Bioinformatics for Computer Scientists
Title | Bioinformatics for Computer Scientists (56420) |
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Quarter | Autumn 2015 |
Instructor | Thomas Binkowski (abinkowski@cs.uchicago.edu) |
Website | http://uchicago.bio |
Syllabus | Course Description Course Content Coursework Week 1: Genomics, Bioinformatics and Molecular Biology A high-level view of increasingly important role of computing in the biological sciences will be presented. Week 2: Genomes, Sequences and Databases A survey of the current state of the art in storing, organizing and analyzing large data sets will be discussed. The advantages and disadvantages of these methods will be explored in the context of academic and commercial research initiatives. Week 3: Sequence Alignment Fast, reliable alignment of text strings started the bioinformatics revolution. This lecture will show how these seemingly simple strings form the basis of almost all bioinformatics research. Week 4: Protein Structure and Function Proteins are central building blocks of all organisms. This lecture will take bioinformatics to the third-dimension, showcasing how the spatial assembly and interactions of proteins support life and cause of disease. Week 5: Protein Motifs and Modeling Understanding protein function holds the promise developing therapeutics and curing diseases, but the computational complexity of analyzing three-dimensional models presents obstacles that have been difficult to overcome. This lecture will discuss approaches to shape analysis and comparison that can be scaled to large data sets. Week 6: High-Performance Computing for Bioinformatics We will discuss how some of the most powerful computing resources in the world are unable answer the simplest questions in bioinformatics. Strategies for conducting large-scale analysis of genes and proteins will be presented. Week 7: Student Presentations Students will present a research topic in bioinformatics of their own choosing. Week 8: Microarray Data Analysis Personalized genomic analysis is being used by consumers to better understand their health and their ancestry. The technologies used to power these services will be introduced as well as the different approaches used to provide web services to analyze the data. Week 9: SNPs and Disease The cause of diseases can be as simple as a single misplaced letter in a DNA sequence. From gene to disease, we will trace the genetic origin of disease. We will explore different approaches to cataloging and analyzing these changes. Week 10: In Silico Drug Discovery Approaches to using computer models to develop new drugs will be presented. We will discuss how years of playing Tetris might be more useful than you thought in combating antibiotic resistant pathogens. Week 11: Final Exam and Final Project Presentations Students will present their final projects. Textbook
The following books are recommended, but not required:
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Prerequisites (Courses) | MPCS 33001 Algorithms and Core Programming requirements. |
Prerequisites (Other) | Lectures and demonstrations will be conducted mostly in Python. Python programming experience will be useful, but is not required as long as students are willing to dedicate sufficient time to obtain basic development and debugging skills in the language. The course is focused on developing solutions to biological problems, not on mastery of any particular language. Final projects will be implemented on Google Could Platform which supports Python, Java, PHP and Go. |
Satisfies | Specialization - Data Analytics
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Time | Mondays, 5:30-8:30 |
Location | Young 306 |