CS 190D/290D – Introduction to Bioinformatics - Fall 2006
Prerequisites:
Undergraduate background in Computer Science
Lectures:
MW 1-3 pm, Phelps 1401
Office Hours: T 4-6 pm, Engr I, Rm. 3119, email:
ambuj@cs.ucsb.edu
Enrollment Code: 70672
Reference material:
Primary
Fundamental
Concepts of Bioinformatics, D.E. Krane and M.L. Raymer, Pearson Education,
2003.
Bioinformatics:
Sequence and genome analysis, D. Mount, Cold Spring Harbor Laboratory Press,
2001.
Algorithms
on strings, trees, and sequences, D. Gusfield, Cambridge university press,
1997.
Genes
VII, B. Lewin, Oxford university press, 2000.
Biochemistry
(5th edition), Berg, Tymoczko, and Stryer, W. H. Freeman and
company, 2001.
Biological sequence
analysis: probabilistic models of proteins and nucleic acids, Richard Durbin et
al., Cambridge University Press, 1998.
Secondary
Computational Molecular Biology: An Algorithmic Approach, P. Pevzner,
MIT press, 2000.
Bioinformatics:
the machine learning approach (2nd edition), P. Baldi and S. Brunak,
MIT press, 2001.
Principles
of data mining, Hand, Mannila, and Smyth, MIT press, 2001.
Post-genome
informatics, M. Kanehisa, Oxford University Press, 2000.
Current
Topics in Computational Molecular Biology, eds. T. Jiang, Y. Xu, and M. Zhang,
MIT press, 2002.
Course Material:
·
Course flyer
·
Lecture outline
·
Reading list
·
Homework assignments
·
Reading assignments
·
Class projects
·
Project milestone 1
External websites:
Human Genome Primer
Public Human Genome Project
Publication In Nature 15 February 2001
Commercial Human
Genome Sequence Published in Science 16 February 2001
NCBI Resources
SWISS-PROT
PDB
ISCB
Conferences and journals:
Bioinformatics
Journal of computational
biology
Briefings in bioinformatics
Nucleic Acids Research
Genome
research
RECOMB
(available from ACM digital library)
ISMB
(available through Bioinformatics journal)
PSB
(available online)