MIT OpenCourseWare

Browse materialsMIT 7.91J · Spring 2014

Foundations of Computational and Systems Biology

Subject: Biology

Art: Ernst Haeckel, Haeckel Hexacoralla 69, 1904 · Public domain

Instructors: Prof. Christopher Burge, Prof. David Gifford, Prof. Ernest Fraenkel
Term: Spring 2014
Level: Graduate
What's inside: 22 videos · 5 problem sets · 5 solutions · 1 reading · 60 other files · 8 web pages
Materials open: Videos here · files on MIT OCW

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About this course

Source: MIT OpenCourseWare 7.91J Foundations of Computational and Systems Biology, Spring 2014, Prof. Christopher Burge, Prof. David Gifford, Prof. Ernest Fraenkel — original course page on ocw.mit.edu ↗. License: CC BY-NC-SA 4.0. Study order: MIT's own listing order, section by section. Taken from MIT's published course files, downloaded from ocw.mit.edu on September 23, 2026. How RedLectern is built.

Materials are grouped the way MIT organized them. A verified, course-wide order has not been established here.

Has MIT solutions 5 files in this course are named by MIT as solutions.

Before you start

Prerequisites are not listed here. Check MIT's own syllabus for this course.

This course’s cited books, in our reading lists: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

How this course was organized

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Materials by section

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Lecture Slides

20 files

Recitations

14 files

Assignments

13 problem sets

Project

Presentation TipsPDF Download

Other materials from this course

22 video transcripts

5 images

MIT OpenCourseWare, Prof. Christopher Burge, Prof. David Gifford, Prof. Ernest Fraenkel, 7.91J Foundations of Computational and Systems Biology, Spring 2014.

License: CC BY-NC-SA 4.0 · Edition: Spring 2014 · Open the original course on OCW ↗

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Foundations of Computational and Systems Biology

Before you start

What's here, and what isn't

Not included here

Materials by section

Lecture Slides

Recitations

Assignments

Project

Other materials from this course

Lecture 1: Introduction to Computational and Systems Biology

Lecture 2: Local Alignment (BLAST) and Statistics

Lecture 3: Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM)

Lecture 4: Comparative Genomic Analysis of Gene Regulation

Lecture 5: Library Complexity and Short Read Alignment (Mapping)

Lecture 6: Genome Assembly

Leture 7: ChIP-seq Analysis; DNA-protein Interactions

Lecture 8: RNA-sequence Analysis: Expression, Isoforms

Lecture 9: Modeling and Discovery of Sequence Motifs

Lecture 10: Markov and Hidden Markov Models of Genomic and Protein Features

Lecture 11: RNA Secondary Structure – Biological Functions and Prediction

Leture 12: Introduction to Protein Structure; Structure Comparison and Classification

Lecture 13: Predicting Protein Structure

Lecture 14: Predicting Protein Interactions

Lecture 15: Gene Regulatory Networks

Lecture 16: Protein Interaction Networks

Lecture 17: Logic Modeling of Cell Signaling Networks

Lecture 18: Analysis of Chromatin Structure

Lecture 19: Discovering Quantitative Trait Loci (QTLs)

Lecture 20: Human Genetics, SNPs, and Genome Wide Associate Studies

Lecture 21: Synthetic Biology: From Parts to Modules to Therapeutic Systems

Lecture 22: Causality, Natural Computing, and Engineering Genomes