• Department of Computer Science and Information Engineering, National Taiwan University, Fall, 2003
• Lecturer: Prof. Hsueh-I Lu
• Time: 10:20AM-1:10PM, Tuesday. Classroom: Room 103, 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
  • WABI Proceedings: 2003 2002
  Roughly 80 percent of lectures by the lecturer, and 20 percent of student presentations.
• Lecture slides
  • Office XP is required to see some animation effects in the slides.
  • Lecture 1, September 23, 2003: ppt.
  • Lecture 2, September 30, 2003: ppt.
  • Lecture 3, October 7, 2003: ppt.
  • Lecture 4, October 14, 2003: ppt.
  • Lecture 5, October 21, 2003: ppt.
  • Lecture 6, October 28, 2003: ppt.
  • Lecture 7, November 4, 2003: ppt.
  • Lecture 8, November 11, 2003: ppt.
  • Lecture 9, November 18, 2003: ppt.
  • Lecture 10, December 2, 2003: ppt.
  • Lecture 11, December 16, 2003: ppt and pdf.
• Students' implementation in Java
  • Ukkonen's algorithm for constructing suffix trees
    • author: ­S®a»¨
    • source: SuffixTree.java and Suffix.java
    • give it a test by clicking here.
• Midterm: problem set (pdf) and solutions to Problems 4 and 5 (prepared by TAs).
• Final: problem set (ps).
• Grades: txt.
• Final presentations.
• Solution for homeworks
  • homework 2's solution and a modification.
  • homework 3's solution a and solution b.
• The webpage for the same course in 2002 can be found here, including slides, scribed notes, material for final presentations.
• 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:
  • Check the presentation pages from previous years: 2002 2001. These papers are excluded.
  • Conference proceedings:
    • RECOMB
    • WABI: 2004 (will be in Norway) 2003 2002 2001
    • CPM: 2004 (will be in Turkey) 2003 2002 2001
    • BIBE: 2004 (will be in Taichung, Taiwan) 2003 2001 2000
    • ISMB:
  • Journals: Bioinformatics, Journal of Computational Biology Journal of Molecular Biology
  • 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:
  • Journal of Bioinformatics and Computational Biology
  • a course on phylogenetic trees
  • a course at VT
  • an interesting paper
  • Springer's bioinformatics page
  • An ANSI C implementation of suffix tree
  • Mark Nelson's implementation of the suffix-tree algorithm.
  • a java implementation of 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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