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1 Introduction to Bioinformatics / 1 2 What is Bioinformatics / Computational Biology? NIH 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.) Computational Biology (The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. ) Walter Gilbert (1932- ) Harvard University, Biological Laboratories W. Gilbert, Towards A Paradigm Shift in Biology, Nature, 349(1991)99 Bioinformatics Computational Biology

2 :50~18: / 2/2 16 2= hqzhu@pku.edu.cn Tel: (office) 3 URL

3 ~ 4 ~ 6 50% 50% 50% 1. Westhead et al., Bioinformatics Durbin, Biological sequence analysis, Brown Pevsner Boogerd Klipp Google

5 1.1 HGP HGP 20 HGP ( ) 1961Kennedy (1962 Kennedy Kennedy Rice) ( ) (HGP Human Genome Project) 1 2

6 DNA (Genome) bp2 DNA: () A, C, G, T Gene DNA HGP DNA DulbeccoScience : (DOE) 1987 NIH Watson HGP HGP DNA Watson,1990, Science James Watson Walter Gilbert

7 HGP 15( ) 30DNA (H. inf) 1996 HGP DNA HGP H.Inf Saccharomyces cerevisiae Caenorhabditis elegans 1997 (E. coli) 1998 Celera Celera Celera Nature Science Celera Drosophila melanogaster Arabidopsis thaliana

8 Nature Science At the White House on June 26, Francis Collins (r), Director of the National Human Genome Research Institute, President Clinton, and J. Craig Venter, President of Celara Genomics, lauded the thousands of scientists who contributed to the genome sequence

9 5,700 (Archaea) (Bacteria) (Eukaryo) (Virus) (Viroid) (Phage) (Organelle) (Plasmid) , ,

10 Gene-swapping collectives Microbiome Metagenomics Microbiome DNA Bacterial genome dynamics. There are three main forces that shape bacterial genomes: gene gain, gene loss and gene change. All three of these can take place in a single bacterium. Some of the changes that result from the interplay of these forces are shown. (Pallen & Wren, Nature, 2007)

11 HGP Celera / The Sun, the Genome, and the Internet Tools of Scientific Revolution Freeman Dyson

12 HGP HGP: Pandora's Box DNA DNA X 1.2

13 Walter Gilbert (1932- ) Harvard University, Biological Laboratories W. Gilbert, Towards A Paradigm Shift in Biology, Nature, 349(1991) / /

14 What is Bioinformatics / Computational Biology? NIH 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.) Computational Biology (The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. ) Bioinformatics Computational Biology Bioinformatics Dr. Hwa A. Lim 1987 Bio-informatique Bioinformatics 1955Bioinformatics University of Texas at Dallas Adjunct Professor 1981(Imperial College, London University)1986 Rochester University D Trends Biothechnology Information Nano Binformatics / / DNA RNA DNA

15 When I give talks to young scientists seeking advice about areas of future intense scientific excitement, computational biology is my number one recommendation. Francis Collins, Director of HGP at NIH The next step in the project is the interpretation phase. That is really the fun part of the whole project because then we finally have the complete order of all layers of genetic codes and we have to discover what it all means. J. Craig Venter, Head of Celera Genomics Inc. 1.3

16 / Data-mining, Knowledge Discovery Extracts the hidden patterns from huge quantities of experimental data, and forms hypotheses as a result. DNA RNA Simulation-based Analysis Tests hypotheses with in silico experiments, providing predictions to be tested by in vitro and in vivo studies. data-mining, knowledge discovery () () ( ) AQ

17 McCulloch-Pitts RNA RNA / / (HMM) () Motif / /

18 1.3.2 DNA RNA Predict the dynamics of systems so that the validity of the underlying assumptions can be tested. (Computation) 1 (System Analysis) (New Biotechnologies) (Systems Biology) 2Petri (Experimental Data)

19 System Nodes Edges 1.4 (Systems Biology) (General Biology) (Experimental, Theoretical, Computational Biology ) (Biotechnology)

20 Like it or not, big biology is here to stay

21 1 2 1 What is life

22 Markov MarkovHMM ANN DNA RNA 1 2 3BLAST

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untitled Course No. 00333280 will lead you Computational Biology / Bioinformatics? NIH Computational Biology (The development and application of data-analytical and theoretical methods, mathematical modeling and