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CSCE 590I Bioinformatics Algorithms and Data Structures

This special topics course aims to familiarize students with algorithms and data structures for computational molecular biology, and contribute to developing a bioinformatics curriculum. It is an experimental course offered by CSE at USC, with collaboration opportunities in various fields. The course requires a background in biology, computer science, statistics, and math. Required materials include the book "Algorithms on Strings, Trees, and Sequences" by Dan Gusfield and research papers assigned by Dr. Rose. For more information, visit the course webpage.

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CSCE 590I Bioinformatics Algorithms and Data Structures

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  1. CSCE 590I Bioinformatics Algorithms and Data Structures Spring 2003 Instructor: Dr. John Rose January 14, 2002

  2. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Purpose of CSCE 590I • Familiarize students with algorithms & data structures for computational molecular biology • Develop a cadre of bioinformatics researchers in CSE • Contribute to developing a bioinformatics curriculum • This course will eventually become a standard course offering.

  3. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • CSE at USC is aggressively entering the field of bioinformatics. • We offer fellowships in computational molecular biology: http://www.engr.sc.edu/release.asp?PID=10013 • We currently collaborate with researchers in Biology, Statistics, Mathematics, Pharmacy, and Medicine • We need more capable student researchers. • Dr. Rose always has an ulterior motive for anything he does.

  4. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Ideal Background: (listed in no particular order) • Biology • Computer Science • Statistics • Biochemistry • Mathematics • In short, bioinformatics is the domain of the renaissance scholar.

  5. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • CSE students are expected to have adequate STAT and MATH background but probably not BIOL & CHEM • Basic sequence in molecular biology & genetics • BIOL 302 • BIOL 303 • BIOL 545 • Prerequisites for the above sequence: • BIOL 101 and 102 • CHEM 111, 112, 333, and 334 • Appropriate labs for listed BIOL and CHEM courses

  6. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Non-CSE students are expected to have adequate STAT, MATH, BIOL & CHEM but probably not CSE. • Basic CSE analytic background • CSCE 350 • Transitive closure of CSE prerequisites for CSCE 350 • CSCE 145 • CSCE 146 • CSCE 240 • CSCE 245 • Appropriate labs for listed CSCE courses

  7. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Expected Background:(listed in no particular order) • Biology or • Computer Science or • Math or • Statistics or • Biochemistry • The consequence is that you will have to apply yourself to wrap your mind around ideas from other disciplines.

  8. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Course Materials: • Algorithms on Strings, Trees, and Sequencesby Dan Gusfield, Cambridge University Press, 1997 (reprinted in 1999). • Research papers that Dr. Rose assigns. • Excerpts from books that Dr. Rose will provide.

  9. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Additional information describing this course can be found on the course webpage. • This page will be updated regularly to reflect the developments in this experimental course. • Yes, you are part of an experiment! • Now we will look at the class webpage and go over course topics, grading, cheating policy, etc. http://www.cse.sc.edu/~rose/590I

  10. CSCE 590I Special Topics: Bioinformatics Algorithms and Data Structures • Good Luck! • Enjoy Yourself!! • Work Hard!!! • Don’t Sleep!!!!

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