presented by liu qi an introduction to bioinformatics algorithms qi liu email: [email protected]
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Presented by Liu QiPresented by Liu Qi
An introduction to An introduction to Bioinformatics AlgorithmsBioinformatics Algorithms
Qi LiuQi Liu
email: [email protected]: [email protected]
Presented By Liu QiPresented By Liu Qi
Description of the CourseDescription of the Course introduce the basic computational issues and introduce the basic computational issues and
methods used in molecular biologymethods used in molecular biologyTopics will include basic algorithms for Topics will include basic algorithms for
alignment of biological sequences and alignment of biological sequences and structures. These include, for example, structures. These include, for example, dynamic programming algorithms for dynamic programming algorithms for alignment, motif definition and computation, alignment, motif definition and computation, Hidden Markov Models, neural networks etc.Hidden Markov Models, neural networks etc.
Presented By Liu QiPresented By Liu Qi
Related CoursesRelated Courses University of Washington University of Washington （（ Computational Biology)Computational Biology)
http://www.cs.washington.edu/education/courses/527/09au/ http://www.cs.washington.edu/education/courses/527/09au/ Tel Aviv University School of Computer Science Tel Aviv University School of Computer Science
(Algorithms in Molecular Biology )(Algorithms in Molecular Biology ) http://www.cs.tau.ac.il/~rshamir/algmb/algmb-archive.htmhttp://www.cs.tau.ac.il/~rshamir/algmb/algmb-archive.htm
StanfordStanford((Representations and Algorithms for Representations and Algorithms for Computational Molecular Biology Computational Molecular Biology )) http://www-helix.stanford.edu/courses/bmi214/http://www-helix.stanford.edu/courses/bmi214/
MITMIT((Foundations of Computational and Systems BiologyFoundations of Computational and Systems Biology)) http://ocw.mit.edu/courses/biology/7-91j-foundations-of-http://ocw.mit.edu/courses/biology/7-91j-foundations-of-
computational-and-systems-biology-spring-2004/ computational-and-systems-biology-spring-2004/ Imperial College (Introduction to Bioinformatics)Imperial College (Introduction to Bioinformatics)
http://www.doc.ic.ac.uk/~sgc/teaching/341/http://www.doc.ic.ac.uk/~sgc/teaching/341/
Presented By Liu QiPresented By Liu Qi
Reference BooksReference Books An Introduction to Bioinformatics AlgorithmsAn Introduction to Bioinformatics Algorithms
Neil C. Jones and Pavel A. PevznerNeil C. Jones and Pavel A. Pevzner Bioinformatics: The Machine Learning ApproachBioinformatics: The Machine Learning Approach
by Baldi, Pierre. Brunak, Søren. by Baldi, Pierre. Brunak, Søren. Bioinformatics: Sequence and genome analysis Bioinformatics: Sequence and genome analysis
(cold spring harbor laboratory press) (cold spring harbor laboratory press) Mount, Mount, David W.David W.
Biological sequence analysis: Probabilistic Biological sequence analysis: Probabilistic models of proteins and nucleic acids (Cambridge models of proteins and nucleic acids (Cambridge university press) R. Durbin et al.university press) R. Durbin et al.
Presented By Liu QiPresented By Liu Qi
ContentContent
Pairwise Sequence AlignmentPairwise Sequence AlignmentMultiple sequence alignmentMultiple sequence alignmentMotif discoveryMotif discoveryProtein secondary structure predictionProtein secondary structure predictionMicroarrays, Clustering and ClassificationMicroarrays, Clustering and Classification Topics for DiscussionTopics for Discussion
Presented By Liu QiPresented By Liu Qi
Pairwise Sequence alignmentPairwise Sequence alignment
Dot matrix Dot matrix (intuitive)(intuitive)Dynamic programming Dynamic programming (exact)(exact)
Global Global Needleman-WunschLocal Local Smith-Waterman
Word or k-tuple Word or k-tuple (heuristic) (heuristic)FASTAFASTABLASTBLAST
Presented By Liu QiPresented By Liu Qi
Multiple sequence alignmentMultiple sequence alignment
Dynamic Programming Dynamic Programming Heuristic Alignment MethodsHeuristic Alignment Methods
Progressive alignmentProgressive alignmentclustalwclustalw
Iterative refinementIterative refinementHidden Markov ModelHidden Markov Model
Presented By Liu QiPresented By Liu Qi
Motif discoveryMotif discovery
Greedy SearchGreedy SearchExpectation MaximizationExpectation MaximizationGibbs samplerGibbs sampler……
Presented By Liu QiPresented By Liu Qi
Protein secondary structure Protein secondary structure predictionprediction
Chou-Fasman predictions Garnier, Osguthorpe and Robson Neural networks Nearest neighbor methods Consensus prediction approaches
Presented By Liu QiPresented By Liu Qi
Microarrays, Clustering and Microarrays, Clustering and Classification Classification
NormalizationDifferential Expression Genes DetectionClustering
– Hierarchical– K-means– SOM
Class Prediction Integrating other Biological Knowledge
Topics for DiscussionTopics for Discussion
Proteomics data analysisProteomics data analysisNGS Data AnalysisNGS Data Analysis Integrative analysis of various omics dataIntegrative analysis of various omics data……....
Presented By Liu QiPresented By Liu Qi