Introduction to Bioinformatics

Transcription

1 Introduction to Bioinformatics

2 If the 19 th century was the century of chemistry and 20 th century was the century of physic, the 21 st century promises to be the century of biology...professor Dr. Satoru Miyano Former President of Japanese Society for Bioinformatics International Bioinformatics Conference (2004), Auckland, New Zealand

3 Outline Definition Introduction Biological Data Challenge What Does Bioinformaticians Do? Fields in Bioinformatics Result / Product from Bioinformatics Resource for Bioinformatics

4 Glossary Deoxyribonucleic Acid (DNA): Containing genetic information of a cell to determine the structure, function and behavior of the cell. Gene (a unit of inheritance): Segment of DNA that carry genetic information for encoding specific cellular RNA and proteins. Ribonucleic acid (RNA) : Molecule that translates the instructions encoded (genetic information) in DNA to build proteins. Gene expression: A conversion process that transcribes genetic information in a gene into RNA and then translates to a protein. Gene Expression Level : An amount of RNA being expressed. GENE Protein: Large molecules required for the structure, function, and regulation of the body's cells, tissues, and organs. Each protein has unique functions. GENE EXPRESSION

5 Keyword Biotechnology = research / development of biological processes to develop helpful products and services.

6 Keyword Bioinformatics Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. Biological Science Information Science Engineering, Information Science, Mathematic

7 Overview of Human Biological Cycle

8 Gene: Segment of DNA that carry genetic information for encoding specific cellular RNA and proteins. Gene expression: A process to convert information from the DNA to RNA for protein production. GENE EXPRESSION CELL

9 Central Dogma (Genes) transcription translation DNA RNA Protein Phenotype

10 Biological Data Gene Expression (Microarray) Protein Function Annotation Genome Sequences Protein Expression RNA Sequences Gene Database Protein Database Protein Sequences and Structures Protein-Protein/Protein- DNA Interaction

11 The Data Explosion Gene Sequences Proteins NCBI Web Site June 2000: 4500 Million Base Pairs February 2001: Million Base Pairs PDB Web Site 1995: 4056 Structures 2000: Structures

12 Challenge and Motivation Challenge Data integration: integrate diverse biological information DNA sequences, protein sequences, gene expression, protein-protein interaction data from large-scale screening. Functional discovery: assign functions to the 30K+ human genes Only 5% of known genes have assigned function Without understanding function, no drug discovery can be done in either small molecule, or in biopharmaceuticals Will be the focus of next 20-years of life-science research The complex structure, higher dimensional and explosive growth in the amount of biological data Motivation Bioinformatics approach is used to solve the problems: data integration, functional discovery and huge biological data.

13 What Does a Bioinformaticist Do 1)Designing/applying/improving algorithm/technique/method/tool to solve the biological problem

14 What Does a Bioinformaticist Do 2)Creating database and representation for biological data

15 What Does a Bioinformaticist Do 3)Building graphical interface and visualization tool for examining biological data

16 What Does a Bioinformaticist Do 4) Working closely with biologists Bioinformaticist Biologist

17 What Does a Bioinformaticist Do 5)Analysis and interpretation of various types of biological data

18 Field in Bioinformatics Sequence Genome Assemble Genome Annotate Genes Gene Expression Protein Structure Protein-Protein Interaction Protein Function Pathway Cellular Response Sequence (Organisms)

19 Engineering / Computer Science in Bioinformatics Automated Technique: - DNA sequencing - DNA microarrays - High throughput screening Software: - Molecular modeling - Visualization - Statistic Network: - Sharing resource (data, hardware, software) - Parallel and grid computing Bioinformatics Computer Hardware: - Storage capacity - Computing capability Artificial Intelligence: - Neural network - Genetic algorithm - Support vector machine - Particle swarm optimization - Fuzzy logic - etc

20 Result / Product from Bioinformatics Medicine Health Care Gene Therapy Alternative Energy Waste Cleanup Agriculture

21 Journals

22 Books