• Introduction to Genetic Diversity
• 72 min
  1. The sources of genomic diversity

  • Dr. George Nelson
• 27 min
  2. Bioinformatics tools in conservation biology

  • Dr. Mahmood Shivji
  • Mr. Vincent Richards
• Populations, Samples and Biological Databases
• 48 min
  3. Specimen banking: saving for the future

  • Ms. Elaine Gunter
• Bioinformatics and Genome Analysis
• 44 min
  4. Accessing and using ENCODE data

  • Prof. Peggy Farnham
• 47 min
  5. Information content in sequences and its relation to protein structure prediction

  • Dr. Rosemarie Swanson
• 40 min
  6. Pattern discovery in bioinformatics

  • Prof. Giri Narasimhan
• Human Disease
• 38 min
  7. Genes in common diseases

  • Prof. Jennie Lou
• 42 min
  8. The impact of genomic architecture and diversity on infectious diseases

  • Prof. Vincent Chow
  • Dr. Meena Sakharkar
• 29 min
  9. The predominant clonal evolution (PCE) concept of microbial pathogens and its practical usefulness

  • Dr. Michel Tibayrenc
• Archived Lectures *These may not cover the latest advances in the field
• 29 min
  10. Unity and diversity in microbial genomes

  • Dr. Kishore Sakharkar
• 38 min
  11. Analysis of protein-protein interaction, transcriptional regulation and metabolic networks

  • Dr. Andreas Wagner
• 39 min
  12. Exploring and predicting phenotype and function in cancer biology: working in high dimensional data spaces

  • Prof. Robert Clarke
• 59 min
  13. Widespread structural variations in the human genome

  • Dr. Charles Lee
• 39 min
  14. Human genome variation

  • Dr. Kelly Frazer
• 36 min
  15. Human genetic variation and therapeutic development

  • Dr. Sally John
  • Dr. Nick Davies
• 62 min
  16. Evolving genomic approaches to the study of complex cardiovascular diseases in human populations: genetic and genomic epidemiology

  • Dr. Christopher O'Donnell
• 42 min
  17. Population genetics studies in Africa: curiosity and challenges

  • Prof. Himla Soodyall
• 37 min
  18. Sample collection for human genetics

  • Dr. Michael Dean
• 40 min
  19. Diagnosis of early relapse in ovarian cancer using serum proteomic profiling

  • Dr. Jean Gao

Printable Handouts

PDF

Navigable Slide Index

1. Introduction
2. Outline
3. Patterns
4. Why pattern discovery?
5. "Ton of data"
6. Sequence patterns: examples
7. Sequence patterns in DNA
8. Pattern representations
9. Pattern representations - consensus sequences
10. Pattern representations - weight matrices
11. Pattern representation: weight matrix
12. Formulae
13. Pattern discovery methods
14. Profile method
15. Profile HMMs
16. Profile HMMs with InDels (1)
17. Profile HMMs with InDels (2)
18. Combinatorial methods
19. Combinatorial method: GYM
20. Example: helix-turn-helix motifs
21. DNA binding at HTH motif
22. Example: HTH motifs and patterns
23. Unaligned pattern discovery
24. TEIRESIAS: key features
25. SPLASH
26. Precomputed sequence patterns
27. Gibbs sampling
28. Expectation maximization (EM)
29. Patterns of protein-DNA interactions
30. Ab initio prediction of TF targets
31. Structure patterns in proteins
32. Structure pattern discovery
33. Sequence-structure patterns
34. Trilogy
35. SSP: supervised pattern discovery algorithm
36. Sequence structure patterns (SSP)
37. Zinc finger motifs: TPs and FPs
38. Limitations in selecting training sets
39. Choosing training sets
40. Conclusions
41. Thanks

Topics Covered

• Why pattern discovery?
• Sequence patterns: representations and protein sequence
• Patterns of DNA-protein interactions
• Structure patterns: representations, discovery and applications
• Sequence-structure patterns
• Designing training sets for supervised discovery
• Algorithmic techniques

Links

Series:

• Using Bioinformatics in the Exploration of Genetic Diversity

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Publication History

• Published on October 1, 2007
• Reviewed on February 8, 2018

Financial Disclosures

• Prof. Giri Narasimhan has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.