Biophyiscs Introduction

1、Introduction to Biology- A Structural and Conceptual ViewProf. Bo Yuan, Ph.D.Department of Computer Science and EngineeringShanghai Jiaotong U131-6211-5543Outline The building blocks from molecule to organism The organizations from interaction to system Key developments in biology Key themes and con

2、cepts in biology Building Blocks of ChemistryStructure of the Animal Cell“It has not escaped our notice that the specific pairing we have postulated immediately suggest a possible copying mechanism for heredity.”James Watson and Francis CrickApril 25, 1953Biological SystemOltvai and Barabasi, Scienc

3、e, Oct 25, 2002The Structure of DNAThe Structure of a GeneThe Genetic CodeThe Protein Synthesis (Ribosome)The Backbone of Protein 3D Structures Protein Structures - from 1D to 4DCommon Protein Folds Homology of Human G-ProteinsMetabolic PathwaysSignal Transduction Pathway A ExamplePopulation Evoluti

4、on & DiversificationThe Central Dogma of Biology DNA Replication RNA Transcription and Splicing Protein TranslationDNARNAProteinWhy Biology?The 21st Century Is BiologyGeneration One(before 1980s)Agriculture and ChemistryGeneration Two(1980s)Recombinant DNA Technology (individual gene)Generation

5、Three(1990s)High-Throughput Technology (multiple genes)Generation Four(the 2000s)Integration (informatics, engineering, and systems) Generation Five(2010s)Stem Cells and Synthetic LifeGeneration Six(2020s)Biological Intelligence To Decode the Book of LifeHuman Genome ProjectThe Beginning (1988)Cold

6、Spring Harbor LaboratoryLong Island, New YorkJune 26, 2000 at the WhitehouseInitial Analysisof the Human GenomeThe Central Theme of BiologyEvolution and HeredityEvolution as a Universal AlgorithmS Wright(1889-1989)R Fisher(1890-1962)Human Genome at GlanceGenomic RedundancyVariable Level of Genomic S

7、tabilityComparative Alignment ofthe Human and Mouse GenomesProtein Complexes Have Similar Compositions in Yeast and HumanGavin A, et al., Nature (2002) 415:141-147Biological SystemOltvai and Barabasi, Science, Oct 25, 2002Functional Diversity and Structural RepertoireSusuma TonegawaRudolph JaenischN

8、ature and NurtureEric LanderBiological Networks and DynamicsE DavidsonD EisenbergA ArkinJ DoyleU AlonM NowakSystems BiologyBiology is information and systems sciences. Lee Hood, 1998To Make New LifeCraig VenterBiology - Its Past and Future2000-1900-2000Current Works in the WorldFuture PerspectivesTh

9、e need of mathematical, statistical, and computational abilities to tackle significant biological problems Data RepresentationMathematical FoundationMathematicalRepresentation TypicalAlgorithmTypical BiologicalQuestionTopologyGraph TheoryPartition ProblemRandom GraphNetwork moduleSystem organization

10、LogicAlgebraic LogicRandom Boolean Network, Automata Gene regulatorynetworkCircuit Complex Number and Control TheoryLinearizationStability and controlMetabolic networkReasoningGame TheoryEvolutionary GameNash EquilibriumPopulation geneticsInferenceBayes TheoremBelieve PropagationModel SearchingData

11、miningDiscrete StochasticMarkov-based UpdatingConvergenceMeta-stabilityContext-based Statistical modelsContinuous StochasticStochastic DifferentialsBrownian integralsFokker-PlanckBiological dynamics and controlBiologicalSystemsTypical BiologicalProblemsTypical InformaticAlgorithmsGenomic SequenceHom

12、ology search;Gene predictionSequence alignment; Machine learning;Discriminant analysisSequence VariationHaplotype;Gene AssociationSNP phasing;Linkage analysisRNA ExpressionCo-expressionMicroarray/genechip analysis;Graphic model/causality inferenceRNA RegulationTrans- and cis- acting factorsSequence

13、alignment; HMM Model;MCMC-based regression3D Protein Structure3D Family;From 1D to 3D3D Clustering;Protein threading and folding Problems Protein RegulationProtein modification;Protein stabilityProtein docking problem;Molecular dynamic simulation Biological PathwayProtein-protein interaction; core biologyRegulatory modules and motifs; protein complexes; topology comparisonMetabolic NetworkSystems and control; stability and robustness Gillespie sampling; Langevin stochastic differentials; Pote