Who, Where, When

InstructorAsa Ben-Hur
 Office: 448 in the new computer science building
 Office Hours: Tue 10-11am, Wed after class
LectureMWF 9-9:50am at room 425 in the new building

Course Outline

  • A primer in biology; computational problems arising in biology (week 1)
  • Sequence alignment for DNA and protein sequences (weeks 2 – 4)
    • Concepts: homology, sequence similarity and sequence alignment; dynamic programming algorithms
    • Pairwise alignment
    • Global and local alignment using dynamic programming
    • Heuristic alignment methods: BLAST/FASTA and the statistics of local alignments
    • Multiple sequence alignment
      • Definition, scoring, techniques
      • Aligners for proteins sequences
      • Spliced alignment
  • Motif finding in DNA and proteins (week 5)
  • Hidden Markov models (HMMs) (week 6 – 8)
    • The basic HMM algorithms: forward, backward, Viterbi, Baum-Welch
    • Applications: CpG islands, gene finding, profile HMMs, pair HMMs
  • Genome assembly (week 9)
  • Analysis of high-throughput sequencing data (week 10)
  • Phylogenetic analysis (week 11 – 12)
    • Why phylogeny?
    • Neighbor joining, parsimony, and maximum likelihood methods
  • Comparative genomics: gene regulation, gene finding, genome rearrangements (week 13)
  • High throughput biological data: microarrays, mass spectrometry, and protein-protein interactions (week 14)
  • Student project presentations and class summary (week 15)

Prerequisites:

Some background in statistics and ability to program (R and matlab are good enough)

Textbooks:

Neil C. Jones and Pavel A. Pevzner
An introduction to bioinformatics algorithms
MIT Press, 2004

We will also use:
Richard Durbin, Sean R. Eddy, Anders. Krogh and Graeme Mitchison. Biological Sequence Analysis. Cambridge UP, 1998.

Grading:

Assignments    30%Programing and written assignments
Project30%Includes a written report and class presentation
Exams40%Midterm (15%) and Final (25%)

Important Dates

Midterm: TBA

Final Exam: TBA