6.802
Foundations of Computational and Systems Biology
Spring 2014
Topics
- Course Introduction: History of Computational Biology; Overview of the Course; Course Policies and Mechanics; DNA Sequencing Technologies
- Local Alignment (BLAST) and Statistics
- Statistics; Significance Testing; Bonferroni Correction
- Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM)
- Comparative Genomic Analysis of Gene Regulation
- Clustering, Model Selection, and BIC Scores
- Library Complexity and Short Read Alignment (Mapping)
- Burrows–Wheeler Transform (BWT) and Alignments. Guest Lecture: Heng Li ( Broad Institute )
- Genome Assembly
- ChIP-seq Analysis; DNA-protein Interactions
- Simultaneous ChIP-seq Peak Discovery and Motif Sampling
- RNA-sequence Analysis: Expression, Isoforms
- Modeling and Discovery of Sequence Motifs (Gibbs Sampler, Alternatives)
- Gene Expression Program Discovery Using Topic Models
- Markov and Hidden Markov Models of Genomic and Protein Features
- RNA Secondary Structure—Biological Functions and Prediction
- Probabilistic Grammatical Models of RNA Structure
- Introduction to Protein Structure; Structure Comparison and Classification
- Protein Amino Acid Sidechain Packing Using Markov Random Fields
- Predicting Protein Structure
- Predicting Protein Interactions
- Protein / Protein Interaction Prediction Using Threading
- Gene Regulatory Networks
- Protein Interaction Networks
- Regression Trees
- Logic Modeling of Cell Signaling Networks. Guest Lecture: Doug Lauffenburger
- Analysis of Chromatin Structure
- BayesNets
- Discovering Quantitative Trait Loci (QTLs)
- Narrow Sense Heritability
- Human Genetics, SNPs, and Genome Wide Associate Studies
- Synthetic Biology: From Parts to Modules to Therapeutic Systems. Guest Lecture: Ron Weiss
- Causality, Natural Computing, and Engineering Genomes. Guest Lecture: George Church
- Presentations
- Presentations (cont.)
Readings
- LEC #: 1 · TOPICS: Course Introduction; Overview · READINGS: No readings for this lecture.
- LEC #: 3 · TOPICS: Global Alignment of Protein Statistics · READINGS: No readings for this lecture.
- LEC #: 16 · TOPICS: Protein Interaction Networks · READINGS: No readings for this lecture.
- Leach, Andrew. Molecular Modelling: Principles and Applications . Prentice Hall, 2001. ISBN: 9780582382107.
- Durbin, Richard, Sean R. Eddy, et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids . Cambridge University Press, 1998. ISBN: 9780521629713.
- Gonick, Larry, and Woollcott Smith. The Cartoon Guide to Statistics . Paw Prints, 2008. ISBN: 9781435242715.
Sources
- Course catalogue ↗Historical OpenCourseWare
- MIT OCW readings ↗
- MIT OCW calendar ↗
- MIT OCW syllabus ↗
- Historical MIT OpenCourseWare offering. Named reading entries and schedule topics are automatically extracted from the linked source pages.