Lecture 1 - Introduction to

Bioinformatics

Outline

Introduction to Bioinformatics
History
Applications
Career prospect

Definitions
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.

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.

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

History
The discovery of DNA double helix

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

Applications of Bioinformatics
Second level development of tools and
resources to analyze the data

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

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

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/