This class extends the material covered in COMP462 and/or COMP561. We will introduce fundamental concepts and techniques in computational structural biology and computational system biology.
Computational structural biology aims to model and predict the structure of bio-molecules (e.g., proteins, DNA, RNA), while computational system biology provides methods to model and study biological systems. These fields of study has a broad impact on the understanding of gene regulation processes and biological system mechanisms. It also open new research directions in synthetic biology such as the design of new bio-molecular devices and the re-engineering of biological functions.
The topics covered will range from the classic techniques used in these field (e.g. molecular dynamics, hidden Markov models) to more recent advances in analyzing and predicting molecular structures and systems (e.g. conditional random fields).
We will illustrate this material with applications of classical bioinformatics tools such as GROMACS or the Vienna RNA package.
Prerequisites: Basic understanding of algorithms and basic biological background.
Evaluation: 2 Assignments (15% each), 2 paper reports (15% each), and 1 project (40%).
Instructor: Jérôme Waldispühl
Lectures: Monday-Wednesday 2:30pm - 4:00pm in McConnell 320.
Office hours: By appointment.
Assignment 1 (RNA Bioinformatics)
Due on March 9th, 2014.
Assignment 2 (Protein structure prediction)
Due on April 13th, 2014.
Format for the report:
Introduction to Computational Structural and System Biology Biology. [Slides]
Introduction to RNAs. Classical secondary structure prediction algorithms. [Slides]
Stochastic RNA Secondary Structure Prediction [Slides]
RNA Sequence-Structure alignment [Notes]
RNA secondary structures with pseudo-knots. [Notes]
RNA-RNA interaction. [Slides]
RNA 3D Modeling. [Slides]
RNA in Sequences/Structures Networks. [Slides]
Exploration of RNA mutational landscapes and RNA design. [Slides]
RNA folding dynamics. [Slides]
Introduction to Protein Folding and Secondary Structure Prediction [Slides]
Protein Beta-sheets Prediction. [Slides]
Molecular Dynamics (lectures by Mohamed Smaoui).
Computational Molecular Biology: An Introduction
Peter Clote, Rolf Backofen
Wiley Series in Mathematical and Computational Biology