Course Syllabus
Course Description: The new biotechnologies developed in the past decade are transforming molecular biology research into a quantitative science based on informatics. New platforms are now capable of collecting large amount of DNA/RNA sequences and measuring their activities in cells in single-cell precision and spatial resolution at a population scale. Without doubt, the contents of the collected data offer unprecedented opportunities for a deep understanding of the molecular mechanisms in cell and cell organizations in tissues, which improve mapping of the linkage between individual’s phenotypes and genetic/genomic patterns for disease treatment. Facing the challenges of making sense out of the sheer volume of data, computer algorithms and data analysis models are playing the central role. This course covers an introduction to various types of functional genomic data available and current computational/statistical methods used for analyzing the data to answer questions in functional genomics, systems biology and their applications in disease research. We will cover the analysis of gene expression data, proteomic data and protein-protein interaction data, with a special focus on how they can be used to understand and infer networks. In particular, the course will also cover the recent advances in cancer genomics by applications of the sequencing, array-based and proteomic technologies. The topics are organized as: 1) Introduction to Genomics and Genomic Technologies, 2) Statistical Analysis of Genomic Data, 3) Data Mining and Machine Learning Methods for Genomics, 4) Cancer Genomics and 5) Biological Network Analysis.
Goals: There will be 4 homework assignments, each requiring the implementation of a computational method and its application to a real functional genomic dataset. Each student/group will also present a research paper on cancer genomics in the class. Students will also choose a topic for the final project, and present the results. All the homework assignments are required to be programmed in matlab/python/R and submitted through canvas.
Grading: Homework Assignments: 60%, Course Project: 30%, and Participation/Presentation: 10%.
Text Books:
- Cancer Genomics, Edited by: Graham Dellaire, Jason N. Berman and Robert J. Arceci ISBN: 978-0-12-396967-5 (free online access at http://www.sciencedirect.com/science/book/9780123969675) Links to an external site.
- Analysis of Biological Networks, Björn H. Junker, Falk Schreiber, ISBN: 9780470253489 (free online access from library http://onlinelibrary.wiley.com/book/10.1002/9780470253489 Links to an external site.)
- Bioinformatics and Functional Genomics, Third Edition, Jonathan Pevsner, ISBN: 9781118581766 (free online access https://ebookcentral.proquest.com/lib/umn/detail.action?docID=4036479 Links to an external site.) [Background readings]
Prerequisites: Some programming skills are required for this course. Biology or other non-CS students are required to take Csci 3003 or an equivalent programming course as a prerequisite or get instructor approval. Prior knowledge of basic molecular biology is highly recommended.
Intended Audience: This course is primarily for graduate and senior undergraduate students in computer science, math, statistics, biological sciences and biomedical sciences with interest in computational biology.
Course Summary:
Date | Details | Due |
---|---|---|
Thu Jan 21, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 1:15pm to 2pm |
Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm | |
Tue Jan 26, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 1:15pm to 2pm |
Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm | |
Wed Jan 27, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Jan 28, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 1:15pm to 2pm |
Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm | |
Mon Feb 1, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Feb 2, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 1:15pm to 2pm |
Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm | |
Wed Feb 3, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Feb 4, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 1:15pm to 2pm |
Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm | |
Mon Feb 8, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Feb 9, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Feb 10, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Feb 11, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm | |
Mon Feb 15, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Feb 16, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Assignment Homework 1 | due by 11:59pm | |
Wed Feb 17, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Feb 18, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Mon Feb 22, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Wed Feb 24, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Feb 25, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Mon Mar 1, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Mar 2, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Mar 3, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Assignment Homework 2 | due by 11:59pm | |
Thu Mar 4, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Mon Mar 8, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Mar 9, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Mar 10, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Mar 11, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Mon Mar 15, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Mar 16, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Mar 17, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Mar 18, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Sun Mar 21, 2021 | Assignment Homework 3 | due by 11:59pm |
Mon Mar 22, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Mar 23, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Mar 24, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Mar 25, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Mon Mar 29, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Mar 30, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Mar 31, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Quiz Selection of Paper for Presentation and Project | due by 11:59pm | |
Thu Apr 1, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Mon Apr 5, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Wed Apr 7, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Mon Apr 12, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Apr 13, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Apr 14, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Apr 15, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Sun Apr 18, 2021 | Assignment Paper Presentation and Project Idea | due by 11:59pm |
Mon Apr 19, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Apr 20, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Apr 21, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Apr 22, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Mon Apr 26, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue Apr 27, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Wed Apr 28, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Thu Apr 29, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Sun May 2, 2021 | Assignment Homework 4 | due by 11:59pm |
Mon May 3, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 9am to 10am |
Tue May 4, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Thu May 6, 2021 | Calendar Event CSCI 5461 (Spring 2021) - Q&A sessions | 2:15pm to 3pm |
Thu May 13, 2021 | Calendar Event CSCI 5461 (001, 881) Functional Genomics, Systems Biology, and Bioinformatics (Spring 2021) | 2:15pm to 3pm |
Sun May 16, 2021 |
Assignment
Final Project
(001 UMNTC CSCI 5461 (Spring 2021))
|
due by 11:59pm |
Assignment
Final Project
(883 UMNTC CSCI 5461 (Spring 2021))
|
due by 11:59pm | |
Assignment
Final Project
(881 UMNTC CSCI 5461 (Spring 2021))
|
due by 11:59pm |