7.91J Fundamentals of Computational and Systems Biology (Spring 2014, MIT OCW) | Biology and Biological Engineering

7.91J Fundamentals of Computational and Systems Biology

7.91J Fundamentals of Computational and Systems Biology (Spring 2014, MIT OCW). Instructors: Prof. Christopher Burge, Prof. David Gifford, and Prof. Ernest Fraenkel. This course is an introduction to computational biology emphasizing the fundamentals of nucleic acid and protein sequence and structural analysis; it also includes an introduction to the analysis of complex biological systems.

The MIT Initiative in Computational and Systems Biology 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. (from ocw.mit.edu)

Introduction

Lecture 01 - Introduction to Computational and Systems Biology

Lecture 02 - Local Alignment (BLAST) and Statistics

Lecture 03 - Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM)

Lecture 04 - Comparative Genomic Analysis of Gene Regulation

Lecture 05 - Library Complexity and Short Read Alignment (Mapping)

Lecture 06 - Genome Assembly

Lecture 07 - ChIP-seq Analysis; DNA-protein Interactions

Lecture 08 - RNA-sequence Analysis: Expression, Isoforms

Lecture 09 - 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

Lecture 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

References

Fundamentals of Computational and Systems Biology
Instructors: Prof. Christopher Burge, Prof. David Gifford, and Prof. Ernest Fraenkel. Lecture Notes. Projects (no examples). Assignments and Solutions. Download Course Materials.