341: Introduction to Bioinformatics, Spring 2016
Department of Computing, Imperial College London
Course Overview
Instructor Information
E-mail: natasha [at] imperial [dot] ac [dot] uk
Office: 407 C Huxley
Time and Location
Lecture time and location: Tuesdays, 2-4pm and Fridays 4-6pm
Office hours: Tuesdays after the class, 407 C 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 be part of the coursework assignment and will include individual work on either: (a) development of code for a bioinformatics algorithm, or (b) data analysis. You will choose which option you will do. Completing only one of these two options will result in full marks. If you do both, both will be marked and you will be given the higher grade of the two.
Course Syllabus
For information about course goals, topics, organization, grading scheme, textbooks and readings, etc., please see the course introduction.
Class Materials
Lecture Notes:
Tuesday Lectures (2-4pm):
- January 19, Lecture 1: Course overview and Introduction to Biology (Dr. Przulj). (in pdf)
- January 19, Lecture 2: Sequencing and Genomics (Dr. Rice). (in pdf)
- January 26, Lecture 5: Functional Genomics and Microarray Analysis (Dr. Rice). (in pdf)
- January 26, Lecture 6: Functional Genomics and Microarray Analysis continued (Dr. Rice). (in pdf)
- February 2, Lecture 7-8:Introduction to biological networks. (in pdf)
- February 9, Lectures 9-10: Introduction to graph theory. (in pdf)
- (OPTIONAL: Review of more graph algorithms; after slide 11 is optional reading and will not be assessed.)
- February 16, Lectures 11-12: Network properties. (in pdf)
- Coursework – given out on Feb 16, 2016, due on March 4, 2016 by 2pm.
- February 23, Lecture 15: Network properties (continued). (in pdf)
- February 23, Lecture 16: Network models. (in pdf)
- March 1, Lecture 17: Network models (continued). (in pdf)
- March 1, Lecture 18: Network comparisons and alignments. (in pdf)
- March 8, Lecture 21: Network comparisons and alignments (continued). (in pdf)
- March 8, Lecture 22: Course review.
- Optional Lectures 23-24: Graph clustering; interplay of network topology and biological function. (in pdf)
Friday Lectures (4-6pm):
- January 22, Lecture 3: Sequence Analysis (Dr. Rice). (in pdf)
- January 22, Lecture 4: Sequence Analysis (Dr. Rice). (in pdf)
- January 29: Tutorial 1 questions; Tutorial 1 answers.
- January 29: Tutorial 2 questions; Tutorial 2 answers.
- February 5, Tutorial 3 questions; Tutorial 3 answers.
- February 5, Tutorial 4a: NCBI, Uniprot, BLAST; Tutorial 4b: Cytoscape. Tutorial 4c: Questions and Answers.
- February 12, Tutorial 5a questions; Tutorial 5a answers. Tutorial 5b: GraphCrunch Tutorial.
- February 12, Tutorial 6 questions; Tutorial 6 answers.
- February 19, Lectures 13-14: Protein 3D structure (Dr. Noel Malod-Dognin)
- February 26, Tutorial 7 questions and answers.
- March 4, Lectures 19-20: Computational Methods for Network Integration
- March 11, Tutorial 8: Coursework model answers.
Additional Readings
- Sequence alignment: pdf, doc.
- 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.
- Vladimir Gligorijevic and Natasa Przulj, “Methods for Biological Data Integration“, J. Roy. Soc. Interface, 20015.
Useful Links
Coursework
- Coursework (Given out on February 16, 2016. Due on March 4, 2016 by 2pm.)
- Sample solution to coursework.
- Exam (Date to be determined.)
