341: Introduction to Bioinformatics, Spring 2012
Department of Computing, Imperial College London
Course Overview
Instructor Information
E-mail: natasha [at] imperial [dot] ac [dot] uk
Office: 407 A Huxley
Time and Location
Lecture time: Fridays, 3 – 6 pm (2 hours of lecture and 1 hour of tutorial)
Location: 145 Huxley
Office hours: Fridays after class, 407 A Huxley
Course Summary
The course will cover basic biological concepts related to the issues of sequence analysis and alignment, microarray data analysis, biological networks, fundamental graph theoretic algorithms, computational complexity and challenges in network analysis, existing post-genomic approaches for analyzing, modeling, and comparing biological networks, and applications of these approaches to understanding biological function, disease, and evolution. For more details, see the course syllabus below.
Practical work will include teamwork development of research applications for Android embedded mobile devices. The winning team will be awarded a visit to Google and lunch with the Google’s development team behind Android. Implementing apps for Android is quite straightforward, as it is basically Java code with a couple of additional APIs for accessing the additional features, so Computing students should have no problem with it. Bioengineering students are familiar with C/C++; Java is quite similar, so they are not expected to have trouble contributing to building a high-quality app in a number of aspects apart from contributing biological background and knowledge.
Course Syllabus
For information about course goals, topics, organization, grading scheme, textbooks and readings, etc., please see the course syllabus.
Class Materials
Lecture Notes:
- Lecture 1: Course overview and Introduction to Biology. (in pdf)
- Lecture 2: Sequencing and Genomics (Prof. Guo)
- Lecture 3: Sequence Analysis (Prof. Guo). (in pdf)
- Lecture 4: Sequence Analysis (Prof. Guo). (in pdf)
- Tutorial 1 questions; Tutorial 1 answers.
- Lecture 5: Functional Genomics and Microarray Analysis (Prof. Guo). (in pdf)
- Lecture 6: Functional Genomics and Microarray Analysis continued (Prof. Guo). (in pdf)
- Tutorial 2 questions; Tutorial 2 answers.
- Lectures 7 and 8: Bioinformatics of Protein-DNA Interactions
- Tutorials 3 and 4: Developing Android Applications (in pdf); Example.
- Coursework 1 – due on March 9, 2012 at 3pm.
- Coursework 2 – due on March 16, 2012 at 3pm.
- Lectures 9 and 10: Introduction to biological networks. (in pdf)
- Lectures 11 and 12: Introduction to graph theory. (in pdf)
- OPTIONAL: Review of more graph algorithms; after slide 11 is optional reading and will not be assessed.
- Tutorial 5 questions; Tutorial 5 answers.
- Lectures 13, 14 and 15: Network properties. (in pdf)
- Tutorial 6 questions; Tutorial 6 answers.
- Lectures 15 and 16: Network properties and models. (in pdf)
- Tutorial 7: Cytoscape demo notes; GraphCrunch demo notes.
- Lectures 17 and 18: Network comparisons and alignments. (in pdf)
- Lecture 18a: Software tools for network analysis and modeling
- Tutorial 8: Coursework 1 and Coursework 2 model solutions.
- Optional Lectures 17 and 18: Graph clustering; interplay of network topology and biological function. (in pdf)
Recommended readings:
Additional Readings
- Survey: “Graph-theoretic approaches for studying biological networks“, Tijana Milenkovic, PhD advancement, Univeristy of California, Irvine, 2008.
- Natasa Przulj and Tijana Milenkovic, “Computational Methods for Analyzing and Modeling Biological Networks“, a chapter in “Biological Data Mining”, edited by Jake Chen and Stefano Lonardi, Chapman & Hall/CRC; 1 edition, September 1, 2009.
- Sequence alignment (pdf, doc)
Useful Links
Coursework
- Coursework 1 (Given out on February 10, 2012. Due on March 9, 2012 at 3pm.)
- Sample solution to coursework 1
- Coursework 2 (Given out on February 10, 2012. Due on March 16, 2012 at 3pm. No late submissions will be allowed.)
- Sample solution to coursework 2
- Exam (Date to be determined.)
