• Department of Computer Science and Information Engineering, National Taiwan University, Fall, 2002
• Lecturer: Prof. Hsueh-I Lu
• Time: 2PM-5PM, Wednesday. Classroom: Room 101, Department building of CSIE
• Prerequisites: (a) Data Structures, (b) Algorithms. Background in biology is welcome but not required for taking this course.
• We will study fundamental algorithms related to bioinformatics based on the following course materials:
  • "Algorithms on Strings, Trees, and Sequences --- Computter Science and Computational Biology", by Dan Gusfiled, 1997
  • "Computational Molecular Biology --- An Algorithmic Approach", by Pavel A. Pevzner, 2000
  • RECOMB Proceedings
  Roughly 80 percent of lectures by the lecturer, and 20 percent of student presentations.
• Midterm
  • The problem set is here (pdf).
  • Updated midterm grades.
• Final grade is here.
• Lecture slides
  • Lecture 1, September 25, 2002. (slides)
  • Lecture 2, October 2, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 3, October 9, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 4, October 16, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 5, October 23, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 6, October 30, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 7, November 13, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 8, November 20, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 9, November 27, 2002. (slides and Tzhua Chen's scribed note)
  • Lecture 10, December 4, 2002. (slides and Tzhua Chen's scribed note)
• Solution for homework 1 by Tak-man.
• Final presentation
• The webpage for the same course in 2001 can be found here, including slides, scribed notes, material for final presentations.
• Possible sources for papers to be presented:
  • Conferences: RECOMB, WABI, BIBE, ISMB. (See the conference pages for 2002 and 2001.)
  • Journals: Bioinformatics, Journal of Computational Biology Journal of Molecular Biology
  • Other sources: see the bibliography of the textbooks.
  • affix tree
• Join the mailing list called 'bioinfoalg@coollist.com' by filling out this form, and you will automatically receive the broadcasting messages of this course.
• Interesting URLs:
  • a course on phylogenetic trees
  • an interesting paper
  • Mark Nelson's implementation of the suffix-tree algorithm.
  • ECCB'03
  • CMSB'03
  • Conferences related to computational biology. ECCB2002 CG 2001
  • An interesting online course with videos and lecture notes on Algorithms offered by MIT (jointly for Singapore).
  • DNA from the Beginning
  • Primer on Molecular Genetics.
  • Discovering the Double Helix, an online lecture by Jim Watson, who discovered the double helix structure of DNA.

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