Bioinformatics, Computational Biology — An Introduction

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Bioinformatics,Bioinformatics,Computational BiologyComputational Biology — An Introduction — An Introduction

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“…the most wondrous map ever produced by mankind” — Bill Clinton

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DNA

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The difference between you & chimp is ~1.24% The difference between you and Maggie is ~0.1%

Post Genome Era Why small variation, BIG DIFFERENCE?

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Genetics:

From DNA topopulation

Source: gsk

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Introduction – Gene History

1865 Mendel: The basic unit of inheritance is a gene.

Mendel’s work was forgotten until 1900s.1944 The gene was known to be made of

DNA (Deoxyribonucleic Acid).1953 James Watson and Francis Crick :

Double helical structure of DNA.

( 雙股螺旋 )

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Introduction – Gene History (Cont.)

1990 The Human Genome Project ( 人類基 因體計畫 ) started.

1995 The first free-living organism to be sequenced : haemophilus influenzae

( 流行性感冒嗜血桿菌 )1998 CELERA joined the gene research.2000 The human DNA sequence draft was completed (published in 2001).

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動物細胞 ( 細胞核、細胞質、細胞膜 )DNA 位於細胞核內之「核仁」

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DNA Sequence

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DNA Length

The total length of the human DNA is about 3109 (30 億 ) base pairs.1% ~ 1.5% of DNA sequence is useful.# of human genes: 30,000~40,000 Conclusion from the human genome proj

ect Expected # is 100,000 originally.

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DNA Double Helix ( 雙股螺旋）

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DNA/RNA 核甘酸分子核甘酸 (Nucleotide) 包含：- 五碳糖 ( 去氧核糖 , deoxyribose)- 磷酸基 (phosphate group)- 四種含氮鹼基之一 (A 、 G 、 C 、 T/U)

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Backbone of DNA and RNA

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Watson-Crick Base Pairs

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DNA Double Helix ( 雙股螺旋）

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From DNA to RNA to Protein

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Biochemical Context of Genomics and Proteomics

DNA

mRNA

Proteins

Cell functions

Genome “Genomics”

Proteome“Proteomics”

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What is Bioinformatics?

Deduction of knowledge by computer analysis of biological data

See 988000 pages on this issue on the WWWInformation stored in the genetic code (DNA), protein sequencesProtein 3D structures, chromosome structureProtein interaction, transcription factor, motifMicro array gene expression, functional MRI, 2D-gelExperimental resultsPatient statisticsScientific literatureAnalysis tools

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Computational Biology & Bioinformatics

Computational Biology

Biological Hypothesis

Formal Specifications

AlgorithmsRaw Data

Information

Bioinformatics End with Experiments

___

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Key Strategy for Analysis

Information

Consensus

Clustering

Distance Measurement

Data

FESS

Evolution

Functions

StructuresSequences

In Computer Sciences In Biology

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Key Strategy for System Biology Experiment Computer Aided Design Specification, Simulation and Reverse Engineering

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Reverse Engineering StrategyHypothesis

Simulation Results

Candidate Set

Match 實際Microarray 輸出結果

Believe it or not是否唯一吻合

重新假設

再作 Distinguishable實驗

是

否

y

n

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Problems on Different Levels

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Some Problems in Bioinformatics

Sequence comparison Longest common subsequence Edit distance Similarity Multiple sequence alignment

Fragment assembly of DNA sequences Shortest common superstring

Physical mapping Double digest problem Consecutive ones problem

Evolutionary treesMolecular structure prediction

Protein folding

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Bioinformatics and Computer Science

Algorithm: all computing problems.Image processing: 3D images of RNA folds or protein.Database: massive database and retrieval.Distributed system and parallel processing: massive storage and accelerating computation.

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Conclusion

Biology easily has 500 years of exciting problems to work on.

-- Donald E. Knuth

Nano

Cognition

Biology

Informatics !

Go working for Integrating

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Reference – Journals

Bioinfomatics (SCI)Bulletin of Mathematical Biology (SCI)Computer Applications in the BiosciencesJournal of Computational Biology (SCI expanded)Journal of Mathematical Biology (SCI)Journal of Molecular Biology (SCI)Nucleic Acids Research (SCI)Gene (SCI)Science (SCI)

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Reference – Web Sites

BioWeb http://bioweb.uwlax.edu/MIT Biology Hypertextbook http://esg-www.mit.edu:8001/esgbio/Bioinformatics Related Journals http://www.iscb.org/journals.htmlNCBI http://www.ncbi.nlm.nih.gov/