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Page 1: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Introduction to Bioinformatics

Page 2: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

“If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises to be the century of biology”

...Professor Dr. Satoru Miyano…nFormer President of Japanese Society for

BioinformaticsnInternational Bioinformatics Conference

(2004), Auckland, New Zealand

Page 3: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

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

Outline

Page 4: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

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

GENE

GENE EXPRESSION

GlossaryDefinition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 5: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Keyword§ Biotechnology = research /

development of biological processes to develop helpful products and services.

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 6: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

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

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 7: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Overview of Human Biological CycleDefinition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 8: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Gene: Segment of DNA that carry genetic information for encoding specific cellular RNA and proteins.

GENE EXPRESSION

Gene expression: A process to convert information from the DNA to RNA for protein production.

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

CELL

Page 9: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Central Dogma

DNA RNA Proteintranscription translation

Phenotype

(Genes)

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 10: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Biological Data

Genome Sequences

RNA Sequences

Protein Sequences and Structures

Gene Expression (Microarray)

Protein Expression

Protein Function

Annotation

Protein-Protein/Protein-DNA Interaction

Gene Database

Protein Database

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 11: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

The Data Explosion

NCBI Web SiteJune 2000: 4500 Million Base Pairs

February 2001: 11000 Million Base Pairs

PDB Web Site1995: 4056 Structures

2000: 12777 Structures

Gene Sequences Proteins

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 12: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Challenge and Motivation

§ 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

§ Bioinformatics approach is used to solve the problems: data integration, functional discovery and huge biological data.

Challenge

Motivation

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 13: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

What Does a Bioinformaticist Do1)Designing/applying/improving

algorithm/technique/method/tool to solve the biological problem

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 14: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

What Does a Bioinformaticist Do2)Creating database and representation for

biological data

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 15: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

What Does a Bioinformaticist Do3)Building graphical interface and

visualization tool for examining biological data

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 16: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

What Does a Bioinformaticist Do4) Working closely with biologists

Bioinformaticist

Biologist

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 17: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

What Does a Bioinformaticist Do

5)Analysis and interpretation of various types of biological data

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 18: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Field in BioinformaticsSequence

.

.

.

.

.

.

.

.

.

.

.(Organisms)

Sequence Genome

Assemble Genome

Annotate Genes

Protein Structure

Protein Function

Gene Expression

Protein-Protein Interaction

Pathway

Cellular Response

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Gene Expression

Page 19: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Engineering / Computer Science in Bioinformatics

Bioinformatics

Automated Technique:- DNA sequencing- DNA microarrays- High throughput screening

Computer Hardware:- Storage capacity- Computing capability

Network:- Sharing resource (data, hardware, software)- Parallel and grid computing

Software:- Molecular modeling - Visualization- Statistic

Artificial Intelligence:- Neural network- Genetic algorithm- Support vector machine- Particle swarm optimization - Fuzzy logic- etc…

Definition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 20: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

Result / Product from BioinformaticsDefinition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Medicine Gene TherapyHealth Care

Waste CleanupAlternative Energy Agriculture

Page 21: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

JournalsDefinition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Page 22: Introduction to Bioinformatics · Introduction to Bioinformatics “If the 19th century was the century of chemistry and 20th century was the century of physic, the 21st century promises

BooksDefinition Biological Data ResourcesProblems BioinformaticianIntroduction Fields Products

Pw point physic

Electricity for physic

Physic investigatory project

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Lecture 22 physic

Complete Physic As

human physic human physic bio chem test ready stuff of test

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Radiology Physic Review

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Physic P2 F5

Physic (37pages)

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Newton Law - Physic

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Practical 1 Physic

The physic of_dance

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A Hedgerow Walk to Dilston Physic Garden on 4 July 2018A Hedgerow Walk to Dilston Physic Garden on 4TH July 2018 On 4th stJuly 2018, the 21 Century Northumbria Herbal Project held

Physic 2-boonya

Textbook of Physic

English for physic

Geo Physic A

Physic Study Guide

Chemistry and Physic

1.4 Muon Physic

Physic Final Review

X Ray Physic

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