Foundations of Computational and Systems Biology
As taught in: Spring 2004
Gibbs Sampler - Strong Motif example. (Figure by Prof. Chris Burge.)
Instructors:
Prof. Christopher Burge
Prof. Michael Yaffe
Dr. Peter Woolf
Prof. Amy Keating
MIT Course Number:
7.91J / 7.36J / 20.490J
Level:
Undergraduate / Graduate
Course Highlights
The MIT Initiative in Computational and Systems Biology (CSBi) is a campus-wide research and education program that links biology, engineering, and computer science in a multidisciplinary approach to the systematic analysis and modeling of complex biological phenomena. This course is one of a series of core subjects offered through the CSB Ph.D program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology.
This course site includes an extensive listing of bioinformatics tools with links to online resources in the tools section as well as a full set of lecture notes.
Course Description
Serving as an introduction to computational biology, this course emphasizes the fundamentals of nucleic acid and protein sequence analysis, structural analysis, and the analysis of complex biological systems. The principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling are covered. Students are also exposed to currently emerging research areas in the fields of computational and systems biology.
Lecture Notes
CB = Professor Chris Burge
AK = Professor Amy Keating
MY = Professor Michael Yaffe
LEC # TOPICS LECTURERS
1 Introduction/Sequence Comparison and Dynamic Programming (PDF - 2.6 MB)
MY
2 Multiple Sequence Alignments
I (PDF)
MY
3 Multiple Sequence Alignments
II (PDF)
MY
4 Phylogenetic Analysis (PDF) MY
5 Literature Discussion (PDF) MY
6 Genome Sequencing and DNA Sequence Analysis (PDF)
CB
7 DNA Sequence Comparison
and Alignment (PDF)
CB
8 DNA Motif Modeling and
Discovery (PDF)
CB
9 Markov and Hidden Markov
Models for DNA Sequences (PDF)
CB
10 DNA Sequence Evolution (PDF) CB
11 RNA Secondary Structure Prediction (PDF)
CB
12 Literature Discussion on Predicting the Functions of
DNA/RNA Sequences
CB
13 Midterm Exam – in class – Protein and DNA Sequence Analysis
14 Protein Secondary Structure MY
LEC # TOPICS LECTURERS Prediction (PDF)
15 Introduction to Protein
Structure and Classification
(PDF - 1.8 MB)
AK
16 Comparing Protein Structures
Molecular Modeling: Methods
and Applications (PDF)
AK
17 Using Computational Methods
to Analyze, Predict, and Design Protein Sequences and
Structures
Solving Structures using X-ray Crystallographpy and NMR (PDF)
AK
18 Solving Structures using X-ray Crystallographpy and NMR (cont.)
Homology Modeling (PDF)
AK
19 Methods for Protein Structure Prediction: Homology
Modeling and Fold Recognition (PDF)
AK
20 Threading and ab
initio Structure Prediction
Computational Protein Design (PDF)
AK
21 Introduction to Systems
Biology
MY
22 Feedback Systems and
Coupled Differential Equations
MY
23 DNA Microarrays and
Clustering (PDF - 1.8 MB)
CB
LEC # TOPICS LECTURERS
24 Literature Discussion on DNA Microarrays and Clustering
CB
25 Computational Annotation of
the Proteome (PDF)
AK
26 Literature Discussion on Computational Annotation of
the Proteome
AK
Assignments ASSIGNMENTS SUPPORTING FILES
Homework 1 (PDF) prob2seqs.fa (FA)
prob3inputseqs.fa (FA)
prob4seq.txt (TXT)
Sample run for problem 6 (TXT)
Homework 2 (PDF) dino1.fa (FA)
dino2.fa (FA)
pombe.fa (FA)
motifs.txt (TXT) random.fa (FA)
5primesplicesites.txt (TXT) 3primesplicesites.txt (TXT) splicing.run (TXT)
motif.run (TXT)
Homework 3 (PDF) 1fxd.pdb (PDB) rmsd.py (PY)
Homework 4 (PDF) hw4.m (M)
repressilator.m (M) Repressilator model based on: Elowitz M. B., and S. Leibler "A synthetic oscillatory network of transcriptional regulators." Nature403, no. 6767 (20 Jan 2000): 335-8.
Exams
Throughout the semester, four lecture sessions will be designated for literature discussion in order to link lecture material with current research. Reading assignments for two journal articles and a literature discussion quiz covering the main points of the papers are due at the beginning of these discussion sessions.
Below are the three literature discussion quizzes. The Lec # column in the table denotes when the discussion session takes place and when the quizzes are due. There is no quiz for the fourth discussion session which takes place during Lec #26.
LEC # EXAMS
5 Literature Discussion Quiz 1 (PDF)
12 Literature Discussion Quiz 2 (PDF)
24 Literature Discussion Quiz 3 (PDF)
26 No Quiz for Literature Discussion 4
The midterm and final exams for this course are not available.