Autumn2021

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Revision as of 10:27, 18 March 2024 by WikiSysop (talk | contribs) (Created page with "= Course 22140 (previously 36040) - plan for autumn 2021 = <!-- = General information = --> '''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:


DTU Learn


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.


Cytoscape

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

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:

  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 2021

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: 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 (PDF) NOTE: Review paper - easy to read
Exercise: Introduction to Cytoscape and working with networks - 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 (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 (Sep 16th) - Intro 3

Lecture: Network topology - Lars Rønn Olsen
Slides: On CampusNet.
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: Cytoscape, topology/statistics/modules 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. Answers to Cytoscape exercise

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 (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 (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: Gene Ontology - yeast cell cycle examples - 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 (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 (PDF)
Slides: To appear on CampusNet
Exercise: Yeast cell cycle: single point arrest DNA microarray studies - Answers: ([1])

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

Lecture: How proteins collaborate during the phases of cell devision - Rasmus Wernersson. (Recorded lecture).
Readings: Cyclebase paper - (skim it - make sure to understand Fig 1).
Slides: To appear on CampusNet
Exercise: Mapping temporal expression data onto networks Answers: ([2])

Autumn vacation (Week 42)

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 (PDF)
  • Concentrate on: Figure 1 and Box 3
Heart development video: https://www.youtube.com/watch?v=5DIUk9IXUaI
Extra: (not curriculum)
Slides: To appear on CampusNet
Exercise: Working with "Virtual Pulldowns" - Answers: "Virtual Pulldown" answers

Lecture 09 (Nov 4th) - Systems Biology in Biomedical Research (Heart diseases) 2

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 (Article link)
  • Make sure you understand how Bonferroni adjustment works.
Extra: (not curriculum)
Slides: To appear on CampusNet
Exercise:
  1. Multiple testing (text mining example) - Answers: Multiple testing answers
  2. Clustering - Answers: ([3])


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 (Article link)
Slides: To appear on DTU Learn
Exercise: ([4]) Answers ([5])


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: Exploring human networks - 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


Lars Rønn will present a new cancer disease case + an exercise analyzing multiple lines of evidence in the context of networks.


Old exam sets

  • On DTU Inside (file sharing)


Links & curriculum summary


Exam

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