WikiSysop: Created page with "= Course 22140 (previously 36040) - plan for autumn 2022 = '''Teachers:''' * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant) - '''contact:''' [mailto:gimo@dtu.dk gimo@dtu.dk] * Lars Rønn Olsen (course organizer) is on parental lea..."

2024-03-05T16:11:56Z

Created page with "= Course 22140 (previously 36040) - plan for autumn 2022 =  '''Teachers:''' * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant) - '''contact:''' [mailto:gimo@dtu.dk gimo@dtu.dk] * Lars Rønn Olsen (course organizer) is on parental lea..."

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= Course 22140 (previously 36040) - plan for autumn 2022 =

'''Teachers:'''
* Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk]
* [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk]
* Giorgia Moranzoni (teaching assistant) - '''contact:''' [mailto:gimo@dtu.dk gimo@dtu.dk]
* Lars Rønn Olsen (course organizer) is on parental leave and will therefore not respond. Contact Kristoffer instead.



= DTU Learn =
* Link: [https://learn.inside.dtu.dk/d2l/home/126026 Course 22140, Autumn 2022 @ DTU Learn]
<br>

= 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.
* [https://teaching.healthtech.dtu.dk/22111/ Course 22111] - ''Introduction to Bioinformatics''
* [[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>

= Cytoscape =
[[Image:Cytoscape_icon.png‎|right]]
For many of the computer exercise we will be using Cytoscape for inspecting and analyzing the biological networks. Cytoscape is Open Source and freely available for Windows, Mac and Linux. Make sure to have Cytoscape installed on your laptop prior to the course: http://www.cytoscape.org/



= Weekly assignments =
[[Image:Office-notes-line_drawing.png|40px|left]]
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 Learn system. We collect the reports and give a general feedback to the entire class the following week.

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



= Lecture plan, autumn 2022 =

== When and Where ==
* '''When:''' Each '''Thursday''' from '''13:00-17:00'''
* '''Where:''' Building '''303A''' auditorium/group-room '''045'''
<hr>


== Block #1: Introduction ==
'''Responsible for this block:''' Rasmus Wernersson, Kristoffer Vitting-Seerup
----
=== Lecture 01 (Sep 1st) - Intro 1 ===

:'''Lecture:''' ''Introduction to Systems Biology and biological networks'' - Rasmus Wernersson.
:'''Slides:''' To appear on DTU Learn
:'''Readings:''' ''Can a Biologist fix a radio?'' - Lazebnik Y., Cancer Cell 2002 ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/W01_Lazebnik_CancerCell2002.pdf PDF]) NOTE: Review paper - easy to read

:'''Exercise:''' [[ExCytoscapeIntro_v2|Introduction to Cytoscape and working with networks]] - '''Answers:''' [[ExCytoscapeIntro_Answers|Exercise #1 answers]]

=== Lecture 02 (Sep 8th) - Intro 2 ===

:'''Lecture:''' ''Protein-protein interaction networks. Experimental methods and interpretation.'' - Rasmus Wernersson

:'''Slides:''' To appear on DTU Learn
:'''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.
:'''Readings:'''
<blockquote>
* 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])
* ''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])
</blockquote>

:'''Exercise:'''
:* Building protein-protein interaction networks from experimental data ([[file:W02_exercises_v7_corrected.pdf|PDF]])) 
:* Note taking sheet for help with ex. 5,7,8,9 ([https://teaching.healthtech.dtu.dk/27040/exercises/Exercise_help_sheet.pdf PDF]) - PRINT OUT and take notes.
:* Computer-exercise: [[ExPpiDataVisualization|Visualization of the networks from the hand-out exercise]] - '''Answers''': [[ExPpiDataVisualization_Answers|Ex. 10+11 answers]]

=== Lecture 03 (Sep 15th) - Intro 3 ===

:'''Lecture:''' ''Network topology'' - Kristoffer Vitting-Seerup
:'''Slides:''' On DTU Learn.

:'''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.
:'''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'''.

:'''Exercises:'''
<blockquote>
#'''Handout exercise:''' Network topology exercise ([https://teaching.healthtech.dtu.dk/27040/teachingmaterials/W03_Network_topology_exercise_v3.pdf PDF])
#'''Computer exercise:''' Cytoscape, topology/statistics/modules [[ExTopology1|Network topology and statistics]] '''Answers''': See slides on DTU Learn (week 3). [[ExTopology1_answers|Answers to Cytoscape exercise]]
</blockquote>

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

=== Lecture 04 (Sep 22nd) - 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 ([https://teaching.healthtech.dtu.dk/27040/exercises/Budding_Yeast_Cell_Cycle_Model.pdf 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:''' [[ExYeastSysBio1|Yeast cell cycle 1 - introduction to data and methods]] '''Answers:''' [[ExYeastSysBio1_answers|Yeast 1 answers]]

=== Lecture 05 (Sept 29th) - 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''' - [[File:Bbr002.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''' - [[File:GO_NATURE_GENETICS_2000.pdf]] (NEW LINK)
:**Describes more the general idea behind GO and why it is useful.
:'''Slides:''' On DTU Learn

:'''Exercise:''' [[ExGeneOntology_Yeast1.5|Gene Ontology - yeast cell cycle examples]] - '''Answers:''' [[ExGeneOntology_Yeast1.5_answers|wiki answers]]

=== Lecture 06 (Oct 6th) - Yeast Systems Biology 3 ===

:'''Lecture:''' ''Introduction to transcriptomics'' - Kristoffer Vitting-Seerup
:'''Readings:''' ''A brief introduction to DNA micro-arrays'' ([https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/510349/View DTU Learn]) - 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/27040/teachingmaterials/informationtheory_primer.pdf PDF])
:'''Slides:''' To appear on DTU Learn

:'''Exercise:''' [[ExYeastCellCycleTranscriptomics1|Yeast cell cycle: single point arrest DNA microarray studies]] - '''Answers:''' ([https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479103/View])

=== Lecture 07 (Oct 13th) - Yeast Systems Biology 4 ===

:'''Lecture:''' ''How proteins collaborate during the phases of cell devision'' - Rasmus Wernersson.
:'''Readings:''' [[Media:Cyclebase1_2008.pdf‎|Cyclebase paper]] - (skim it - make sure to understand '''Fig 1''').
:'''Slides:''' To appear on DTU Learn

:'''Exercise:''' [[ExYeastCellCycleTranscriptomics2|Mapping temporal expression data onto networks]] '''Answers:''' ([https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479132/View])

<hr>
<div align="center">
'''Autumn vacation'''
(Week 42)
</div>
<hr>

== Block #3: Case: Human disease biology ==
'''Responsible for this block:''' Rasmus Wernersson, Kristoffer Vitting-Seerup
----

=== Lecture 08 (Oct 27th) - Systems Biology in Biomedical Research (Heart diseases) 1 ===

:'''Lecture:''' ''Systems Biology of Heart Disease'' - Rasmus Wernersson
:'''Readings:'''
:* ''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'''
:'''Heart development video:''' https://www.youtube.com/watch?v=5DIUk9IXUaI
:'''Extra:''' (not curriculum)
:* The heart disease paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/
:'''Slides:''' To appear on DTU Learn

:'''Exercise:''' [[ExHumanSysbio1|Working with "Virtual Pulldowns"]] '''Answers:''' [[ExHumanSysbio1_answers|"Virtual Pulldown" answers]]

=== Lecture 09 (Nov 3rd) - Systems Biology in Biomedical Research (Heart diseases) 2 ===
[[Image:XKCD_significant.png|80px|thumb|right]]
:'''Lecture:''' ''Clustering, multiple testing correction & text mining'' - Kristoffer Vitting-Seerup and Rasmus Wernersson.
:'''Readings:'''
:* Read the cartoon to the right - it nicely illustrates the multiple testing problem (source: XKCD.org)
:* ''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.
:'''Extra:'''
:* The MCODE paper: http://www.biomedcentral.com/1471-2105/4/2
:'''Slides:''' To appear on DTU Learn

:'''Exercise:'''
:# [[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 (Nov 10th) - Integrating multiple omics data types for cancer research ===
:'''Lecture:''' ''Functional cancer phenotyping: follicular thyroid cancer case'' - Kristoffer Vitting-Seerup
:'''Readings:'''
:* ''The Hallmarks of Cancer'', Hanahan & Weinberg 2011 ([https://www.cell.com/fulltext/S0092-8674(11)00127-9 Article link])
:'''Slides:''' To appear on DTU Learn
:'''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 11 (Nov 17th) - Systems Biology in Biomedical Research (inBio Discover framework, drug targets) 3 ===
:'''Lecture:''' ''Biomarker and drug target identification'' - Rasmus Wernersson.
:'''Readings:'''
:* ''Systems biology investigation of COVID-19'': '''https://www.intomics.com/covid19/'''
:* It's a web-page with a written explanation of the COVID-19 analysis + links to interactive networks.
:* 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:'''
:* [[ExInBioDiscover_v2|Exploring drug target and disease networks]] - '''Answers:''' [[ExInBioDiscover_v2_answers|ANSWERS]]
:* OPTIONAL: [[ExHumanSysbio3|Exploring human networks]] (If time allows) - '''Answers:''' [[ExHumanSysbio3_answers|Exploring human networks
ANSWERS]]
:'''Link to inBio Discover:''' '''https://inbio-discover.com/'''
:*'''Please register''' your email with inBio Discover before the exercise.

<br>

=== Lecture 12 (Nov 24th) - Isoform Switches in Cancer - Part 1 ===
:'''Lecture:''' Kristoffer Vitting-Seerup

:'''Readings:''' [https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/526969/View Isoform Switches in Cancer]

:'''Slides:''' [https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/531621/View On DTU Learn]. Note slides with solutions will be available after lecture

:'''Exercise:''' [https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479148/View Isoform exercise]

<br>

=== Lecture 13 (Dec 1st) - Isoform Switches in Cancer - Part 2, QnA, Course summary ===
:'''Content''':
:* Isoform switches in cancer - part 2
:* Exam info and QnA
:* Course summary

:'''Lecture:''' Kristoffer Vitting-Seerup

:'''Readings:''' [https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/526969/View Isoform Switches in Cancer]

:'''Slides:''' [https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/531621/View On DTU Learn]. Note slides with solutions will be available after lecture

:'''Exercise:''' [https://learn.inside.dtu.dk/d2l/le/content/126026/viewContent/479148/View Isoform exercise]

<br>

= Old exam sets =

* On DTU Inside (file sharing)



= Exam =
* '''Date: 7/12 2022
* '''Time: 09:00-13:00
* '''Where: (will be) available via https://eksamensplan.dtu.dk/

Autumn2022 - Revision history