WikiSysop: Created page with "= Course 22140 (previously 36040) - plan for autumn 2021 = '''Teachers:''' * [https://www.biosurf.org 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] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant..."

2024-03-18T09:27:41Z

Created page with "= Course 22140 (previously 36040) - plan for autumn 2021 =  '''Teachers:''' * [https://www.biosurf.org 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] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant..."

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= Course 22140 (previously 36040) - plan for autumn 2021 =

'''Teachers:'''
* [https://www.biosurf.org 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]
* [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk]
* Giorgia Moranzoni (teaching assistant) - '''contact:''' [mailto:gimo@dtu.dk gimo@dtu.dk]



= DTU Learn =
* Link: [https://learn.inside.dtu.dk/d2l/home/81276 Course 22140, Autumn 2021 @ DTU Learn]
<br>

= Bioinformatics =
Besides knowledge about basic molecular biology and biochemistry, a prerequisite for this course is bioinformatics (usually from course 27611 or 27622). If you need to read up on some bioinformatics topics, please use the links below.
* [http://teaching.healthtech.dtu.dk/36611 Course 36611] - ''Introduktion til Bioinformatik'' (in danish)
* [[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 2021 =

== 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, Lars Rønn Olsen
----
=== Lecture 01 (Sep 2nd) - Intro 1 ===

:'''Lecture:''' ''Introduction to Systems Biology and biological networks'' - Rasmus Wernersson.
:'''Slides:''' To appear on CampusNet
:'''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 9th) - Intro 2 ===

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

:'''Slides:''' To appear on CampusNet
:'''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]]) - '''NEW LINK! (Sept. 9th 2021)''') - - '''Answers''': (NEW - updated Feb 16th) [[file:W02_exercises_with_answers_2021_CORRECTED.pdf]] (We will also show some slides about this on Tuesday)
:* 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 16th) - Intro 3 ===

:'''Lecture:''' ''Network topology'' - Lars Rønn Olsen
:'''Slides:''' On CampusNet.

:'''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). Wiki answers comming as soon as we have updated the plots to show Cytoscape 3.8 results. [[ExTopology1_answers|Answers to Cytoscape exercise]]
</blockquote>

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

=== Lecture 04 (Sep 23rd) - Yeast Systems Biology 1 ===

:'''Lecture:''' ''Yeast Cell Cycle introduction'' - Rasmus Wernersson.
:'''Slides:''' Will be uploaded to CampusNet
:'''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 30th) - Yeast Systems Biology 2 ===

:'''Lecture:''' ''Gene Ontology and large scale data analysis'' - Lars Rønn Olsen
:'''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 CampusNet

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

=== Lecture 06 (Oct 7th) - Yeast Systems Biology 3 ===

:'''Lecture:''' ''Introduction to transcriptomics'' - Kristoffer Vitting-Seerup
:'''Readings:''' ''A brief introduction to DNA micro-arrays'' ([http://www.cbs.dtu.dk/~raz/teaching/IntroToMicroArrays_2013.pdf PDF]) - 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 CampusNet

:'''Exercise:''' [[ExYeastCellCycleTranscriptomics1|Yeast cell cycle: single point arrest DNA microarray studies]] - '''Answers:''' ([https://learn.inside.dtu.dk/d2l/le/content/81276/viewContent/340241/View])

=== Lecture 07 (Oct 14th) - Yeast Systems Biology 4 ===

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

:'''Exercise:''' [[ExYeastCellCycleTranscriptomics2|Mapping temporal expression data onto networks]] '''Answers:''' ([https://learn.inside.dtu.dk/d2l/le/content/81276/viewContent/354860/View])

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

== Block #3: Case: Human disease biology ==
'''Responsible for this block:''' Rasmus Wernersson, Lars Rønn Olsen
----

=== Lecture 08 (Oct 28th) - 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 CampusNet


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

=== Lecture 09 (Nov 4th) - Systems Biology in Biomedical Research (Heart diseases) 2 ===
[[Image:XKCD_significant.png|80px|thumb|right]]
:'''Lecture:''' ''Clustering, multiple testing correction & text mining'' - Lars Rønn Olsen 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:''' (not curriculum)
:* The MCODE paper: http://www.biomedcentral.com/1471-2105/4/2
:'''Slides:''' To appear on CampusNet

:'''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/81276/viewContent/354865/View])

=== Lecture 10 (Nov 11th) - Integrating multiple omics data types for cancer research ===
:'''Lecture:''' ''Functional cancer phenotyping: follicular thyroid cancer case'' - Lars Rønn Olsen.
:'''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/81276/viewContent/346362/View]) '''Answers''' ([https://learn.inside.dtu.dk/d2l/le/content/81276/viewContent/348132/View])

=== Lecture 11 (Nov 18th) - 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:''' [[ExHumanSysbio3|Exploring human networks]] - '''Answers:''' [[ExHumanSysbio3_answers|Exploring human networks ANSWERS]] (Link fixed)
:'''Link to inBio Discover:''' '''https://inbio-discover.intomics.com/'''
:*'''Please register''' your email with inBio Discover before the exercise.

=== Lecture 12 (Nov 25th) - A (cancer) case of isoform switches, functional class scorring and topology analysis ===
:'''Lecture: TBD''' - Kristoffer Vitting-Seerup.
:'''Readings: TBD'''
:'''Slides:''' To appear on CampusNet
:'''Exercise: TBD'''

=== Lecture 13 (Dec 2nd) - Advanced topics, Wrap-up, "Spørgetime" (Q&A session) ===

:'''Lecture:''' ''TBA

:'''Slides:''' To appear on CampusNet

<blockquote style="background-color: lavender; border: solid thin grey;">
Lars Rønn will present a new cancer disease case + an exercise analyzing multiple lines of evidence in the context of networks.
</blockquote>





= Old exam sets =

* On DTU Inside (file sharing)

= Links & curriculum summary =
* [[Links and curriculum|Links and curriculum index]]

= Exam =
* '''When & where: '''December 7th 2021'' ; 15:00 - 19:00 (some have extra time), '''TBD''

Autumn2021 - Revision history