Week 1 (Jan 24, 2005):
Course Overview
Lecture 1: Inroduction to Molecular Biology
Reading
assignment: Hunter, L., Molecular Biology for Computer Scientists.
Artificial Intelligence for Molecular Biology, Ed. L. Hunter, pp. 1-46,
AAAI Press, 1993. (download)
Homework 1 (due in class, Jan 31)
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Week 2:
(Jan 31, 2005):
Lecture
2: Inroduction to Molecular Biology (Part 2)
Reading
assignment: Hunter, L., Molecular Biology for Computer Scientists.
Artificial Intelligence for Molecular Biology, Ed. L. Hunter, pp. 1-46,
AAAI Press, 1993. (download)
Lecture
2: Introduction to Bioinformatics
Reading
assignment: NM Luscombe, D Greenbaum, M Gerstein, What is
bioinformatics? A proposed definition and overview of the field, Methods
Inf Med 40: 346-58. 2001 (download)
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Week 3:
(Feb 07, 2005):
Lecture 3: Basic algorithms for pairwise sequence
alignment Course material: Lecture notes from Mark
Craven's BMI/CS 576
Introduction to Bioinformatics course ("Pairwise
Sequence Alignment", "Primer
on Probability for Discrete Variables")
Reading assignment: Chapter 2 from Durbin textbook
Homework 2 (due Feb 14, in class; you can download the necessary
files from
here)
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Week 4:
(Feb 14, 2005):
Lecture 4: Alignment Statistics, Substitution Scores, Intro to
Multiple Alignment Course material: Lecture notes from Mark
Craven's BMI/CS 576
Introduction to Bioinformatics course ("Alignment
Statistics, Substitution Scores", "Multiple
Alignments") Reading assignment: Chapters 2, 6 from Durbin textbook
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Week 5:
(Feb 21, 2005):
Lecture
5: Multiple Sequence Alignment (ClustalW, Gibbs sampling)
Course material: Lecture notes from Mark
Craven's BMI/CS 576
Introduction to Bioinformatics course ("Multiple
Alignments", "Heuristic
Algorithms for Sequence Database Searching") Course material: Lecture notes from
Russ Altman's
Biomedical
Informatics 214 Representations and Algorithms for Computational
Molecular Biology course (Multiple Sequence Alignment lecture)
Homework
3 (due Feb 28, in class)
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Week 6:
(Feb 28, 2005):
Canceled
due to snow storm NOTE: HW3 is due
in class on Mar 14.
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Week 7:
(Mar 14, 2005):
Lecture
7: Heuristic Algorithms for Sequence Database Searching (BLAST),
1D Motifs, Markov Chain Models
Course material: Lecture notes from Mark
Craven's BMI/CS 576
Introduction to Bioinformatics course and
Russ Altman's
Biomedical
Informatics 214 Representations and Algorithms for Computational
Molecular Biology course
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Week 8:
(Mar 21, 2005):
Lecture 8: Markov Chain Models, Hidden Markov Models
Course material: Lecture notes from Mark
Craven's BMI/CS 576
Introduction to Bioinformatics course ("Markov
Chain Models", "Hidden
Markov Models")
Homework
4 (due Mar 28, in class)
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Week 9:
(Mar 28, 2005):
Lecture 9: Hidden Markov Models Applications; Supervised and
Unsupervised Learning for Bioinformatics
Course material: Lecture notes from Mark
Craven's BMI/CS 576
Introduction to Bioinformatics course ("More
on Hidden
Markov Models")
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Week 10: (Apr 04, 2005)
MIDTERM
Lecture 10: Supervised and
Unsupervised Learning for Bioinformatics; Project Topics Discussion,
Prediction of Protein Structure
Homework
5 (due Apr 11, in class)
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Week 11: (Apr 11, 2005)
Lecture 11: Microarray Data Analysis
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Week 12: (Apr 18, 2005)
Lecture 12: Interesting Topics: Structural Alignment, Genetic
Networks, Comparative Genomics, Text Mining
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Week 13: (Apr 25, 2005)
Presentations:
Uros (Epitope Prediction)
Prasanna (Human Genome Project)
Benjamin (Quest algorithm for 2D Gels)
Rajesh (CATH database)
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Week 14: (May 02, 2005)
Presentations:
Shamika (Prediction of Protein Contacts)
Weigen (Prediction of Protein Location)
Wei (Predicting Deleterious Amino Acid Substitutions)
Tek (Protein-Protein Interaction Prediction)
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