Autumn2024: Difference between revisions

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:'''Exercise:'''  
:'''Exercise:'''  
:* [[Media:W02_exercises_v7_corrected.pdf|Building protein-protein interaction networks from experimental data]] '''Answers''': [[Media:W02_exercises_with_answers_2021_CORRECTED.pdf|Handout answers]]
:* [[Media:W02_exercises_v7_corrected.pdf|Building protein-protein interaction networks from experimental data]] - '''Answers''': [[Media:W02_exercises_with_answers_2021_CORRECTED.pdf|Handout answers]]
:* [[Media:Exercise_help_sheet.pdf|Note taking sheet for help with ex. 5,7,8,9]] - Consider printing this for taking notes
:* [[Media:Exercise_help_sheet.pdf|Note taking sheet for help with ex. 5,7,8,9]] - Consider printing this for taking notes
:* [[Ex_handouts_igraph|Visualization of the networks from the hand-out exercise]] - '''Answers''': [[Ex_handouts_igraph_solution|Exercise #2 answers]]
:* [[Ex_handouts_igraph|Visualization of the networks from the hand-out exercise]] - '''Answers''': [[Ex_handouts_igraph_solution|Exercise #2 answers]]
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<blockquote>
<blockquote>
#'''Handout exercise:''' Network topology exercise ([https://teaching.healthtech.dtu.dk/material/22140/W03_Network_topology_exercise_v3.pdf PDF])
#'''Handout exercise:''' Network topology exercise ([https://teaching.healthtech.dtu.dk/material/22140/W03_Network_topology_exercise_v3.pdf PDF])
#'''Computer exercise:''' Topology/statistics/modules [[ExTopology1_igraph|Network topology and statistics]] - '''Answers''': [[ExTopology1_igraph_solutions|Answers to igraph exercise]]
#'''Computer exercise:''' Topology/statistics/modules [[ExTopology1_igraph|Network topology and statistics]] - '''Answers''': [[ExTopology1_igraph_solutions|Answers to network topology exercise]]
</blockquote>
</blockquote>


== Block #2: Case: Yeast systems biology ==
== Block #2: Case: Yeast systems biology ==
'''Responsible for this block:''' Rasmus Wernersson and Kristoffer Vitting-Seerup
'''Responsible for this block:''' Rasmus Wernersson and Lars Rønn Olsen
----
----


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=== Lecture 06 (October 10) - Yeast Systems Biology 3 ===
=== Lecture 06 (October 10) - Yeast Systems Biology 3 ===


:'''Lecture:''' ''Introduction to transcriptomics'' - Kristoffer Vitting-Seerup
:'''Lecture:''' ''Introduction to transcriptomics'' - Lars Rønn Olsen
:'''Readings:''' ''A brief introduction to DNA micro-arrays'' ([https://learn.inside.dtu.dk/d2l/le/content/167355/viewContent/691406/View DTU Learn]) - Rasmus Wernersson
:'''Readings:''' ''[[media:IntroToMicroArrays 2013.pdf|A brief introduction to DNA micro-arrays]]'' - Rasmus Wernersson
:'''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/material/22140/informationtheory_primer.pdf PDF])
:'''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/material/22140/informationtheory_primer.pdf PDF])
:'''Slides:''' To appear on DTU Learn
:'''Slides:''' To appear on DTU Learn
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:'''Exercise:''' [[ExYeastCellCycleTranscriptomics_R|Yeast cell cycle: single point arrest DNA microarray studies]] - '''Answers:''' [[ExYeastCellCycle_answers|Answers]]
:'''Exercise:''' [[ExYeastCellCycleTranscriptomics_R|Yeast cell cycle: single point arrest DNA microarray studies]] - '''Answers:''' [[ExYeastCellCycle_answers|Answers]]


=== Lecture 07 (October 12) - Yeast Systems Biology 4 ===
=== Lecture 07 (October 24) - Yeast Systems Biology 4 ===


:'''Lecture:''' ''How proteins collaborate during the phases of cell devision'' - Rasmus Wernersson.
:'''Lecture:''' ''How proteins collaborate during the phases of cell devision'' - Lars Rønn Olsen.
:'''Readings:''' [https://teaching.healthtech.dtu.dk/material/22140/Cyclebase1_2008.pdf PDF Cyclebase paper] - (skim it - make sure to understand '''Fig 1''').
:'''Readings:''' [https://teaching.healthtech.dtu.dk/material/22140/Cyclebase1_2008.pdf PDF Cyclebase paper] - (skim it - make sure to understand '''Fig 1''').
:'''Slides:''' To appear on DTU Learn
:'''Slides:''' To appear on DTU Learn
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== Block #3: Case: Human disease biology ==
== Block #3: Case: Human disease biology ==
'''Responsible for this block:''' Lars Rønn Olsen, Rasmus Wernersson, and Kristoffer Vitting-Seerup  
'''Responsible for this block:''' Lars Rønn Olsen, Kristoffer Vitting-Seerup and Rasmus Wernersson
----
----


=== Lecture 08 (October 24) - Systems Biology in Biomedical Research  (Heart diseases) 1 - CANCELLED ===
=== Lecture 08 (October 31) - Systems Biology in Biomedical Research  (Heart diseases) 1 ===


<!--- :'''Lecture:''' ''Systems Biology of Heart Disease'' - Rasmus Wernersson (recorded lecture)
:'''Lecture:''' ''Systems Biology of Heart Disease'' - Rasmus Wernersson
:'''Readings:'''  
:'''Readings:'''  
:* ''Human diseases through the lens of network biology'' ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/Furlong_Cell2012.pdf PDF])
:*[https://www.sciencedirect.com/science/article/pii/S0168952512001886?via%3Dihub|''Human diseases through the lens of network biology'']
:* Concentrate on: '''Figure 1''' and '''Box 3'''
:* Concentrate on: '''Figure 1''' and '''Box 3'''
:'''Heart development video:''' https://www.youtube.com/watch?v=5DIUk9IXUaI
:'''Heart development video:''' https://www.youtube.com/watch?v=5DIUk9IXUaI
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:* The heart disease paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/
:* The heart disease paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/
:'''Slides:''' To appear on DTU Learn
:'''Slides:''' To appear on DTU Learn
:'''Exercise:''' [[ExHumanSysbio1|Working with "Virtual Pulldowns"]] '''Answers:''' [[ExHumanSysbio1_answers|"Virtual Pulldown" answers]]--->
:'''Exercises:''' [[DiscoNet|Working with "Virtual Pulldowns]] - '''Answers:''' [[DiscoNet_answers|"Virtual Pulldown" answers]]
 
=== Lecture 09 (November 7) - Systems Biology in Biomedical Research  (Heart diseases) 2 ===


=== Lecture 09 (October 31) - Systems Biology in Biomedical Research  (Heart diseases) 2 ===
[[Image:XKCD_significant.png|80px|thumb|right]]
[[Image:XKCD_significant.png|80px|thumb|right]]
:'''Lecture:''' ''Virtual pulldown and protein complex detection'' - Lars Rønn Olsen and Giorgia Moranzoni
:'''Lecture:''' ''Virtual pulldown and protein complex detection'' - Rasmus Wernersson
:'''Readings:'''
:'''Readings:'''
:* ''Human diseases through the lens of network biology'' ([https://teaching.healthtech.dtu.dk/material/22140/Furlong_Cell2012.pdf PDF]) - Concentrate on: '''Figure 1''' and '''Box 3'''
:* ''Human diseases through the lens of network biology'' ([https://teaching.healthtech.dtu.dk/material/22140/Furlong_Cell2012.pdf PDF]) - Concentrate on: '''Figure 1''' and '''Box 3'''
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:* The heart disease paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/
:* The heart disease paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/
:* The MCODE paper: http://www.biomedcentral.com/1471-2105/4/2
:* The MCODE paper: http://www.biomedcentral.com/1471-2105/4/2
:'''Exercises:''' [[DiscoNet|DiscoNet]] - '''Answers:''' [[DiscoNet_answers|DiscoNet answers]]
:'''Exercises:''' Same as last week
 
=== Lecture 10 (November 14) - Protein isoforms 1 ===
 
Isoform exercise
 
=== Lecture 11 (November 21) - Protein isoforms 2 ===


<!---:* Read the cartoon to the right - it nicely illustrates the multiple testing problem (source: XKCD.org)
Isoform exercise continued + *QnA*
:* ''How does multiple testing correction work?'', Noble 2009 ([https://www.nature.com/articles/nbt1209-1135 Article link])
 
:* Make sure you understand how '''Bonferroni adjustment''' works.
=== Lecture 12 (November 28) - Integrating multiple omics data types for cancer research ===
:'''Extra:'''
:'''Slides:''' To appear on DTU Learn
:'''Exercises:'''
[[ExTM+MulTest|Multiple testing (text mining example)]] <br>
:# [[ExTM+MulTest|Multiple testing (text mining example)]] - '''Answers:'''  [[ExTM+MulTest_answers|Multiple testing answers]]
:# [[ExHumanSysbio2|Clustering]] - '''Answers:''' ([https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479133/View]) --->


=== Lecture 10 (November 7) - Integrating multiple omics data types for cancer research ===
:'''Lecture:''' ''Systems Biology in Cancer'' - Lars Rønn Olsen
:'''Lecture:''' ''Systems Biology in Cancer'' - Kristoffer Vitting-Seerup
:'''Readings:'''  
:'''Readings:'''  
:* ''The Hallmarks of Cancer'', Hanahan & Weinberg 2011 ([https://www.cell.com/fulltext/S0092-8674(11)00127-9 Article link])
:* ''The Hallmarks of Cancer'', Hanahan & Weinberg 2011 ([https://www.cell.com/fulltext/S0092-8674(11)00127-9 Article link])
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:'''Exercises:''' [[DiscoNet2|Multiomics data integration]] '''Answers:''' [[DiscoNet2_answers|answers]]
:'''Exercises:''' [[DiscoNet2|Multiomics data integration]] '''Answers:''' [[DiscoNet2_answers|answers]]


<!--- :'''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]) --->
=== Lecture 13 (December 5) - Multiple choice test (EXAM! Participation is mandatory) + Q&A ===


=== Lecture 11 (November 14) - Essential R functions + exam exercise ===
TBA


:'''Lecture:''' Week 10 (and to some extent week 9) exercise walk-through
= Old exam sets =
:'''Slides:''' To appear on DTU Learn
:'''Exercise:''' Old exam set (adapted to R)


<br>
To appear on Learn


=== Lecture 12 (November 21) - QnA / AMA ===
= Written exam with aids =
* '''Date: 9/12 2024
* '''Time: (will be) available via https://eksamensplan.dtu.dk/
* '''Where: (will be) available via https://eksamensplan.dtu.dk/


:'''Lecture:''' Kristoffer Vitting-Seerup
:'''Topics:''' Anything you would like to a refresher about


<br>
<!---
 
=== Lecture 13 (December 5) - Systems Biology in Biomedical Research 3 (ZS Revelen framework, drug targets) ===
=== Lecture 13 (November 28) - Systems Biology in Biomedical Research 3 (ZS Revelen framework, drug targets) ===
:'''Lecture:''' ''Biomarker and drug target identification'' - Rasmus Wernersson.
:'''Lecture:''' ''Biomarker and drug target identification'' - Rasmus Wernersson.
:'''Readings:'''  
:'''Readings:'''  
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:* It's a document with a written explanation of the COVID-19 analysis. (PDF of Intomics web-page, apologies for the sub-optimal formatting)  
:* It's a document with a written explanation of the COVID-19 analysis. (PDF of Intomics web-page, apologies for the sub-optimal formatting)  
:* Please read all of it - ''including methods''. It is written for a non-technical audience and should be easy to understand.
:* Please read all of it - ''including methods''. It is written for a non-technical audience and should be easy to understand.
 
--->
:'''Slides:''' To appear on DTU Learn
:'''Exercise:'''
:* PDF on Learn
:'''Link to ZS Revelen:''' '''https://zs-revelen.com/'''
:*'''Please register''' your email with ZS Revelen before the exercise. '''Please use your DTU email.'''
<br>
 
= Old exam sets =
 
* On Learn
 
 
<!--- = Links & curriculum summary =
* [[Links and curriculum|Links and curriculum index]] --->
 
= Exam =
* '''Date: 9/12 2024
* '''Time: (will be) available via https://eksamensplan.dtu.dk/
* '''Where: (will be) available via https://eksamensplan.dtu.dk/

Latest revision as of 12:01, 14 November 2024

Course 22140 - plan for autumn 2024

Teachers:

  • Lars Rønn Olsen (course organizer) - contact: lronn@dtu.dk
  • Kristoffer Vitting-Seerup (course organizer) - contact: krivi@dtu.dk
  • Rasmus Wernersson (external lecturer) - contact: rawe@dtu.dk
  • Dimitrios Kanakoglou (teaching assistant) - contact: dimkan@dtu.dk


DTU Learn


Bioinformatics

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.


R

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 here.

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".

Weekly assignments

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.

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.

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.

Allowed formats:

  1. Plain text + figures as extra files
  2. Microsoft Word (*.doc, *.docx)
  3. PDF: use ANY word-processing software you like (e.g. "Pages") and save/print the result to a PDF.


Lecture plan, autumn 2024

When and Where

  • When: Each Thursday from 13:00-17:00
  • Where: Building 303A auditorium/group-room 045


Block #1: Introduction

Responsible for this block: Lars Rønn Olsen and Rasmus Wernersson

Lecture 01 (September 5) - Intro 1

Lecture: Introduction to Systems Biology and biological networks - Rasmus Wernersson.
Slides: Will be uploaded to DTU Learn
Readings: Can a Biologist fix a radio? - Lazebnik Y., Cancer Cell 2002 (PDF)
Exercise: Introduction to working with networks in R - Answers: Exercise #1 answers

Lecture 02 (September 12) - Intro 2

Lecture: Protein-protein interaction networks. Experimental methods and interpretation. - Lars Rønn Olsen
Slides: To appear on DTU Learn
Hand-outs: SnapShot: Protein-Protein Interaction Networks - Seebacher & Gavin, Nature 2011 (PDF) - focus on the EXPERIMENTAL METHODS part for this week.
Readings:
  • Lecture note on quality scoring of protein-protein interaction data, notes and examples (PDF)
  • Comparative assessment of large-scale data sets of protein-protein interactions - von Mering C, et al. Nature 2002 (PDF)
Exercise:

Lecture 03 (September 19) - Intro 3

Lecture: Network topology - Lars Rønn Olsen
Slides: On DTU Learn.
Hand-outs: SnapShot: Protein-Protein Interaction Networks - (SAME AS LAST WEEK) (PDF) - read the rest for this week.
Readings: Global network properties. Barabasi& Oltvai, Nat Rev Genet 2004 (PDF) - concentrate on Box 1 and Box 2.
Exercises:
  1. Handout exercise: Network topology exercise (PDF)
  2. Computer exercise: Topology/statistics/modules Network topology and statistics - Answers: Answers to network topology exercise

Block #2: Case: Yeast systems biology

Responsible for this block: Rasmus Wernersson and Lars Rønn Olsen

Lecture 04 (September 26) - Yeast Systems Biology 1

Lecture: Yeast Cell Cycle introduction - Rasmus Wernersson.
Slides: Will be uploaded to DTU Learn
Readings:
  • Background on budding yeast cell cycle and cell cycle regulation (PDF).
  • 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].
  • 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.
Saccharomyces Genome Database: http://www.yeastgenome.org/
Exercise: Yeast cell cycle 1 - introduction to data and methods - Answers: Yeast 1 answers

Lecture 05 (October 3) - Yeast Systems Biology 2

Lecture: Gene Ontology and large scale data analysis - Rasmus Wernersson
Readings: Two introductory papers to The Gene Ontology (GO). Choose the one you prefer.
  • Intro for bioinformaticians: The what, where, how and why of gene ontology - a primer for bioinformaticians - PDF (NEW LINK) (focus on the first three pages).
    • Focuses mostly on the structure of the GO, the evidence behind the annotations and relations of the genes/proteins to the categories.
  • Intro for biologists: Gene Ontology: tool for the unification of biology - PDF (NEW LINK)
    • Describes more the general idea behind GO and why it is useful.
Slides: On DTU Learn
Exercise: Gene Ontology - yeast cell cycle examples - Answers: answers

Lecture 06 (October 10) - Yeast Systems Biology 3

Lecture: Introduction to transcriptomics - Lars Rønn Olsen
Readings: A brief introduction to DNA micro-arrays - Rasmus Wernersson
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 (PDF)
Slides: To appear on DTU Learn
Exercise: Yeast cell cycle: single point arrest DNA microarray studies - Answers: Answers

Lecture 07 (October 24) - Yeast Systems Biology 4

Lecture: How proteins collaborate during the phases of cell devision - Lars Rønn Olsen.
Readings: PDF Cyclebase paper - (skim it - make sure to understand Fig 1).
Slides: To appear on DTU Learn
Exercise: Mapping temporal expression data onto networks Answers: answers

Autumn vacation (Week 42)

Block #3: Case: Human disease biology

Responsible for this block: Lars Rønn Olsen, Kristoffer Vitting-Seerup and Rasmus Wernersson

Lecture 08 (October 31) - Systems Biology in Biomedical Research (Heart diseases) 1

Lecture: Systems Biology of Heart Disease - Rasmus Wernersson
Readings:
Heart development video: https://www.youtube.com/watch?v=5DIUk9IXUaI
Extra: (not curriculum)
Slides: To appear on DTU Learn
Exercises: Working with "Virtual Pulldowns - Answers: "Virtual Pulldown" answers

Lecture 09 (November 7) - Systems Biology in Biomedical Research (Heart diseases) 2

Lecture: Virtual pulldown and protein complex detection - Rasmus Wernersson
Readings:
Extra: (not curriculum)
Exercises: Same as last week

Lecture 10 (November 14) - Protein isoforms 1

Isoform exercise

Lecture 11 (November 21) - Protein isoforms 2

Isoform exercise continued + *QnA*

Lecture 12 (November 28) - Integrating multiple omics data types for cancer research

Lecture: Systems Biology in Cancer - Lars Rønn Olsen
Readings:
  • The Hallmarks of Cancer, Hanahan & Weinberg 2011 (Article link)
Slides: On DTU Learn
Exercises: Multiomics data integration Answers: answers

Lecture 13 (December 5) - Multiple choice test (EXAM! Participation is mandatory) + Q&A

TBA

Old exam sets

To appear on Learn

Written exam with aids


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