Jean-Christophe (JC) Nebel

Bioinformatics & Genomic Signal Processing Group

j.nebel@kingston.ac.uk

Kingston University London

Bioinformatics

What is bioinformatics?

Bioinformatics: word was coined in 1978

Bio-: life Informatics: information systems & computer science

Analysis of molecular biology data using techniques from information systems, computer science, artificial intelligence, statistics and mathematics~computational biology (USA)

Molecular biology data?

DNA, RNA, genes, proteins…

Health

• disease prevention: • detect people at risk

• change of lifestyle, diet…e.g. risk of cardiovascular diseases – exercise…

• study virus evolutione.g. bird flu virus

• treatment:• quantitative evaluation of disease spread• rational drug design

e.g. first efficient drug against HIV (Norvir 1996)• gene therapy

e.g. “bubble” kids with no immune system• animal model

e.g. zebra fish is the new mouse

Aim of bioinformatics“To improve the quality of life” by understanding how it works

Ethical issues!

Forensic (DNA fingerprints)

• criminal suspects (UK: database of 3M people) • paternity tests

1/25 child is NOT from the expected father!• identification of victims (Titanic, earthquakes…)• prevent illegal trade (drugs, ivory…)

Paleoanthropology & archaeology

• Human evolutione.g. where is the first American from?

Food industry

• GMOs (Genetically Modified Organisms) Famine buster or Frankenfood?

Other applications

Ethical issues!

$300 million to $1.7 billion and up to 20 years, only 1/10 projects succeeds

~6 years, only 1/1000 compounds are tested in a clinical trial

In silico

~8 years, fewer than 6% of compounds get approval

In vivo

In vitro

1. Biochemical assays ($400 per compound)Drug target in solution with compound

2. Cell-based assays ($4,000 per compound)Culture of living cells in solution with compound

3. Animal testing ($10,000-1,000,000 per compound)

4. Human clinical trials• Phase I: side effects on (20-50) healthy volunteers

30% of drugs are rejected (unsafe)• Phase II: positive effect on (20-300) patients

66% of drugs are rejected (poor efficacy)• Phase III: positive effect on variety of (300–3,000) patients

75% of drugs are rejected

HumanClinicalTrials

[1] D Young, Computational drug design, N.J: John Wiley & Sons, 2009

Bringing a new drug to the market [1]

0. (Computational) ‘rational’ drug design

Course structure5 lectures (2x45’):

45’: Biological background and probleme.g.: what is DNA? + how to detect genes?

45’: Informatics solution (databases, algorithms…)

-> handouts provided-> lecture notes available after lecture

5 workshops (1h30’):

Use of bioinformatics tools