Post on 04-Oct-2015
description
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/