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An overview of Bioinformatics

An overview of Bioinformatics. Cell and Central Dogma. Source: “Post-genome Informatics” by M Kanehisa. Source: “Post-genome Informatics” by M Kanehisa. Deduction and Analogy. Biological System (Organism) Reductionistic Synthetic

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An overview of Bioinformatics

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  1. An overview ofBioinformatics

  2. Cell and Central Dogma

  3. Source: “Post-genome Informatics” by M Kanehisa

  4. Source: “Post-genome Informatics” by M Kanehisa

  5. Deduction and Analogy

  6. Biological System (Organism) Reductionistic Synthetic Approach Approach (Experiments) (Bioinformatics) Building Blocks (Genes/Molecules) Source: “Post-genome Informatics” by M Kanehisa

  7. Principles Known Physics Chemistry Biology Matter Compound Organism Elementary Elements Genes Particles Yes Yes No Source: “Post-genome Informatics” by M Kanehisa

  8. Searching and learning problems in biology Source: “Post-genome Informatics” by M Kanehisa

  9. Sequence Comparison: Algorithms and Approaches

  10. Homology Search New sequence Sequence database (Primary data) retrieval Similar sequences Expert knowledge Sequence interpretation Source: “Post-genome Informatics” by M Kanehisa

  11. Pairwise sequence alignment by dynamic programming Needleman Wunsch alogrithm Source: “Post-genome Informatics” by M Kanehisa

  12. Database Search for Similar Sequences

  13. Web Lab

  14. Motif

  15. Source: “Introduction to Protein Structure” by Branden & Tooze

  16. Web Lab

  17. Motif Search Sequence database (Primary data) New sequence Expert knowledge Motif library (Empirical rules) inference Sequence interpretation Source: “Post-genome Informatics” by M Kanehisa

  18. Introduction to Structural Biology

  19. Source: “Introduction to Protein Structure” by Branden & Tooze

  20. Source: “Introduction to Protein Structure” by Branden & Tooze

  21. Web Lab

  22. Web Lab

  23. Web Lab

  24. Genome Project

  25. Web Lab

  26. Genome Sequencing and Genome Annotation

  27. A general model of the structure of genomicsequences Source: “Bioinformatics” by D W Mount

  28. Microarray

  29. Joe Sutliff for Science 291 p1224 (2001) What kind of solution Genomics can provide with ?  High Throughput Gene Discovery

  30. 165 genes are up-regulated in 75% tumors (MAPK pathway, APC, promotion of mitosis; 69 unknown) • 170 genes are down-regulated in 65% tumors (hepatocyte-specific gene products, retinoid metabolism; 75 unknown) • Hierarchical Clustering • K-means • Self Organization Map • Support Vector • Single Value Decomposition

  31. Gene Expression and Transcriptome

  32. Web Lab

  33. Proteomics and Functional Genomics

  34. Source: “Post-genome Informatics” by M Kanehisa

  35. Web Lab

  36. Integrative Genomics

  37. Network of physical interactions between nuclear proteins

  38. Attributes of generic network structures

  39. Living Cell Perturbation Environmental change Gene disruption Gene overexpression Dynamic Response Changes in: Gene expression profiles, Etc. Biological Knowledge Molecular and Cellular Biology,Biochemistry, Genetics, etc Basic Principles Practical Applications Virtual Cell Complete Genome Sequences Source: “Post-genome Informatics” by M Kanehisa

  40. Take Home Message • Define the biological problem. • Why is bioinformatics important ? A synthesis approach. • Prediction is a dangerous game. Always try your best to validate in the bench side. • The devil is in the detail. Always try different bioinformatic tools and databases. • Your knowledge rests on your own practice.

  41. Reference Books you will find useful: Bioinformatics -sequence and genome analysis by D W Mount Introduction to Bioinformatics by A M Lesk Post-genome Informatics by M Kanehisa

  42. Evolution of molecular biology databases Database category Data content Examples 1. Literature database Bibliographic citations MEDLINE(1971) On-line journals 2. Factual Database Nucleic acid sequences GenBank(1982) Amino acid sequences EMBL(1982) 3D molecular structures DDBJ(1984) SWISS_PROT(1986) PDB(1971) 3. Knowledge base Motif libraries PROSITE(1988) Molecular classification SCOP(1994) Biochemical pathways KEGG(1995)

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