https://teaching.healthtech.dtu.dk/22140/index.php?action=history&feed=atom&title=Autumn2023
Autumn2023 - Revision history
2026-05-03T13:12:56Z
Revision history for this page on the wiki
MediaWiki 1.41.0
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=86&oldid=prev
WikiSysop: /* Lecture 09 (Nov 2) - Systems Biology in Biomedical Research (Heart diseases) 2 */
2024-03-05T15:55:40Z
<p><span dir="auto"><span class="autocomment">Lecture 09 (Nov 2) - Systems Biology in Biomedical Research (Heart diseases) 2</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:55, 5 March 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Virtual pulldown and protein complex detection'' - Lars Rønn Olsen and Giorgia Moranzoni</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Virtual pulldown and protein complex detection'' - Lars Rønn Olsen and Giorgia Moranzoni</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:'''</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:'''</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:* ''Human diseases through the lens of network biology'' ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/Furlong_Cell2012.pdf PDF]) - Concentrate on: '''Figure 1''' and '''Box 3'''</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:* ''Human diseases through the lens of network biology'' ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/Furlong_Cell2012.pdf PDF]) - Concentrate on: '''Figure 1''' and '''Box 3'''</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* '''Heart development video:''' https://www.youtube.com/watch?v=5DIUk9IXUaI</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* '''Heart development video:''' https://www.youtube.com/watch?v=5DIUk9IXUaI</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Extra:''' (not curriculum)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Extra:''' (not curriculum)</div></td></tr>
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WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=78&oldid=prev
WikiSysop: /* Lecture 02 (Sep 7) - Intro 2 */
2024-03-05T15:43:53Z
<p><span dir="auto"><span class="autocomment">Lecture 02 (Sep 7) - Intro 2</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:43, 5 March 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' To appear on DTU Learn</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' To appear on DTU Learn</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:'''Hand-outs:''' ''SnapShot: Protein-Protein Interaction Networks'' - Seebacher & Gavin, Nature 2011 ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/SnapShot_Cell2011.pdf PDF]) - focus on the EXPERIMENTAL METHODS part for this week.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:'''Hand-outs:''' ''SnapShot: Protein-Protein Interaction Networks'' - Seebacher & Gavin, Nature 2011 ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/SnapShot_Cell2011.pdf PDF]) - focus on the EXPERIMENTAL METHODS part for this week.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><blockquote></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><blockquote></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Lecture note on ''quality scoring of protein-protein interaction data, notes and examples'' ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/W02_scoring_of_PPI.pdf PDF])</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Lecture note on ''quality scoring of protein-protein interaction data, notes and examples'' ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/W02_scoring_of_PPI.pdf PDF])</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* ''Comparative assessment of large-scale data sets of protein-protein interactions'' - von Mering C, ''et al''. Nature 2002 ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/W02_Comparative_assessment_of_large-scale_data_sets_of_protein-protein.pdf PDF])</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* ''Comparative assessment of large-scale data sets of protein-protein interactions'' - von Mering C, ''et al''. Nature 2002 ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/W02_Comparative_assessment_of_large-scale_data_sets_of_protein-protein.pdf PDF])</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></blockquote></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></blockquote></div></td></tr>
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WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=75&oldid=prev
WikiSysop: /* Lecture 01 (August 31) - Intro 1 */
2024-03-05T15:35:21Z
<p><span dir="auto"><span class="autocomment">Lecture 01 (August 31) - Intro 1</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Introduction to Systems Biology and biological networks'' - Rasmus Wernersson.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Introduction to Systems Biology and biological networks'' - Rasmus Wernersson.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' Will be uploaded to DTU Learn</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' Will be uploaded to DTU Learn</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' ''Can a Biologist fix a radio?'' - Lazebnik Y., Cancer Cell 2002 ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/W01_Lazebnik_CancerCell2002.pdf PDF])</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' ''Can a Biologist fix a radio?'' - Lazebnik Y., Cancer Cell 2002 ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/W01_Lazebnik_CancerCell2002.pdf PDF])</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Exercise:''' [[igraphIntro_Ex_v1|Introduction to working with networks in R]] - '''Answers:''' [[igraphIntro_Answers_v1|Exercise #1 answers]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Exercise:''' [[igraphIntro_Ex_v1|Introduction to working with networks in R]] - '''Answers:''' [[igraphIntro_Answers_v1|Exercise #1 answers]]</div></td></tr>
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WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=74&oldid=prev
WikiSysop: /* Lecture 07 (Oct 12) - Yeast Systems Biology 4 */
2024-03-05T15:33:41Z
<p><span dir="auto"><span class="autocomment">Lecture 07 (Oct 12) - Yeast Systems Biology 4</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''How proteins collaborate during the phases of cell devision'' - Rasmus Wernersson.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''How proteins collaborate during the phases of cell devision'' - Rasmus Wernersson.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' [<del style="font-weight: bold; text-decoration: none;">[Media</del>:Cyclebase1_2008.<del style="font-weight: bold; text-decoration: none;">pdf|</del>Cyclebase paper<del style="font-weight: bold; text-decoration: none;">]</del>] - (skim it - make sure to understand '''Fig 1''').</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' [<ins style="font-weight: bold; text-decoration: none;">https</ins>:<ins style="font-weight: bold; text-decoration: none;">//teaching.healthtech.dtu.dk/material/22140/</ins>Cyclebase1_2008.<ins style="font-weight: bold; text-decoration: none;">pdf PDF </ins>Cyclebase paper] - (skim it - make sure to understand '''Fig 1''').</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' To appear on DTU Learn</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' To appear on DTU Learn</div></td></tr>
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WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=69&oldid=prev
WikiSysop: /* Lecture 06 (Oct 5) - Yeast Systems Biology 3 */
2024-03-05T15:26:25Z
<p><span dir="auto"><span class="autocomment">Lecture 06 (Oct 5) - Yeast Systems Biology 3</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Introduction to transcriptomics'' - Kristoffer Vitting-Seerup</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Introduction to transcriptomics'' - Kristoffer Vitting-Seerup</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' ''A brief introduction to DNA micro-arrays'' ([https://learn.inside.dtu.dk/d2l/le/content/167355/viewContent/691406/View DTU Learn]) - Rasmus Wernersson</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' ''A brief introduction to DNA micro-arrays'' ([https://learn.inside.dtu.dk/d2l/le/content/167355/viewContent/691406/View DTU Learn]) - Rasmus Wernersson</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:'''Background:''' (Optional) - If you need a reminder about how the Log2 function works, then have a look at '''Appendix A''' in Thomas Schneider's '' Information Theory Primer'' ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/informationtheory_primer.pdf PDF])</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:'''Background:''' (Optional) - If you need a reminder about how the Log2 function works, then have a look at '''Appendix A''' in Thomas Schneider's '' Information Theory Primer'' ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/informationtheory_primer.pdf PDF])</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' To appear on DTU Learn</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' To appear on DTU Learn</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
</table>
WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=52&oldid=prev
WikiSysop: /* Lecture 05 (Sept 28) - Yeast Systems Biology 2 */
2024-03-05T14:47:32Z
<p><span dir="auto"><span class="autocomment">Lecture 05 (Sept 28) - Yeast Systems Biology 2</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:47, 5 March 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Gene Ontology and large scale data analysis'' - Rasmus Wernersson</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Lecture:''' ''Gene Ontology and large scale data analysis'' - Rasmus Wernersson</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' Two introductory papers to The Gene Ontology (GO). Choose the one you prefer. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' Two introductory papers to The Gene Ontology (GO). Choose the one you prefer. </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:* Intro for bioinformaticians: '''The what, where, how and why of gene ontology - a primer for bioinformaticians''' - [<del style="font-weight: bold; text-decoration: none;">[File</del>:Bbr002.pdf<del style="font-weight: bold; text-decoration: none;">]</del>] (NEW LINK) (focus on the first three pages).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:* Intro for bioinformaticians: '''The what, where, how and why of gene ontology - a primer for bioinformaticians''' - [<ins style="font-weight: bold; text-decoration: none;">https</ins>:<ins style="font-weight: bold; text-decoration: none;">//teaching.healthtech.dtu.dk/material/22140/</ins>Bbr002.pdf <ins style="font-weight: bold; text-decoration: none;">PDF</ins>] (NEW LINK) (focus on the first three pages).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:**Focuses mostly on the structure of the GO, the evidence behind the annotations and relations of the genes/proteins to the categories.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:**Focuses mostly on the structure of the GO, the evidence behind the annotations and relations of the genes/proteins to the categories.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:* Intro for biologists: '''Gene Ontology: tool for the unification of biology''' - [<del style="font-weight: bold; text-decoration: none;">[File</del>:GO_NATURE_GENETICS_2000.pdf<del style="font-weight: bold; text-decoration: none;">]</del>] (NEW LINK)</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:* Intro for biologists: '''Gene Ontology: tool for the unification of biology''' - [<ins style="font-weight: bold; text-decoration: none;">https</ins>:<ins style="font-weight: bold; text-decoration: none;">//teaching.healthtech.dtu.dk/material/22140/</ins>GO_NATURE_GENETICS_2000.pdf <ins style="font-weight: bold; text-decoration: none;">PDF</ins>] (NEW LINK)</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:**Describes more the general idea behind GO and why it is useful.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:**Describes more the general idea behind GO and why it is useful.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' On DTU Learn</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' On DTU Learn</div></td></tr>
</table>
WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=51&oldid=prev
WikiSysop: /* Lecture 04 (Sep 21) - Yeast Systems Biology 1 */
2024-03-05T14:28:26Z
<p><span dir="auto"><span class="autocomment">Lecture 04 (Sep 21) - Yeast Systems Biology 1</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:28, 5 March 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' Will be uploaded to DTU Learn</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' Will be uploaded to DTU Learn</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:* Background on budding yeast cell cycle and cell cycle regulation ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">exercises</del>/Budding_Yeast_Cell_Cycle_Model.pdf PDF]).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:* Background on budding yeast cell cycle and cell cycle regulation ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/Budding_Yeast_Cell_Cycle_Model.pdf PDF]).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* Source: http://mpf.biol.vt.edu/research/budding_yeast_model/pp/index.php (much more information about modelling the yeast cell cycle can be found here) [NOT part of the curriculum].</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* Source: http://mpf.biol.vt.edu/research/budding_yeast_model/pp/index.php (much more information about modelling the yeast cell cycle can be found here) [NOT part of the curriculum].</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* '''Important:''' You don't need to understand all the finer points about the regulation, but make sure you known the '''phases''' of the cell cycle. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* '''Important:''' You don't need to understand all the finer points about the regulation, but make sure you known the '''phases''' of the cell cycle. </div></td></tr>
</table>
WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=43&oldid=prev
WikiSysop: /* Lecture 03 (Sep 14) - Intro 3 */
2024-03-05T14:11:24Z
<p><span dir="auto"><span class="autocomment">Lecture 03 (Sep 14) - Intro 3</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:11, 5 March 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' On DTU Learn.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Slides:''' On DTU Learn.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:'''Hand-outs:''' SnapShot: Protein-Protein Interaction Networks - (SAME AS LAST WEEK) ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/SnapShot_Cell2011.pdf PDF]) - read the rest for this week.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:'''Hand-outs:''' SnapShot: Protein-Protein Interaction Networks - (SAME AS LAST WEEK) ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/SnapShot_Cell2011.pdf PDF]) - read the rest for this week.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' Global network properties. Barabasi& Oltvai, Nat Rev Genet 2004 ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/W03_Barabasi_Oltvai_NatRevGen2004.pdf PDF]) - concentrate on '''Box 1''' and '''Box 2'''.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:'''Readings:''' Global network properties. Barabasi& Oltvai, Nat Rev Genet 2004 ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/W03_Barabasi_Oltvai_NatRevGen2004.pdf PDF]) - concentrate on '''Box 1''' and '''Box 2'''.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Exercises:''' </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Exercises:''' </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><blockquote></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><blockquote></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>#'''Handout exercise:''' Network topology exercise ([https://teaching.healthtech.dtu.dk/<del style="font-weight: bold; text-decoration: none;">27040</del>/<del style="font-weight: bold; text-decoration: none;">teachingmaterials</del>/W03_Network_topology_exercise_v3.pdf PDF])</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>#'''Handout exercise:''' Network topology exercise ([https://teaching.healthtech.dtu.dk/<ins style="font-weight: bold; text-decoration: none;">material</ins>/<ins style="font-weight: bold; text-decoration: none;">22140</ins>/W03_Network_topology_exercise_v3.pdf PDF])</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#'''Computer exercise:''' Topology/statistics/modules [[ExTopology1_igraph|Network topology and statistics]] - '''Answers''': [[ExTopology1_igraph_solutions|Answers to igraph exercise]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#'''Computer exercise:''' Topology/statistics/modules [[ExTopology1_igraph|Network topology and statistics]] - '''Answers''': [[ExTopology1_igraph_solutions|Answers to igraph exercise]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></blockquote></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></blockquote></div></td></tr>
</table>
WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=39&oldid=prev
WikiSysop: /* Block #1: Introduction */
2024-03-05T14:04:54Z
<p><span dir="auto"><span class="autocomment">Block #1: Introduction</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:04, 5 March 2024</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Exercise:''' </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:'''Exercise:''' </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>:* [[Media:W02_exercises_v7_corrected.pdf|Building protein-protein interaction networks from experimental data]] (solutions now on <del style="font-weight: bold; text-decoration: none;">learn</del>)</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:* [[Media:W02_exercises_v7_corrected.pdf|Building protein-protein interaction networks from experimental data]] (solutions now on <ins style="font-weight: bold; text-decoration: none;">DTU Learn</ins>)</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* [[Media:Exercise_help_sheet.pdf|Note taking sheet for help with ex. 5,7,8,9]] - Consider printing this for taking notes</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* [[Media:Exercise_help_sheet.pdf|Note taking sheet for help with ex. 5,7,8,9]] - Consider printing this for taking notes</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* [[Ex_handouts_igraph|Visualization of the networks from the hand-out exercise]] - '''Answers''': [[Ex_handouts_igraph_solution|Exercise #2 answers]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:* [[Ex_handouts_igraph|Visualization of the networks from the hand-out exercise]] - '''Answers''': [[Ex_handouts_igraph_solution|Exercise #2 answers]]</div></td></tr>
</table>
WikiSysop
https://teaching.healthtech.dtu.dk/22140/index.php?title=Autumn2023&diff=10&oldid=prev
WikiSysop: Created page with "= Course 22140 - plan for autumn 2023 = <!-- = General information = --> '''Teachers:''' * Lars Rønn Olsen (course organizer) - '''contact:''' [mailto:lronn@dtu.dk lronn@dtu.dk] * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * Rasmus Wernersson (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Hanxi Li (teaching assistant) - '''contact:''' [mailto:hanxli@dtu.dk hanxli@dtu.dk] <!-- '''Main cour..."
2024-03-05T11:05:06Z
<p>Created page with "= Course 22140 - plan for autumn 2023 = <!-- = General information = --> '''Teachers:''' * Lars Rønn Olsen (course organizer) - '''contact:''' [mailto:lronn@dtu.dk lronn@dtu.dk] * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * Rasmus Wernersson (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Hanxi Li (teaching assistant) - '''contact:''' [mailto:hanxli@dtu.dk hanxli@dtu.dk] <!-- '''Main cour..."</p>
<p><b>New page</b></p><div>= Course 22140 - plan for autumn 2023 =<br />
<!-- = General information = --><br />
'''Teachers:'''<br />
* Lars Rønn Olsen (course organizer) - '''contact:''' [mailto:lronn@dtu.dk lronn@dtu.dk]<br />
* Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk]<br />
* Rasmus Wernersson (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk]<br />
* Hanxi Li (teaching assistant) - '''contact:''' [mailto:hanxli@dtu.dk hanxli@dtu.dk]<br />
<br />
<br />
<!-- '''Main course page:''' [[Course36040|36040 - wiki page]] --><br />
<br />
= DTU Learn =<br />
* Link: [https://learn.inside.dtu.dk/d2l/home/167355 Course 22140, Autumn 2022 @ DTU Learn]<br />
<br><br />
<br />
= Bioinformatics =<br />
Besides knowledge about basic molecular biology and biochemistry, a prerequisite for this course is bioinformatics (usually from course 22211 or one of its variants). If you need to read up on some bioinformatics topics, please use the links below.<br />
* [https://teaching.healthtech.dtu.dk/22111/ Course 22111] - ''Introduction to Bioinformatics'' <br />
* [[Exercise:_The_protein_database_UniProt|UniProt exercise]] ([[ExUniProt-answers|answers]]) - This is an important one, as we use UniProt a lot in this course.<br />
<br><br />
<br />
= R =<br />
For the computer exercises we will be using R to process data, analyze, and visualize the biological networks. R is Open Source and freely available for Windows, Mac and Linux. We will be utilizing a RStudio server cloud solution to make sure that everyone uses the same version of R and the needed packages. You can log in with your DTU credentials [https://teaching.healthtech.dtu.dk/22140/rstudio.php here].<br />
<br />
'''NOTE''': In order to produce plots with RStudio server, you need to have the appropriate graphics device activated. If you have X11 installed, this should work without any further actions. If you do not, you will get an error whenever you try to plot anything. To mitigate this, open Rstudio server, go to "Tools" (options bar at the top of the screen), select "Global options" from the drop down menu, select the "Graphics" tab, and change "Backend" to "Cairo".<br />
<br><br><br />
<br />
= Weekly assignments =<br />
[[Image:Office-notes-line_drawing.png|40px|left]]<br />
As part of the computer exercises you (or your group) should keep a "log book" and answer the questions/report observations as you work though the exercise. The parts you need to document will be marked with the small "report icon" also seen here.<br />
<br />
Following the exercise the reports will be handed in using the peer grade system. We will assign your report to three co-students to provide you with feedback.<br />
<br />
'''Important:''' The reports are not as such mandatory, but it is HIGHLY recommended to turn them in, as this is excellent training for the exam.<br />
<br />
'''Allowed formats:''' <br />
# Plain text + figures as extra files<br />
# Microsoft Word (*.doc, *.docx)<br />
# PDF: use ANY word-processing software you like (e.g. "Pages") and save/print the result to a PDF.<br />
<br />
<br />
= Lecture plan, autumn 2023 =<br />
<br />
<br />
== When and Where ==<br />
* '''When:''' Each '''Thursday''' from '''13:00-17:00'''<br />
* '''Where:''' Building '''303A''' auditorium/group-room '''045''' <br />
<hr><br />
<br />
<br />
<br />
== Block #1: Introduction ==<br />
'''Responsible for this block:''' Lars Rønn Olsen and Rasmus Wernersson<br />
----<br />
=== Lecture 01 (August 31) - Intro 1 ===<br />
<br />
:'''Lecture:''' ''Introduction to Systems Biology and biological networks'' - Rasmus Wernersson.<br />
:'''Slides:''' Will be uploaded to DTU Learn<br />
:'''Readings:''' ''Can a Biologist fix a radio?'' - Lazebnik Y., Cancer Cell 2002 ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/W01_Lazebnik_CancerCell2002.pdf PDF])<br />
:'''Exercise:''' [[igraphIntro_Ex_v1|Introduction to working with networks in R]] - '''Answers:''' [[igraphIntro_Answers_v1|Exercise #1 answers]]<br />
<br />
=== Lecture 02 (Sep 7) - Intro 2 ===<br />
<br />
:'''Lecture:''' ''Protein-protein interaction networks. Experimental methods and interpretation.'' - Lars Rønn Olsen<br />
<br />
:'''Slides:''' To appear on DTU Learn<br />
:'''Hand-outs:''' ''SnapShot: Protein-Protein Interaction Networks'' - Seebacher & Gavin, Nature 2011 ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/SnapShot_Cell2011.pdf PDF]) - focus on the EXPERIMENTAL METHODS part for this week.<br />
:'''Readings:''' <br />
<blockquote><br />
* Lecture note on ''quality scoring of protein-protein interaction data, notes and examples'' ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/W02_scoring_of_PPI.pdf PDF])<br />
* ''Comparative assessment of large-scale data sets of protein-protein interactions'' - von Mering C, ''et al''. Nature 2002 ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/W02_Comparative_assessment_of_large-scale_data_sets_of_protein-protein.pdf PDF])<br />
</blockquote><br />
<br />
:'''Exercise:''' <br />
:* [[Media:W02_exercises_v7_corrected.pdf|Building protein-protein interaction networks from experimental data]] (solutions now on learn)<br />
:* [[Media:Exercise_help_sheet.pdf|Note taking sheet for help with ex. 5,7,8,9]] - Consider printing this for taking notes<br />
:* [[Ex_handouts_igraph|Visualization of the networks from the hand-out exercise]] - '''Answers''': [[Ex_handouts_igraph_solution|Exercise #2 answers]]<br />
<br />
=== Lecture 03 (Sep 14) - Intro 3 ===<br />
<br />
:'''Lecture:''' ''Network topology'' - Lars Rønn Olsen <br />
:'''Slides:''' On DTU Learn.<br />
<br />
:'''Hand-outs:''' SnapShot: Protein-Protein Interaction Networks - (SAME AS LAST WEEK) ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/SnapShot_Cell2011.pdf PDF]) - read the rest for this week.<br />
:'''Readings:''' Global network properties. Barabasi& Oltvai, Nat Rev Genet 2004 ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/W03_Barabasi_Oltvai_NatRevGen2004.pdf PDF]) - concentrate on '''Box 1''' and '''Box 2'''.<br />
<br />
:'''Exercises:''' <br />
<blockquote><br />
#'''Handout exercise:''' Network topology exercise ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/W03_Network_topology_exercise_v3.pdf PDF])<br />
#'''Computer exercise:''' Topology/statistics/modules [[ExTopology1_igraph|Network topology and statistics]] - '''Answers''': [[ExTopology1_igraph_solutions|Answers to igraph exercise]]<br />
</blockquote><br />
<br />
== Block #2: Case: Yeast systems biology ==<br />
'''Responsible for this block:''' Rasmus Wernersson and Kristoffer Vitting-Seerup<br />
----<br />
<br />
=== Lecture 04 (Sep 21) - Yeast Systems Biology 1 ===<br />
<br />
:'''Lecture:''' ''Yeast Cell Cycle introduction'' - Rasmus Wernersson.<br />
:'''Slides:''' Will be uploaded to DTU Learn<br />
:'''Readings:''' <br />
:* Background on budding yeast cell cycle and cell cycle regulation ([https://teaching.healthtech.dtu.dk/27040/exercises/Budding_Yeast_Cell_Cycle_Model.pdf PDF]).<br />
:* Source: http://mpf.biol.vt.edu/research/budding_yeast_model/pp/index.php (much more information about modelling the yeast cell cycle can be found here) [NOT part of the curriculum].<br />
:* '''Important:''' You don't need to understand all the finer points about the regulation, but make sure you known the '''phases''' of the cell cycle. <br />
<br />
:'''Saccharomyces Genome Database:''' http://www.yeastgenome.org/<br />
:'''Exercise:''' [[ExYeastSysBio_R|Yeast cell cycle 1 - introduction to data and methods]] - '''Answers:''' [[ExYeastSysBio_R_answers|Yeast 1 answers]]<br />
<br />
=== Lecture 05 (Sept 28) - Yeast Systems Biology 2 ===<br />
<br />
:'''Lecture:''' ''Gene Ontology and large scale data analysis'' - Rasmus Wernersson<br />
:'''Readings:''' Two introductory papers to The Gene Ontology (GO). Choose the one you prefer. <br />
:* Intro for bioinformaticians: '''The what, where, how and why of gene ontology - a primer for bioinformaticians''' - [[File:Bbr002.pdf]] (NEW LINK) (focus on the first three pages).<br />
:**Focuses mostly on the structure of the GO, the evidence behind the annotations and relations of the genes/proteins to the categories.<br />
:* Intro for biologists: '''Gene Ontology: tool for the unification of biology''' - [[File:GO_NATURE_GENETICS_2000.pdf]] (NEW LINK)<br />
:**Describes more the general idea behind GO and why it is useful.<br />
:'''Slides:''' On DTU Learn<br />
<br />
:'''Exercise:''' [[ExGeneOntology_Yeast_R|Gene Ontology - yeast cell cycle examples]] - '''Answers:''' [[ExGeneOntology_Yeast_R_answers|answers]]<br />
<br />
=== Lecture 06 (Oct 5) - Yeast Systems Biology 3 ===<br />
<br />
:'''Lecture:''' ''Introduction to transcriptomics'' - Kristoffer Vitting-Seerup<br />
:'''Readings:''' ''A brief introduction to DNA micro-arrays'' ([https://learn.inside.dtu.dk/d2l/le/content/167355/viewContent/691406/View DTU Learn]) - Rasmus Wernersson<br />
:'''Background:''' (Optional) - If you need a reminder about how the Log2 function works, then have a look at '''Appendix A''' in Thomas Schneider's '' Information Theory Primer'' ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/informationtheory_primer.pdf PDF])<br />
:'''Slides:''' To appear on DTU Learn<br />
<br />
:'''Exercise:''' [[ExYeastCellCycleTranscriptomics_R|Yeast cell cycle: single point arrest DNA microarray studies]] - '''Answers:''' [[ExYeastCellCycle_answers|Answers]]<br />
<br />
=== Lecture 07 (Oct 12) - Yeast Systems Biology 4 ===<br />
<br />
:'''Lecture:''' ''How proteins collaborate during the phases of cell devision'' - Rasmus Wernersson.<br />
:'''Readings:''' [[Media:Cyclebase1_2008.pdf|Cyclebase paper]] - (skim it - make sure to understand '''Fig 1''').<br />
:'''Slides:''' To appear on DTU Learn<br />
<br />
:'''Exercise:''' [[ExYeastCellCycleTranscriptomics2_R|Mapping temporal expression data onto networks]] '''Answers:''' [[ExYeastCellCycleTranscriptomics2_R_answers|answers]]<br />
<br />
<hr><br />
<div align="center"><br />
'''Autumn vacation'''<br />
(Week 42)<br />
</div><br />
<hr><br />
<br />
== Block #3: Case: Human disease biology ==<br />
'''Responsible for this block:''' Lars Rønn Olsen, Rasmus Wernersson, and Kristoffer Vitting-Seerup <br />
----<br />
<br />
=== Lecture 08 (Oct 26) - Systems Biology in Biomedical Research (Heart diseases) 1 - CANCELLED ===<br />
<br />
<!--- :'''Lecture:''' ''Systems Biology of Heart Disease'' - Rasmus Wernersson (recorded lecture)<br />
:'''Readings:''' <br />
:* ''Human diseases through the lens of network biology'' ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/Furlong_Cell2012.pdf PDF])<br />
:* Concentrate on: '''Figure 1''' and '''Box 3'''<br />
:'''Heart development video:''' https://www.youtube.com/watch?v=5DIUk9IXUaI<br />
:'''Extra:''' (not curriculum)<br />
:* The heart disease paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/<br />
:'''Slides:''' To appear on DTU Learn<br />
:'''Exercise:''' [[ExHumanSysbio1|Working with "Virtual Pulldowns"]] '''Answers:''' [[ExHumanSysbio1_answers|"Virtual Pulldown" answers]]---><br />
<br />
=== Lecture 09 (Nov 2) - Systems Biology in Biomedical Research (Heart diseases) 2 ===<br />
[[Image:XKCD_significant.png|80px|thumb|right]]<br />
:'''Lecture:''' ''Virtual pulldown and protein complex detection'' - Lars Rønn Olsen and Giorgia Moranzoni<br />
:'''Readings:'''<br />
:* ''Human diseases through the lens of network biology'' ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/Furlong_Cell2012.pdf PDF]) - Concentrate on: '''Figure 1''' and '''Box 3'''<br />
:* '''Heart development video:''' https://www.youtube.com/watch?v=5DIUk9IXUaI<br />
:'''Extra:''' (not curriculum)<br />
:* The heart disease paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/<br />
:* The MCODE paper: http://www.biomedcentral.com/1471-2105/4/2<br />
:'''Exercises:''' [[DiscoNet|DiscoNet]] - '''Answers:''' [[DiscoNet_answers|DiscoNet answers]]<br />
<br />
<!---:* Read the cartoon to the right - it nicely illustrates the multiple testing problem (source: XKCD.org) <br />
:* ''How does multiple testing correction work?'', Noble 2009 ([https://www.nature.com/articles/nbt1209-1135 Article link])<br />
:* Make sure you understand how '''Bonferroni adjustment''' works.<br />
:'''Extra:'''<br />
:'''Slides:''' To appear on DTU Learn <br />
:'''Exercises:''' <br />
[[ExTM+MulTest|Multiple testing (text mining example)]] <br><br />
:# [[ExTM+MulTest|Multiple testing (text mining example)]] - '''Answers:''' [[ExTM+MulTest_answers|Multiple testing answers]]<br />
:# [[ExHumanSysbio2|Clustering]] - '''Answers:''' ([https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479133/View]) ---><br />
<br />
=== Lecture 10 (Nov 9) - Integrating multiple omics data types for cancer research ===<br />
:'''Lecture:''' ''Systems Biology in Cancer'' - Kristoffer Vitting-Seerup<br />
:'''Readings:''' <br />
:* ''The Hallmarks of Cancer'', Hanahan & Weinberg 2011 ([https://www.cell.com/fulltext/S0092-8674(11)00127-9 Article link])<br />
:'''Slides:''' [https://learn.inside.dtu.dk/d2l/le/content/167355/viewContent/704041/View On DTU Learn]<br />
:'''Exercises:''' [[DiscoNet2|Multiomics data integration]] '''Answers:''' [[DiscoNet2_answers|answers]]<br />
<br />
<!--- :'''Exercise:''' ([https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479122/View]) - '''Answers''' ([https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479141/View]) ---><br />
<br />
=== Lecture 11 (Nov 16) - Essential R functions + exam exercise ===<br />
<br />
:'''Lecture:''' Week 10 (and to some extent week 9) exercise walk-through<br />
:'''Slides:''' To appear on DTU Learn<br />
:'''Exercise:''' Old exam set (adapted to R)<br />
<br />
<br><br />
<br />
=== Lecture 12 (Nov 23) - QnA / AMA ===<br />
<br />
:'''Lecture:''' Kristoffer Vitting-Seerup<br />
:'''Topics:''' Anything you would like to a refresher about<br />
<br />
<br><br />
<br />
=== Lecture 13 (Nov 30) - Systems Biology in Biomedical Research 3 (ZS Revelen framework, drug targets) ===<br />
:'''Lecture:''' ''Biomarker and drug target identification'' - Rasmus Wernersson.<br />
:'''Readings:''' <br />
:* ''Systems biology investigation of COVID-19'': ''' Network analysis of COVID19 – Intomics''' (PDF on DTU Learn)<br />
:* It's a document with a written explanation of the COVID-19 analysis. (PDF of Intomics web-page, apologies for the sub-optimal formatting) <br />
:* Please read all of it - ''including methods''. It is written for a non-technical audience and should be easy to understand.<br />
<br />
:'''Slides:''' To appear on DTU Learn<br />
:'''Exercise:'''<br />
:* PDF on Learn<br />
:'''Link to ZS Revelen:''' '''https://zs-revelen.com/'''<br />
:*'''Please register''' your email with ZS Revelen before the exercise. '''Please use your DTU email.'''<br />
<br><br />
<br />
= Old exam sets =<br />
<br />
* On Learn<br />
<br />
<br />
<!--- = Links & curriculum summary =<br />
* [[Links and curriculum|Links and curriculum index]] ---><br />
<br />
= Exam =<br />
* '''Date: 6/12 2022<br />
* '''Time: 15:00-19:00<br />
* '''Where: (will be) available via https://eksamensplan.dtu.dk/</div>
WikiSysop