Lecture 1

Lecture 1 - Introduction to Bioinformatics

Outline

Introduction to Bioinformatics History Applications Career prospect

Definitions

The crea%on and development of advanced informa/on and computa/onal technologies for problems in biology, most commonly molecular biology (but increasingly in other areas of biology). As such it deals with methods for storing, retrieving and analyzing biological data, such as nucleic acid and protein sequences, structures, func%on, pathways and gene%c interac/ons.

Bioinforma/cs is conceptualizing biology molecules and applying informa/cs techniques (derived from disciplines such as applied math, computer science and sta/s/cs) to understand and organize the informa/on associated with this molecules, on a large scale.

Introduction

Introductions At cellular level

Plasma membrane lipids, proteins Cytoplasm - organelles Nucleus genetic material

Genes and Proteins Genes: Director of the cell

contain genetic information DNA replication Transcription and translation

Proteins are the tool of the cell Structural proteins Transport proteins Receptors Immunological proteins Blood carrier Enzymes

Central dogma of molecular biology The expression of biomolecules is governed by

central dogma of molecular biology which can be stated as DNA makes RNA makes proteins

DNA and protein play critical role at various functional sites

Molecular biology and bioinformatics Bioinformatics has close connection with molecular

biology (understanding molecular biology at the molecular level)

Biological processes involve biomolecules (eg. Lipids, nucleic acids, carbohydrate, proteins) that forms biological structures (eg. Organelle, membrane, tissue etc.)

The information on the expression and regulation of these molecules is decoded in the genetics material (DNA)

Molecular biology deals with biological activity at the molecular level

The discovery of DNA double helix

History

History 1955- The sequence of the first protein bovine insulin was

analyzed by F.Sanger. 1970s - genetic engineering (eg. DNA recombinant

technology, Sanger sequencing method) 1980s - development of PCR for DNA amplification 1990s revolution in high-throughput molecular

measurement system (eg. DNA microarray) 1995- TheHaemophilus influenzea genome(1.8) is sequenced

( Fleischmannet al.,Science269:496-512 (1995). 1996- The genome for yeast, Saccharomyces cerevisiae (12.1

Mb) is sequenced. 1997- The genome for E.coli (4.7 Mbp) is published.

History 1998- The genomes for C.elegans and yeast are published 1988 - the Human Genome Organization (HUGO) was

founded. 1999- First Human Chromosome Completely Sequenced.

On December 1, researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22.

2000- The genome for Pseudomonas aeruginosa (6.3 Mbp) is published. The A.thaliana genome (100 Mb) is sequenced. The D.melanogaster genome (180 Mb) is sequenced.

2003-Human Genome Project Completion, April 2003.

Human Genome Project

Sequence of entire human genome (3 billion bps) Implications: Unlocking the secret of gene and possibilities of new

discoveries, publicly available Valuable information for biotechnology and

pharmaceutical industry potential new drug targets Lead to the genome sequencing projects for other

organisms and ongoing development of more robust sequencing technology

1000 genomes project The first human genome, published in 2003, took

more than a decade to complete, but the 1,000 Genomes Project completed the bulk of its sequencing work in less than a year.

A genome can nowadays be fully sequenced in just a few days!.

DNA sequences made freely available by the 1,000 Genomes Project will be used to uncover the genetic roots of disease

hCp://www.1000genomes.org/

Nature and diversity of data

Data explosion from Eg. Genome sequencing projects, proteomics,

expression studies The completely sequence genomes are stored in

databases Continue to increase Supported by automation Development of rapid sequencing technology All the data need to be stored, organized and indexed

so that it can be retrieved and used

What Bioinformatics can help?

Gene expression analysis, prediction of gene functions and establishment of gene library

The ability to use genome sequences to identify protein functions, protein interactions, modification and functions i.e proteomics

Elucidation the function of a molecule based on its structure

Molecular modeling and molecular dynamics to predict function from sequence structure

Identification of gene causing disease Data from functional genomic and proteomic can aid in

drug discovery

Applications of Bioinformatics

At the first/basic level to store and organize and manage the large amount of biological data PDB GenBank

Second level development of tools and resources to analyze the data

Applications of Bioinformatics

hCp://blast.ncbi.nlm.nih.gov/Blast.cgi

hCp://www.ebi.ac.uk/Tools/sss/fasta/

Applications of Bioinformatics

Third level the use of these tools to analyze data and to interpret the results in a biologically meaningful manner

Applications of Bioinformatics

Information search and retrieval eg. development of algorithms

Genetics related applications eg. gene prediction

Sequence comparison pairwise alignment, multiple sequence alignment

Phylogenetic analysis Next generation sequencing and genome

assembly

Applications of Bioinformatics

Genome annotations Proteomics Pharmacogenomics Drug discovery and computer aided drug

design Systems biology And many more

Career path

Postgraduate study taught course or MSc (by research) Bioinformatics Computer science

MSc/PhD - computer science or Bioinformatics

Career prospect

With bioinformatics skills/knowledge or degree Bioinformatics scientist Bioinformatics software and application developer Bioinformatics analyst Bioinformatics engineer Bioinformatics graphic and multimedia designer Bioinformatics information scientist Bioinformatics system and database administrator Bioinformatics web development engineer other

Career prospect

There are thousands of biology-based companies In Malaysia

over 100 companies are with Bionexus status which is exclusively given to stable and large bioinformatics and Biotechnology companies with good performance and passed the standard set by the BioNexus Bill of Guarantees

-source BiotechCorp website h4p://www.biotechcorp.com.my/bionexus/