The CRISPR Revolution: Engineering the Genome for Basic Science and Clinical Medicine
Provides a conceptual and technical understanding of genome editing systems and their research and clinical applications. Focuses on fundamental CRISPR biology in bacteria, methodologies for manipulating the genome with CRISPR, and the application of genome engineering in research and medicine. Combines lectures and literature discussions with critical analysis and assigned readings, with the goal of better understanding how key discoveries were made and how these are applied in the real work. Class work includes brief writing assignments as well as a final research proposal and scientific presentation. Students taking the graduate version explore the subject in greater depth, in part through additional assignments.
Spring 2014 · Foundations of Computational and Systems Biology
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.
Prerequisites & course information
Subject meets with 7.36 Prereq: Permission of instructor G (Fall) 3-0-9 units
Sources
- Course catalogue ↗2026–2027
- MIT OpenCourseWare ↗Spring 2014
- 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.