Autumn2017

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General information

Teachers:


CampusNet

Cytoscape

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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/


Windows 8/10: Description about how to fix the Java 32bit vs. 64bit issue is described here: http://www.cytoscape.org/release_notes_3_4_0.html

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.

  • [27611] - Introduktion til Bioinformatik (in danish)
  • UniProt exercise - This is an important one, as we use UniProt a lot in this course.

Weekly assignments

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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 CampusNet 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 2017

When and Where

  • When: Each Thursday from 13:00-17:00
  • Where: Building 210 rooms 042 + 048 (both lecture and computer exercise)

Block #1: Introduction

Responsible for this block: Rasmus Wernersson, Lars Rønn Olsen


Lecture 01 (Sep 7th) - 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 14th) - 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 21st) - Intro 3

Lecture: Network topology - Rasmus Wernersson
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: Answers to Cytoscape exercise

Block #2: Case: Yeast systems biology

Responsible for this block: Rasmus Wernersson, Lars Rønn Olsen


Lecture 04 (Sep 28th) - 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 (Oct 5th) - 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.
Slides: On CampusNet
Exercise: Gene Ontology - yeast cell cycle examples - Answers: wiki answers

Lecture 06 (Oct 12th) - Yeast Systems Biology 3

Lecture: Introduction to transcriptomics - Lars Rønn Olsen.
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: Slides on CampusNet (after next lecture) + full writtten answers as a PDF on CampusNet as well (already uploaded).

Autumn vacation (Week 42)


Lecture 07 (Oct 26th) - Yeast Systems Biology 4

Lecture: How proteins collaborate during the phases of cell devision - Rasmus Wernersson.
Readings: Cyclebase paper - (skim it - make sure to understand Fig 1).
Slides: To appear on CampusNet
Exercise: Mapping temporal expression data onto networks - Answers: Slides on CampusNet + full writtten answers as a PDF on CampusNet as well.

Block #3: Case: Prokaryote systems biology

Responsible for this block: Jan Martinussen


Lecture 08 (Nov 2nd) - Metabolomics #1: Purine metabolism in Lactococcus lactis

Lecture: Purine metabolism in Lactococcus lactis - Jan Martinussen.
Readings:
Slides: To appear on CampusNet
Exercise: Latococcus exercise#1

Lecture 09 (Nov 9th) - Metabolomics #2: Purine metabolism in Lactococcus lactis (cont.)

Lecture: Purine metabolism in Lactococcus lactis (part 2) - Jan Martinussen.
Readings:
Slides: To appear on CampusNet
Exercise: Latococcus exercise#2

Block #4: Case: Human disease biology

Responsible for this block: Rasmus Wernersson, Lars Rønn Olsen


Lecture 10 (Nov 16th) - Exam prep

LAST MINUTE CHANGE: Due to illness the introduction to the Human Disease Systems Biology case has been postponed to next week. Instead we'll work with an old exam set (December 2016 - all files are on DTU Inside / file sharing)

Lecture 11 (Nov 23rd) - 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"

Lecture 12 (Nov 30th) - Systems Biology in Biomedical Research (Heart diseases) 2

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Lecture: Clustering, multiple testing correction & text mining - Lars Rønn Olsen and Rasmus Wernersson.
Readings:
  • Read the cartoon to right - it nicely illustrates the multiple testing problem (source: XKCD.org)
  • How does multiple testing correction work?, Noble 2009 (PDF)
  • Make sure you understand how Bonferroni adjustment works.
Extra: (not curriculum)
Slides: To appear on CampusNet
Exercise:
  1. Multiple testing (text mining example)
  2. Clustering

Block #5: Wrap up

Responsible for this block: Rasmus Wernersson, Lars Rønn Olsen


Lecture 13 (Dec 7th) - Advanced topics, Wrap-up, "Spørgetime" (Q&A session)

Lecture: A primer to mathematical models and other more advanced topics - Rasmus Wernersson and guest lecturers.
Slides: To appear on CampusNet
Exercise: Practice on an old exam set - We'll work on the December 2015 exam (found under "File sharing" on CampusNet)

Old exam sets

  • On CamputNet (file sharing)

Links & curriculum summary

Exam

  • When & where: December 12th 2017 ; 9:00 - 13:00 (some have extra time), Building 116.
  • Exam questions: Will be available on CampusNet (Assignments -> Exam) as soon as the exam opens.