction to Bioconductor (Lecture slides)
Carsten Friis
13.30-14.30
Exercise: Introduction to Bioconductor (Exercise)
Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
14.30-14.45
Break
14.45-16.15
Public data - available for project (1)
Agnieszks Junker
16.15-16.30
Test of the day
H. Bjørn Nielsen

4-Jan-2006 (Wednesday): Data Normalization

09.00-10.00
Normalization and expression index calculation (Section 3.1-3.4) (Lecture slides)
H. Bjørn Nielsen
10.00-10.15
Break
10.15-12.00
Exercise: Normalization methods and expression index calculation (Exercise)
Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
12.00-13.00
Lunch Break
13.00-14.00
Case story: A key regulator of pathogen defense responses in Arabidopsis (Petersen et al. 2000)
H. Bjørn Nielsen
14.00-14.15
Break
14.15-15:00
Project work - problem formulation
15.00-15.30
Case story: Epistasis by microarray
H. Bjørn Nielsen
15.30-15.45
Test of the day
H. Bjørn Nielsen

5-Jan-2006 (Thursday): Statistical analysis

09.00-10.00
Statistical analysis (Section 3.5-3.6) (Lecture slides)
H. Bjørn Nielsen
10.00-10.15
Coffee Break
10.15-12.00
Exercise: Statistical analysis including multiple testing correction (Exercise,data.tab, annotation.tab, Lecture)
Jeppe S. Spicker, Hanni Willenbrock and Carsten Friis
12.00-13.00
Lunch Break
13.00-13.45
Case story: Regulation of the storage protein hordein C production in barley - How to reduce N-waste
Michael Hansen
13.45-14.00
Break
14.00-16.00
Public data - available for project (Human tissue, Spike-in, Cell cycle)
Carsten Friis
16.00-16.15
Test of the day
H. Bjørn Nielsen

6-Jan-2006 (Friday): Data visualization and class prediction

09.00-09.45
Dimension reduction: PCA and Clustering (Chapter 4 and 5) (Lecture slides)
Agnieszka Juncker
09.45-10.00
Break
10.00-11.15
Exercise: Dimension reduction: PCA and Clustering (Exercise)
Jeppe S. Spicker and Agnieszka Juncker
11.15-12.00
Classification (Chapter 8) (Lecture slides)
Agnieszka Juncker
12.00-13.00
Lunch Break
13.00-14.00
Case story: Predicting Toxicity - An Unfinished Case Story
Jeppe S. Spicker
14.00-14.15
Break
14.15-15.00
Exercise: Classification, (Exercise)
Jeppe S. Spicker and Agnieszka Juncker
15.00-15.15
Test of the day
Agnieszka Juncker

9-Jan-2006 (Monday): Gene annotation analysis

09.00-11.00
Gene Onthology (GO), KEGG and ChIp-chip (Lecture slides, Exercise, Solutions)
Agnieszka Juncker and Hanni Willenbrock
11.00-11.15
Break
11.15-12.00
Case story: F.A.R.O.
12.00-13.00
Lunch Break
13.00-13.45
Case story: DNA Chip prognosis of breast cancer - a meta analysis
Steen Knudsen
13.45-14.00
Break
14.00-16.00
Public data - available for project (Leukemia, Plant mutants, Rosetta compendium)
H. Bjørn Nielsen
15.15-15.30
Test of the day
Agnieszka Juncker

10-Jan-2006 (Tuesday): Integrative Biology

09:00-11:00
Integrative Biology (with exercise)
Carsten Friis
11:00-12:00
Project work - (project outline)
12.00-13.00
Lunch Break
13.00-13.45
Comparative Genomic Hybridization (CGH)
Hanni Willenbrock
13.45-14.00
Test of the day
Hanni Willenbrock

11-Jan-2006 (Wednesday): Project Problem Formulation

09.00-11.00
Probe design using OligoWiz 2.0 (lecture notes, Exercise guide, OligoWiz 2.0 server
Rasmus Wernersson
11.00-11.15
Break
11.15-12.00
Case story: From genome sequence to gene expression data in Campylobacter jejuni
Peter F. Hallin
12.00-13.00
Lunch Break
13:00-14:00
Project work - (Deadline for Problem formulation - hand in written P.F.)
14.00-14.15
Break
14:15-15:15
Exercise: Reading Data into R (Exercise)
Carsten Friis
15.15-15.30
Test of the day
Rasmus Wernersson

12-Jan-2006 (Thursday): Problem Presentations

09.00-10.30
Promoter analysis (Lecture slides, Exercise)
H. Bjørn Nielsen and Agnieszka Juncker
10.30-10.45
Break
10.45-12.00
Problem presentations (5min pr. group, one slide)
Project groups
12.00-13.00
Lunch Break
13.00-13.30
course summary
H. Bjørn Nielsen
13.30-
Project work

13-Jan-2006 (Friday) — 19-Jan-2006 (Thursday): Project Work

10.00-12.00
Office Hours - one or more Teacher(s) can be found in auditorium 51

20-Jan-2006 (Friday): Poster Session

10.00-15.00
Poster Session (exam) - In the hall infront of CBS (building 208)

18-Jan-2006 (Wednesday) — 21-Jan-2006 (Saturday)

Course evaluation on CampusNet
Please, use your student number and password to login
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