CISC 889 Bioinformatics

• Lecture 1 (Overview)
• Lecture 2 (Intro to Molecular Biology by Dr. Marsh)
• Lecture 3 (Genome sequencing and mapping)
• Lecture 4 (pairwise sequence alignment)
• Lecture 5 (pairwise sequence alignment- heuristics and score statistics)
• Lecture 6 (multiple sequence alignment)
• Lecture 7 (hidden Markov models I)
• Lecture 8 (hidden Markov models II)
• Lecture 9 (hidden Markov models III)
• Lecture 10 (Gene Finding)
• Lecture 11 (Protein Secondary Structure Prediction)
• Lecture 12 (Phylogenetic trees I)
• Lecture 13 (Phylogenetic trees II)
• Lecture 14 (Phylogenetic trees III)
• Lecture 15 (Stochastic grammars)
• Lecture 17 (Support Vector Machines I)
• Lecture 18 (Support Vector Machines II)
• Lecture 19 (DNA Microarray and Gene Expressions)
• Lecture 20 (Gene Expressions and Genetic Networks)
• Lecture 21 (Gene Expressions and Bayesian Networks)

Links

• Kimball's Biology Pages>
• Molecular Biology for Computer Scientists by L. Hunter
• Biochemistry of Metabolism ( A course at RPI)
• Programming Perl (3rd Edition) by Larry Wall, Tom Christiansen, Jon Orwant Amazon
• Mastering Algorithms With Perl by John Macdonald, Jon Orwant, Jarkko Hietaniemi Amazon
• A gentle introduction to perl by Patrick M. Ryan
• Lincoln Stein's Pages
• BioPerl
• BioJava
• Reference for scoring matrices
• References for sequence alignment algorithms
• References for pathways
• Critical Assessment of Techniques for Protein Structure Prediction (CASP)
• Kernel-based learning methods (www.kernel-machines.org)
• Glossary