systems biology workshop - cbs · 2009-05-12 · introduction to the course systems biology...

Systems Biology Workshop, May 14th-15th, 2009 Thomas Skøt Jensen

Technical University of Denmark

Introduction to the course

Systems Biology Workshop

Thomas Skøt Jensen Center for Biological Sequence Analysis Technical University of Denmark


Technical University of Denmark Teachers

Lars Juhl Jensen Professor, Systems Biology

Irene Kouskoumvekaki Assistant professor, Computational Chemical Biology

Chris Workman Assistant professor, Regulatory Genomics

Thomas Skøt Jensen Assistant professor, Integrative Systems Biology


Technical University of Denmark Course Program


Technical University of Denmark Practical Information

•  Informal course - interrupt and ask questions

•  Feel free to take a coffee break during exercises

•  Lunch is on your own, we recommend the canteen

•  We recommend that exercise are done in teams

•  Rest rooms located below the stairs



A historical perspective on

Systems Biology



“...So God created the great creatures of the sea and every living and moving thing with which the water teems, according to their kinds, and every winged bird according to its kind. And God saw that it was good...”

“... God made the wild animals according to their kinds, the livestock according to their kinds, and all the creatures that move along the ground according to their kinds. And God saw that it was good...”

“... So God created man in his own image, in the image of God he created him; male and female he created them.”

“... God blessed them and said to them, "Be fruitful and increase in number; fill the earth and subdue it. Rule over the fish of the sea and the birds of the air and over every living creature that moves on the ground..."

Source: The Bible, Genesis

Early theories in biology


Technical University of Denmark God is systematic...


Technical University of Denmark Theory of evolution


Technical University of Denmark Darwin’s four postulates

  Each generation more offspring is born than the environment can support - a fraction of offspring dies without leaving any offspring of its own.

  Individuals in a population vary in their characteristics.   Some differences among individuals are based on

genetic differences.   Individuals with favorable characteristics have higher

rates of survival and reproduction.

⇒  Evolution by means of natural selection ⇒  Presence of ”design-like” features in organisms:

quite often features are there “for a reason”


Technical University of Denmark The search for the genetic material

In 1944, Avery, MacLeod and McCarty proved that DNA is the genetic material (not protein)

Oswald Theodore Avery 1877 - 1955

In 1953, Watson and Crick deduced the helical structure of DNA

James D. Watson (1928 - ) Francis Crick (1916 - 2004)


Technical University of Denmark Genome sequencing gave all the parts!


Technical University of Denmark GenBank growth 1982-2005

Source: http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html

Systems Biology


Technical University of Denmark Systems Biology and emergent properties


Technical University of Denmark How radios work and how to fix them...

Radio kindly provided by Lazebnik, Cancer Cell, 2002


Technical University of Denmark 6000 papers a year about “cell cycle”


Technical University of Denmark Models: You say tomato, I say tomato...

Chen et al., Mol. Biol. Cell., 2004


Technical University of Denmark A definition of a (scientific) model

“A model is essentially just a hypothesis, but one that is explicitly stated”


Technical University of Denmark The hierarchy of models



… And then came the grandest idea of all! We actually made a map of the country, on the scale of a mile to the mile!"

"Have you used it much?" I enquired.

"It has never been spread out, yet," said Mein Herr: "the farmers objected: they said it would cover the whole country, and shut out the sunlight! So we now use the country itself, as its own map, and I assure you it does nearly as well.

From Sylvie and Bruno Concluded by Lewis Carroll, first published in 1893.

The 1:1 Lewis Carroll map



Systems Biology: A hypothesis generating discipline

systems biology workshop - cbs · 2009-05-12 · introduction to the course systems biology...

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